Miracle-dz/UniFAR-FTUs huggingface dataset:
Base triples in RNA 3D structures: Identifying, clustering and classifying

Neocles B. Leontis, Research Advisor Base triples are recurrent sets of three interacting RNA nucleotides that hydrogen bond to each other along their base edges. Base triples occur frequently in structured RNAs, usually as parts of recurrent structural motifs or of tertiary interactions between parts of the RNA that are distant in the secondary structure. In almost all base triples, the central base interacts with each of the other bases of the triple to form two base pairs. As described in previous work by Leontis and Westhof, RNA nucleotides pair along their Watson-Crick (W), Hoogsteen (H), or Sugar (S) base edges and the resulting base pairs can be classified by identifying the interacting edges and the mutual orientations of the glycosidic bonds of the interacting nucleotides. The main goal of the present work is to test the hypothesis that the geometric base pair classification of Leontis and Westhof can be extended in a natural way to classify base triples geometrically. To test this hypothesis, the research leveraged the large number of RNA molecules that have been solved to atomic resolution by x-ray crystallography and deposited in the Protein Data Bank (PDB). Using a non-redundant (NR) data set of atomic-resolution, RNA-containing x-ray structures, a comprehensive survey of base triples was carried out in parallel with a combinatoric enumeration of base triple families predicted on the basis of the 12 geometric base triple families defined by the Leontis-Westhof nomenclature. This work predicts 108 potential geometric base triple families. Comprehensive searching of atomic-resolution RNA 3D structures found instances of 68 of the 108 predicted base triple families. Model building was carried out to determine which of the remaining 40 families are sterically feasible. Significantly, the proposed iv classification of base triples accounts for all but a handful of base triples observed in the structure database. The exceptions are intermediate cases in which two bases form a WatsonCrick pair and the third base interacts with both bases along their Hoogsteen or Sugar edges, without making a bona fide base pair with either base. An on-line resource was developed based on this classification of base triples that provides exemplars of all the base triples observed in the structure database and models for unobserved, predicted triples, grouped by base triple family, as well as by three-base combinations (see http://rna.bgsu.edu/Triples). This classification helps to identify recurrent triple motifs which can substitute for each other while preserving RNA 3D structure. It can also assist in producing RNA sequence phylogenies. Moreover, the classification is useful for improving methods for aligning evolutionarily related RNA sequences and modeling RNA 3D structures based on sequence alignments, including applications of RNA 3D structure prediction, such as predicting neutral and lethal mutations in structured RNA molecules.
Dynamics and evolution of trans-posable elements

This text presents the evolution of transposable elements (TE). After a description of the main types of elements, their life and death within a species, including regulation of transposition, and their distribution in natural populations and on chromosomes are discused. The impact of TEs on the host genomes, the putative relationship between environment and transposition rates lead to a discussion of the interaction (or co-evolution) between TEs and their host. These results introduce the analysis of the phylogenies of TEs and their interpretations according to different models, for example, horizontal versus vertical transmission. Finally, the question of the origin and the general evolution of TEs is raised from the comparison of conserved regions. Standing orders placed before 31 December 1996 will receive a 10% reduction off the list price of all volumes published within the series between the order date and 31 December 1997. This offer is valid as of June 1996, on a firm order basis only.
STRUCTURAL AND FUNCTIONAL INSIGHTS ON REGULATION BY PHENOLIC COMPOUNDS.

The shikimate pathway is a primary metabolic pathway involved in the synthesis of aromatic compounds in plants, fungi, apicomplexan parasites and microbes. The absence of this pathway in animals makes it ideal for the synthesis of antimicrobial compounds and herbicides. Additionally, its branching into indole hormone synthesis and phenylpropanoid secondary metabolism makes this pathway attractive for metabolic engineering. Here, the focus is on the first step of the shikimate pathway catalyzed by DAHP synthase. This step consists of the condensation of phosphoenol pyruvate and erythrose-4-phosphate to make DAHP, which undergoes another six catalytic steps to synthesize chorismate, the precursor of the aromatic amino acids. Arabidopsis thaliana contains three DAHP synthase isozymes, which are known to indirectly regulate downstream pathways in response to wounding and pathogen stress. The model presented here proposes that DAHP synthase isozymes are regulated by the end products tyrosine, tryptophan and phenylalanine.
Polyphenols and quality of virgin olive oil in retrospect

Polyphenols influence the oxidative stability and sensory quality of virgin olive oil. Studies from the last 30 years are reviewed and the most significant findings are presented. Information is given on the main phenolic compounds detected and identified in olive fruit and oil. In recent years powerful analytical techniques (GC-MS, HPLC-MS, NMR) have been used to investigate the complex nature of olive oil polyphenols. Tyrosol, hydroxytyrosol, oleuropein aglycon and their derivatives with a non-phenolic acid and elenolic acid in free or esterified forms are the main components of the water-methanol extract of virgin olive oil, known as the polar fraction. Total phenol content as determined colorimetrically correlates well with the oxidative stability of the oil. The contribution of individual phenols to oil stability has not been fully investigated. There is still more to be known about the importance of the presence of phenolic components to the sensory quality of the oil.
The effects of temperature and lighting on flowering of lavender (Lavandula angustifolia ‘Hidcote’)

Summary A series of three experiments was conducted to determine the effects of temperature and lighting on bud initiation and flower expression in lavender. A period of nine weeks at 4°C was shown to satisfy the vernalization requirement for all plants, and after five weeks at 4°C, 50% of plants flowered. Vernalization was shown to occur more slowly at temperatures above 4°C and was observed up to 16°C. Following vernalization, a higher temperature advanced bud appearance, with an optimum temperature of 20°C, but reduced the number of buds. When vernalization was incomplete, a higher temperature delayed bud appearance and reduced the number of buds. A daylength of 15 h compared with 8 h either during or after cold treatment increased the number of buds produced, suggesting that additional lighting may be needed for the winter production of plants in flower. Whilst it was possible to model flower development after bud appearance, unexplained variation between experiments in the time to first visible bud prevented satisfactory mathematical description of floral bud production. It was concluded that the “environmental history” of commercially micro-propagated material had a significant effect on the duration of cold required for vernalization, and that differences in the vernalization requirement of individual meristems led to variation in the cold requirements of plants within a crop. The commercial significance of these conclusions is discussed.
Les parasites intestinaux chez les macaques crabier (Macaca Fascicularis). Etude expérimentale et recommandations pour la diagnose et la gestion des rhizoflagelles et des cilies

Le Macaque crabier est actuellement le primate non-humain le plus utilise pour la recherche biomedicale. Afin d'obtenir un modele le plus standardise, il est necessaire de connaitre le statut sanitaire des animaux. Les infestations parasitaires sont courantes chez les primates non-humains. L'etude effectuee au Centre de Primatologie de Strasbourg a permis de mettre en evidence une infestation parasitaire specifique des primates provenant d'elevage. Les rhizoflagelles et les cilies representent la majorite des parasites retrouves lors d'examens coproscopiques. La reconnaissance et la gestion de ces parasites sont essentielles chez des primates destines a la recherche biomedicale.
Genotype Frequency of Human Papillomavirus Determined by PCR and DNA Sequencing in Korean Women

Human Papilloma viruses (HPVs) are etiological agents for cervical cancer and are classified into lowand high-risk categories. The aim of this study was to determine the frequency of the HPV genotype in the HPV screening test of Korean women using PCR-direct sequencing. Consensus primers of L1 legion were used for the amplification of HPV DNA and the PCR products (450 bps) obtained were analyzed by automatic sequencing. Sequences were compared with those in GenBank by using the BLAST program. Cervical swab samples of 3,978 women (20-73 years) were tested and the average age was 37.6 years. In this study, 1,174 samples were HPV positive out of 3,978 cervical swab samples screened (29.5%) and 136 samples (11.6%) showed a double infection. A total of 1,310 HPV genotypes were analyzed. The HPV positive rate was the lowest in the 20 years group (69.5%) and most of the samples of the > 60 years group were found HPV positive. Among thirty seven different HPV types identified by sequencing, 21 were HPV high risk types and 16 HPV low risk types were 69.8% (914/1,310) and 26.0% (340/1,310), respectively. In HPV high-risk types, 16 (13.21%), was the most frequently found. HPV 53 (9.62%) and 58 (9.24%) were also frequently found. This group was followed by HPV types 70 (5.50%), 33 (4.73%), 66 (4.20%), 18 (4.05%), 52 (4.05%), 31 (3.97%) and 56 (3.51%) in descending order of frequency. Among HPV low-risk types, 62 (4.20%), 6 (3.59%), 81 (3.59%), 84 (3.51%), and 11 (2.6%) were frequently found. In conclusion, PCR-direct sequencing could be used for quick and reliable typing of known and novel HPVs from clinical specimens. This data could be useful for epidemiological study of HPV and it also allows type-specific follow-up of women who have been treated for cervical intraepithelial neoplasia.
PIGMENTATION CHARACTERS: AN EXAMPLE OF SANKOFF CHARACTERS FROM TINAMOU PHYLOGENY

– In a cladistic analysis of tinamous, special attention was paid to character definition and scoring of non-traditional characters for phylogenetic reconstruction of birds. For example, transformation costs between states were applied (Sankoff characters) to analyze the egg coloration on the basis of pigment composition. In this scheme, lesser costs were assigned to transformations between more similar states. This approach is similar to that applied to plumage characters (overlap of pigmentation patterns) in a previous study. The present study shows that changes between several states of pigmentation characters are not a consequence of the imposed penalty in the cost regime, but an interaction with other characters. This is interpreted as evidence that multistate characters with complex costs among characters states (as in pigmentation characters) are not an artifact and should be used to describe relative degrees of similarity. Accepted 28 January 2004.
DISSECTING THE ROLE OF THE GLUCOCORTICOID RECEPTOR IN EMBRYONIC CORTICAL DEVELOPMENT: INSIGHTS FROM IN UTERO GLUCOCORTICOID EXPOSURE

Synthetic glucocorticoids (GCs) such as dexamethasone (DEX), are given to pregnant women to reduce the incidence of respiratory distress syndrome and intraventricular hemorrhage in premature infants. However, animal and human studies reveal adverse effects of DEX on cerebral cortical development. Understanding the basis for these negative neurological consequences of prenatal GCs would be aided by a detailed description of the developmental and spatial expression profile of the glucocorticoid receptor (GR) in neural stem/progenitor cells. This could provide mechanistic understanding of the impact of premature activation of GR signaling in the developing brain, particularly since endogenous GC levels are low during the period of fetal development at which DEX is administered. In this study we show that GR protein is expressed in cortical radial glia cells (RGCs) and intermediate progenitor cells (IPCs) from embryonic day 11.5 in the mouse. Furthermore, in many areas of the fetal brain, GR was primarily nuclear at times when endogenous GCs are expected to be low. We also examined the consequences of prenatal DEX exposure and found that a single, clinically relevant DEX dose at midgestation (E14.5) reduced cortical thickness and surface on E17.5, but increased the number of neurons throughout the cortex, including in deep layer VI. BrdU birthdating revealed that the BrdU+ progeny of the E14.5 progenitors was increased by DEX. Furthermore, while a higher proportion migrated in the cortical plate, a smaller proportion remained in the progenitor zone, suggesting that DEX promoted precocious neurogenesis. Accordingly, after a single, 24 hour exposure on E14.5, DEX induced a neurogenic fate shift in progenitors in an S-phase-specific manner. Specifically in non-S-RGCs DEX promoted the IPC fate, while it induced re-entry of S-phase RGCs and expansion primarily of the neurogenic RGC pool (BrdU+). DEX induced neurogenic divisions of S-phase RGCs and S-phase IPCs causing increase of the BrdU+ cells. FACs analysis verified the neurogenic shift in S-phase BrdU+ progenitors, which accumulated in G0G1 phase. Collectively, these results suggest that premature, DEX-induced activation of GR induces cell cycle phase-dependent precocious neurogenesis and highlights a role for GR in regulating neurogenesis in the developing brain.
Detection of quantitative trait loci for intramuscular fat content and lipogenic enzyme activities in Meishan × Large White F2 pigs.

Institut National de la Recherche Agronomique, France 1 Station de Génétique Quantitative et Appliquée 78352 Jouy-en-Josas Cedex 2 INRA Laboratoire de Génétique Cellulaire, 31326 Castanet Tolosan Cedex 3 INRA Laboratoire de Radiobiologie et d’Etude du Génome 78352 Jouy-en-Josas Cedex 4 INRA Station Expérimentale de Sélection Porcine, 86480 Rouillé 5 INRA Unité Mixte de Recherches sur le Veau et le Porc, 35590 Saint Gilles
Long-Term Dynamics of a Wood Thrush Population Breeding in a Forest Fragment

ABsmAcT. -The dynamics of a population of Wood Thrushes (Hylocichla mustelina) in a Delaware woodlot from 1974 through 1990 did not meet all predictions of the forest-fragmentation hypothesis, which posits that declining abundance of Neotropical, migratory, forest songbirds results from poor reproduction in, and immigration to, forest fragments. Abundance declined at an average rate of 4% per year over the period 1978 through 1987, equalling the national decline found by the Breeding Bird Survey for those years, but recovered by 1990 to pre-decline levels. Abundance of previous residents followed a similar pattern, the only population component to do so. Abundance of new immigrants and of returning, locally produced young was generally stable. Throughout the study, reproductive rates were high enough to maintain the population at the return rates observed early and late in the study. However, a sustained episode of reduced production per female and of an increased percentage of adults failing to produce any young generally coincided with the decline in abundance. When the failure rate later dropped, return rate and abundance subsequently increased. We conclude that a period of elevated, predation-caused failure prompted greater emigration by an ever-younger, less-site-faithful population. High emigration coupled with stable immigration, stable recruitment of local young, and even normal mortality of residents would yield a declining population. A regional predation episode could cause a broader decline in abundance through several mechanisms that could reduce the number of available immigrants. Received 25 March 1991, accepted 9 November 1992.
The 'K' selected oligophilic bacteria: a key to uncultured diversity?

Molecular techniques have made it increasingly clear that a large proportion of bacterial diversity in natural habitats is uncultured and therefore unexplored. We suggest and give evidence in support of a hypothesis that a large proportion, if not all, of the uncultured diversity from a variety of aquatic and terrestrial habitats are oligophilic (oligotrophic) bacteria. Oligophilic bacteria grow only on dilute nutrient media and form small or microscopic colonies. A technique to cultivate and isolate the moderately oligophilic bacteria was developed and 90 cultures isolated, The twelve bacterial cultures characterized showed high growth yield coefficients and carbon conversion efficiencies at low substrate concentrations and progressively decreased with increasing substrate concentrations. Most of the growth yields were substantially higher than those reported in the literature and lie near the theoretical maximum. Slow growth rates and high yields indicate that they are 'K' selected species. 16S rDNA partial sequence analysis of the isolates indicates that it is a novel as well as diverse group.
Vegetative propagation of Strelitzia reginae.

Strelitzia reginae is propagated either by division of naturally developed branches known as fans or by seeds. Vegetative propagation by division is limited by a low rate of multiplication being 0.5–1.5 divisions per branch per year. Branching originates in the division of the apical dome with an absolute abscence of branching from axillary buds. Propagation by seeds is undesirable due to juvenility and genetic variation. Therefore induction of branching to increase the multiplication rate of Strelitzia by elimination of apical dominance was the purpose of this study. Selected plants were excavated and divided in fans. After shortening the roots to 20 cm, the fans were planted in containers and left for recovery and root regeneration. Then the apex was reached by a triangular excision of a part of the plant with a transversal cut 8–12 mm above the basal plate throughout the basal leaf sheaths keeping the leaves in contact with the roots. Thereafter the apex was removed and after 2–6 months lateral sprouts developed, varying in number from 2 to 30 per fan depending on age and size of the fan. In order to obtain shoots with roots most of the old roots were removed and during the next 6 months the newly formed laterals, rooted and could be divided in individual plants. These plants could be treated again from one year on. The total period for the sequential processes took one year
Razvoj in implementacija orodja za določanje individualne ogroženosti za rakom dojk v slovenski populaciji

Various mathematical models for calculating individual breast cancer risk are known nowadays. Currently, the Tyrer-Cuzick algorithm included in the IBIS program is recognized as the most consistent one. In Slovenia, the S-IBIS software was developed within the framework of the Targeted Research Project Development and Implementation of Personalised Breast Cancer Risk Evaluation Tool for Slovenian Population, which is being carried out at the Institute of Oncology Ljubljana. Slovenian IBIS (S-IBIS) is specifically designed to calculate the individual risk of breast cancer in Slovenian women. It is an adjustment of the IBIS software, where Slovenian generation specific population breast cancer risks are applied. S-IBIS is ready for use in the Slovene health system and allows an evidence-based assignment of an asymptomatic individual to a group of general, moderate and high breast cancer risk. As a cut-off for the moderate risk group the S-IBIS life-time risk of 16 percent or more is suggested for a Slovene women at age 25. The cut-offs for ten-years risk are offered as well. Compared with today's system, where the Terms of the health prevention at the primary health care level classifies breast cancer high risk women applying very subjective qualitative criteria, it is today already possible to classify asymptomatic Slovenian women to a group of general, moderate and high breast cancer risk on the basis of individual numerical criteria using S-IBIS software. Pilot testing of the S-IBIS in the national Breast Disease Centers shows encouraging results - we believe that the implementation of S-IBIS in the Slovenian healthcare system could reduce the number of unnecessary preventive interventions, while also reducing the waiting time for justified preventive examinations of moderate and high risk women.
The potentials of multi-nutrient soil extraction with 0.01 M CaCl2 in nutrient management

Key words: 0.01 M CaCl 2 , soil testing, nutrient management, decision-making, multi-nutrient Aim of this thesis is to improve the understanding of nutrient dynamics in soil and thereby to improve decision-making in nutrient management. There is a need for a more mechanistic approach of decision-making because the classical approaches cannot comply with the tightening up of legislation and boundary conditions for sustainable agricultural production. The thesis encompasses eight separate papers in which the mechanistic backgrounds of the 0.01 M CaCl 2 soil extraction procedure has been studied as well as the perspectives of the design of a multi-nutrient CaCl 2 soil testing program. The studies have been focussed on the cations Ca, Mg and K. Although the use of CaCl 2 as a soil extractant is promising, it is concluded that the design of a multi-nutrient CaCl 2 soil testing program is time-consuming and costly. A framework for decision-making in nutrient management has been worked out. In this framework the multi-nutrient 0.01 M CaCl 2 soil extraction procedure is used as a standardized procedure to give a chemical characterization of soils at a pH and ionic strength comparable to field conditions. This characterization is used as input in a soil chemical model to calculate nutrient speciation and nutrient distribution under varying conditions. This nutrient speciation and distribution is used to characterize the pool of plant available soil nutrient. It is proposed to integrate the CaCl 2 soil extraction procedure with a soil chemical model, a crop growth model, a soil microbiological, a soil hydraulic model and an optimization procedure into a practical tool for nutrient management decision-making. This tool can then be used i) to tune plant nutrient requirements for maximal crop production and crop quality to the magnitude of the pool of plant available soil nutrient in time and space, and ii) to optimize farm activities in order to comply with more and stricter legislation and boundary conditions related to nutrient management. It is concluded that the perspectives of the multi-nutrient CaCl 2 soil extraction procedure in mechanistic soil nutrient models and in nutrient management are promising.