bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenomics of species from four genera of New World monkeys by flow sorting and reciprocal chromosome painting
Authors: Dumas Francesca , Stanyon Roscoe , Sineo Luca , Stone Gary , Bigoni Francesca 
Published: August 2007

Abstract

Background
The taxonomic and phylogenetic relationships of New World monkeys (Platyrrhini) are difficult to distinguish on the basis of morphology and because diagnostic fossils are rare. Recently, molecular data have led to a radical revision of the traditional taxonomy and phylogeny of these primates. Here we examine new hypotheses of platyrrhine evolutionary relationships by reciprocal chromosome painting after chromosome flow sorting of species belonging to four genera of platyrrhines included in the Cebidae family: Callithrix argentata (silvered-marmoset), Cebuella pygmaea (pygmy marmoset), Callimico goeldii (Goeldi's marmoset) and Saimiri sciureus (squirrel monkey). This is the first report of reciprocal painting in marmosets.

Results
The paints made from chromosome flow sorting of the four platyrrhine monkeys provided from 42 to 45 hybridization signals on human metaphases. The reciprocal painting of monkey probes on human chromosomes revealed that 21 breakpoints are common to all four studied species. There are only three additional breakpoints. A breakpoint on human chromosome 13 was found in Callithrix argentata, Cebuella pygmaea and Callimico goeldii, but not in Saimiri sciureus. There are two additional breakpoints on human chromosome 5: one is specific to squirrel monkeys, and the other to Goeldi's marmoset.

Conclusion
The reciprocal painting results support the molecular genomic assemblage of Cebidae. We demonstrated that the five chromosome associations previously hypothesized to phylogenetically link tamarins and marmosets are homologous and represent derived chromosome rearrangements. Four of these derived homologous associations tightly nest Callimico goeldii with marmosets. One derived association 2/15 may place squirrel monkeys within the Cebidae assemblage. An apparently common breakpoint on chromosome 5q33 found in both Saimiri and Aotus nancymae could be evidence of a phylogenetic link between these species. Comparison with previous reports shows that many syntenic associations found in platyrrhines have the same breakpoints and are homologous, derived rearrangements showing that the New World monkeys are a closely related group of species. Our data support the hypothesis that the ancestral karyotype of the Platyrrhini has a diploid number of 2n = 54 and is almost identical to that found today in capuchin monkeys; congruent with a basal position of the Cebidae among platyrrhine families.
Montmorillonite protection of an UV-irradiated hairpin ribozyme: evolution of the RNA world in a mineral environment
Authors: Biondi Elisa , Branciamore Sergio , Maurel Marie-Christine , Gallori Enzo 
Published: August 2007

AbstractBackgroundThe hypothesis of an RNA-based origin of life, known as the "RNA world", is strongly affected by the hostile environmental conditions probably present in the early Earth. In particular, strong UV and X-ray radiations could have been a major obstacle to the formation and evolution of the first biomolecules. In 1951, J. D. Bernal first proposed that clay minerals could have served as the sites of accumulation and protection from degradation of the first biopolymers, providing the right physical setting for the evolution of more complex systems. Numerous subsequent experimental studies have reinforced this hypothesis.ResultsThe ability of the possibly widespread prebiotic, clay mineral montmorillonite to protect the catalytic RNA molecule ADHR1 (Adenine Dependent Hairpin Ribozyme 1) from UV-induced damages was experimentally checked. In particular, the self-cleavage reaction of the ribozyme was evaluated after UV-irradiation of the molecule in the absence or presence of clay particles. Results obtained showed a three-fold retention of the self-cleavage activity of the montmorillonite-protected molecule, with respect to the same reaction performed by the ribozyme irradiated in the absence of the clay.ConclusionThese results provide a suggestion with which RNA, or RNA-like molecules, could have overcame the problem of protection from UV irradiation in the RNA world era, and suggest that a clay-rich environment could have favoured not only the formation of first genetic molecules, but also their evolution towards increasingly complex molecular organization.
The primordial metabolism: an ancestral interconnection between leucine, arginine, and lysine biosynthesis
Authors: Fondi Marco , Brilli Matteo , Emiliani Giovanni , Paffetti Donatella , Fani Renato 
Published: August 2007

Abstract

Background
It is generally assumed that primordial cells had small genomes with simple genes coding for enzymes able to react with a wide range of chemically related substrates, interconnecting different metabolic routes. New genes coding for enzymes with a narrowed substrate specificity arose by paralogous duplication(s) of ancestral ones and evolutionary divergence. In this way new metabolic pathways were built up by primordial cells. Useful hints to disclose the origin and evolution of ancestral metabolic routes and their interconnections can be obtained by comparing sequences of enzymes involved in the same or different metabolic routes. From this viewpoint, the lysine, arginine, and leucine biosynthetic routes represent very interesting study-models. Some of the lys, arg and leu genes are paralogs; this led to the suggestion that their ancestor genes might interconnect the three pathways. The aim of this work was to trace the evolutionary pathway leading to the appearance of the extant biosynthetic routes and to try to disclose the interrelationships existing between them and other pathways in the early stages of cellular evolution.

Results
The comparative analysis of the genes involved in the biosynthesis of lysine, leucine, and arginine, their phylogenetic distribution and analysis revealed that the extant metabolic "grids" and their interrelationships might be the outcome of a cascade of duplication of ancestral genes that, according to the patchwork hypothesis, coded for unspecific enzymes able to react with a wide range of substrates. These genes belonged to a single common pathway in which the three biosynthetic routes were highly interconnected between them and also to methionine, threonine, and cell wall biosynthesis. A possible evolutionary model leading to the extant metabolic scenarios was also depicted.

Conclusion
The whole body of data obtained in this work suggests that primordial cells synthesized leucine, lysine, and arginine through a single common metabolic pathway, whose genes underwent a set of duplication events, most of which can have predated the appearance of the last common universal ancestor of the three cell domains (Archaea, Bacteria, and Eucaryotes). The model proposes a relative timing for the appearance of the three routes and also suggests a possible evolutionary pathway for the assembly of bacterial cell-wall.
Global transcription profiling reveals differential responses to chronic nitrogen stress and putative nitrogen regulatory components in Arabidopsis
Authors: Bi Yong-Mei , Wang Rong-Lin , Zhu Tong , Rothstein Steven J 
Published: August 2007

Abstract

Background
A large quantity of nitrogen (N) fertilizer is used for crop production to achieve high yields at a significant economic and environmental cost. Efforts have been directed to understanding the molecular basis of plant responses to N and identifying N-responsive genes in order to manipulate their expression, thus enabling plants to use N more efficiently. No studies have yet delineated these responses at the transcriptional level when plants are grown under chronic N stress and the understanding of regulatory elements involved in N response is very limited.

Results
To further our understanding of the response of plants to varying N levels, a growth system was developed where N was the growth-limiting factor. An Arabidopsis whole genome microarray was used to evaluate global gene expression under different N conditions. Differentially expressed genes under mild or severe chronic N stress were identified. Mild N stress triggered only a small set of genes significantly different at the transcriptional level, which are largely involved in various stress responses. Plant responses were much more pronounced under severe N stress, involving a large number of genes in many different biological processes. Differentially expressed genes were also identified in response to short- and long-term N availability increases. Putative N regulatory elements were determined along with several previously known motifs involved in the responses to N and carbon availability as well as plant stress.

Conclusion
Differentially expressed genes identified provide additional insights into the coordination of the complex N responses of plants and the components of the N response mechanism. Putative N regulatory elements were identified to reveal possible new components of the regulatory network for plant N responses. A better understanding of the complex regulatory network for plant N responses will help lead to strategies to improve N use efficiency.
Large-scale polymorphism of heterochromatic repeats in the DNA of Arabidopsis thaliana
Authors: Davison Jerry , Tyagi Anand , Comai Luca 
Published: August 2007

Abstract

Background
The composition of the individual eukaryote's genome and its variation within a species remain poorly defined. Even for a sequenced genome such as that of the model plant Arabidopsis thaliana accession Col-0, the large arrays of heterochromatic repeats are incompletely sequenced, with gaps of uncertain size persisting in them.

Results
Using geographically separate populations of A. thaliana, we assayed variation in the heterochromatic repeat arrays using two independent methods and identified significant polymorphism among them, with variation by as much as a factor of two in the centromeric 180 bp repeat, in the 45S rDNA arrays and in the Athila retroelements. In the accession with highest genome size as measured by flow cytometry, Loh-0, we found more than a two-fold increase in 5S RNA gene copies relative to Col-0; results from fluorescence in situ hybridization with 5S probes were consistent with the existence of size polymorphism between Loh-0 and Col-0 at the 5S loci. Comparative genomic hybridization results of Loh-0 and Col-0 did not support contiguous variation in copy number of protein-coding genes on the scale needed to explain their observed genome size difference. We developed a computational data model to test whether the variation we measured in the repeat fractions could account for the different genome sizes determined with flow cytometry, and found that this proposed relationship could account for about 50% of the variance in genome size among the accessions.

Conclusion
Our analyses are consistent with substantial repeat number polymorphism for 5S and 45S ribosomal genes among accession of A. thaliana. Differences are also suggested for centromeric and pericentromeric repeats. Our analysis also points to the difficulties in measuring the repeated fraction of the genome and suggests that independent validation of genome size should be sought in addition to flow cytometric measurements.
A new enzymatic route for production of long 5'-phosphorylated oligonucleotides using suicide cassettes and rolling circle DNA synthesis
Authors: Lohmann Jakob S , Stougaard Magnus , Koch Jørn 
Published: August 2007

Abstract

Background
The quality of chemically synthesized oligonucleotides falls with the length of the oligonucleotide, not least due to depurinations and premature termination during production. This limits the use of long oligonucleotides in assays where long high-quality oligonucleotides are needed (e.g. padlock probes). Another problem with chemically synthesized oligonucleotides is that secondary structures contained within an oligonucleotide reduce the efficiency of HPLC and/or PAGE purification. Additionally, ligation of chemically synthesized oligonucleotides is less efficient than the ligation of enzymatically produced DNA molecules.

Results
Chemically synthesized oligonucleotides with hairpin structures were acquired from our standard supplier. The stem of the hairpin contained recognition sequences for the Nt. Alw I nicking enzyme and the Mly I restriction enzyme. These double stranded regions were positioned in a way to allow self-templated circularization of the oligonucleotide. Following ligation, tandem repeats of the complementary sequence of the circular oligonucleotide could be produced through rolling circle DNA synthesis. By running successive rounds of ligation, rolling circle DNA synthesis, and nicking, the original oligonucleotide could be amplified as either the (+)-strand or the (-)-strand. Alternatively, the hairpin structure could be removed by cleavage with the Mly I restriction enzyme, thereby releasing the oligonucleotide sequence contained within the hairpin structure from the hairpin.

Conclusion
We present here a method for the enzymatic production through DNA amplification of oligonucleotides with freely designable 5'-ends and 3'-ends, using hairpin-containing self-templating oligonucleotides. The hairpin comprises recognition sequences for a nicking enzyme and a restriction enzyme. The oligonucleotides are amplified by successive rounds of ligation, rolling circle DNA synthesis and nicking. Furthermore, the hairpin can be removed by cleavage with the Mly I restriction enzyme. We have named such hairpin structures "suicide cassettes".
Between health care and social security – psychiatric patients and the disability pension system in Norway and Russia
Authors: Rezvyy Grigory , Schönfelder Walter , Øiesvold Terje , Olstad Reidun , Midré Georges 
Published: August 2007

Abstract
Background
The official statistics of persons with mental disorders who are granted disability pension (DP) in Russia and Norway indicate large differences between the countries.

Methods
This qualitative explorative hypothesis-generating study is based on text analysis of the laws, regulations and guidelines, and qualitative interviews of informants representing all the organisational elements of the DP systems in both countries.

Results
The DP application process is initiated much later in Norway than in Russia, where a 3 year occupational rehabilitation and adequate treatment is mandatory before DP is granted. In Russia, two instances are responsible for preparing of the medical certification for DP, a patients medical doctor (PD) and a clinical expert commission (CEC) while there is one in Norway (PD). In Russia, the Bureau of Medical-Social Expertise is responsible for evaluation and granting of DP. In Norway, the local social insurance offices (SIO) are responsible for the DP application. Decisions are taken collectively in Russia, while the Norwegian PD and SIO officer often take decisions alone. In Russia, the medical criterion is the decisive one, while rehabilitation and treatment criteria are given priority in Norway. The size of the DP in Norway is enough to cover of subsistences expenditure, while the Russian DP is less than the level required for minimum subsistence.

Conclusion
There were noteworthy differences in the time frame, organisation model and process leading to a DP in the two countries. These differences may explain why so few patients with less severe mental disorders receive a DP in Russia. This fact, in combination with the size of the DP, may hamper reforms of the mental health care system in Russia.
Comparison of PCR-based detection of Plasmodium falciparum infections based on single and multicopy genes
Authors: Oyedeji Segun I , Awobode Henrietta O , Monday Gamaliel C , Kendjo Eric , Kremsner Peter G , Kun Jürgen F 
Published: August 2007

Abstract
PCR-based assays are the most sensitive and specific methods to detect malaria parasites.
This study compared the diagnostic accuracy of three PCR-based assays that do not only differ in their sequence target, but also in the number of copies of their target region, for the detection of Plasmodium falciparum in 401 individuals living in a malaria-endemic area in Nigeria. Compared to a composite reference generated from results of all the 3 PCR assays, the stevor gene amplification had a sensitivity of 100% (Kappa = 1; 95% CI = 1.000–1.000), 83% (Kappa = 0.718; 95% CI = 0.648–0.788) by SSUrRNA gene PCR and 71% (Kappa = 0.552; 95% CI = 0.478–0.627) by the msa-2 gene amplification.
Results from this study indicate that the stevor gene amplification is the most sensitive technique for the detection of P. falciparum. This assay may be an important reference standard, especially when a confirmatory technique with high sensitivity and specificity is needed for ruling out P. falciparum infection.
Variation in Canadian French usage from the 18th to the 19th century
Authors: Martineau France 
Published: August 2007

Abstract
On the basis of private documents (letters, diaries), this article discusses the language use of Canadian French writers from different social classes from the beginning of the 18th century to the end of the 19th century. It first examines the relationship between the writers and the norm and their use of conservative and innovative features with regard to spelling and grammar. Next, it looks into the extent to which non-standard spelling use could be paralleled with vernacular use of morpho-syntactic features.
ne montre pas mon griffonage jan ai honte moi-même
‘Do not show my scribbles, I am ashamed of them’ (18th century)
Writing ability and the written language of Danish private soldiers in the Three Year's War (1848–50)
Authors: Sandersen Vibeke 
Published: August 2007

Abstract
This contribution focuses on letters written by private soldiers from Denmark around the middle of the 19th century. It investigates whether there were statistically significant differences in the orthographic skills between the social groups into which the rural male population could be classified at that time. Apart from the writers' social rank, I look at the correlation between the percentage of norm divergence and the correspondents' place and time of birth, as well as the length of the letter and the repeated use of specific types of divergences by the correspondents.
Differential Response of Adult and Embryonic Mesenchymal Progenitor Cells to Mechanical Compression in Hydrogels
Authors: Terraciano Vanessa , Hwang Nathaniel , Moroni Lorenzo , Park Hyung Bin , Zhang Zijun , Mizrahi Joseph , Seliktar Dror , Elisseeff Jennifer 
Published: August 2007

Abstract
Cells in the musculoskeletal system can respond to mechanical stimuli, supporting tissue homeostasis and remodeling. Recent studies have suggested that mechanical stimulation also influences the differentiation of MSCs, whereas the effect on embryonic cells is still largely unknown. In this study, we evaluated the influence of dynamic mechanical compression on chondrogenesis of bone marrow-derived MSCs and embryonic stem cell-derived (human embryoid body-derived [hEBd]) cells encapsulated in hydrogels and cultured with or without transforming growth factor β-1 (TGF-β1). Cells were cultured in hydrogels for up to 3 weeks and exposed daily to compression for 1, 2, 2.5, and 4 hours in a bioreactor. When MSCs were cultured, mechanical stimulation quantitatively increased gene expression of cartilage-related markers, Sox-9, type II collagen, and aggrecan independently from the presence of TGF-β1. Extracellular matrix secretion into the hydrogels was also enhanced. When hEBd cells were cultured without TGF-β1, mechanical compression inhibited their differentiation as determined by significant downregulation of cartilage-specific genes. However, after initiation of chondrogenic differentiation by administration of TGF-β1, the hEBd cells quantitatively increased expression of cartilage-specific genes when exposed to mechanical compression, similar to the bone marrow-derived MSCs. Therefore, when appropriately directed into the chondrogenic lineage, mechanical stimulation is beneficial for further differentiation of stem cell tissue engineered constructs.
Disclosure of potential conflicts of interest is found at the end of this article.
Static and Dynamic Uncertainty Management for Probabilistic Production Forecast in Chuchupa Field, Colombia
Authors: Rivera Nestor , Meza Nestor , Kim Jeoung , Clark Peter , Garber Raymond , Fajardo Andres , Peña Victoria 
Published: August 2007

SummaryStructural, stratigraphic, and petrophysical uncertainties result in a wide range of geologic interpretations. For fields with a long production and pressure history, 3D dynamic simulations have been very useful in providing feedback to geologic modelers, which results in improved static models. For this study, we developed an integrated static and dynamic workflow to create a range of probabilistic simulation models to forecast dry-gas production under several production scenarios in the Chuchupa field.We selected eight geologic interpretations, representing the range of original gas in place (OGIP) and reservoir geometries determined in the static modeling, to perform dynamic history matches. The OGIP range of the models with very good history matches corresponds closely to the P10 to P90 OGIP range calculated from static modeling.In addition, we calibrated the various models with historical bottomhole and tubinghead flowing pressures and coupled the reservoir model with a network consisting of surface lines and equipment, pipelines from two platforms to the onshore sale-point station, and multistage compression to 1,215 psia. The set of probabilistic models is currently used to evaluate various production and market scenarios.
Using Analytical Solutions in Compositional Streamline Simulation of a Field-Scale CO2-Injection Project in a Condensate Reservoir
Authors: Seto C. J. , Jessen K. , Orr F. M. 
Published: August 2007

Summary
This paper applies compositional streamline simulation to model a real field-scale project that is a combination of enhanced condensate recovery and geologic storage of CO2. These processes are inherently compositional, and detailed compositional fluid descriptions must be used to represent the displacement behavior accurately. We demonstrate that compositional streamline simulation, along with the use of analytical solutions for condensate displacement, is computationally efficient enough to permit high resolution of spatial heterogeneity as well as detailed characterization of the fluid system.
We present a simulation study comparing streamline and finite-difference results for 2D and 3D examples to demonstrate that the compositional streamline method is an efficient computational method for modeling CO2 storage and condensate vaporization in gas reservoirs. Although the streamline method makes many simplifications regarding the effects of gravity and capillary crossflow, in heterogeneity-dominated systems such as the condensate system presented, comparison of finite-difference and streamline results confirms that these simplifications are reasonable.