Electrophoretic mobility of supercoiled, catenated and knotted DNA molecules.

We systematically varied conditions of two-dimensional (2D) agarose gel electrophoresis to optimize separation of DNA topoisomers that differ either by the extent of knotting, the extent of catenation or the extent of supercoiling. To this aim we compared electrophoretic behavior of three different families of DNA topoisomers: (i) supercoiled DNA molecules, where supercoiling covered the range extending from covalently closed relaxed up to naturally supercoiled DNA molecules; (ii) postreplicative catenanes with catenation number increasing from 1 to ∼15, where both catenated rings were nicked; (iii) knotted but nicked DNA molecules with a naturally arising spectrum of knots. For better comparison, we studied topoisomer families where each member had the same total molecular mass. For knotted and supercoiled molecules, we analyzed dimeric plasmids whereas catenanes were composed of monomeric forms of the same plasmid. We observed that catenated, knotted and supercoiled families of topoisomers showed different reactions to changes of agarose concentration and voltage during electrophoresis. These differences permitted us to optimize conditions for their separation and shed light on physical characteristics of these different types of DNA topoisomers during electrophoresis.

Viticulture under climate change : understanding vulnerability and adaptive capacity of wineries and growers. A case study in El Penedès region, Catalonia

Climate change may pose challenges and opportunities to viticulture, and much research has focused in studying the likely impacts on grapes and wine production in different regions worldwide. This study assesses the vulnerability and adaptive capacity of the viticulture sector under changing climate conditions, based on a case study in El Penedès region, Catalonia. Farm assets, livelihood strategies, farmer-market interactions and climate changes perceptions are analysed through semi-structured interviews with different types of wineries and growers. Both types of actors are equally exposed to biophysical stressors but unevenly affected by socioeconomic changes. While wineries are vulnerable because of the current economic crisis and the lack of diversification of their work, which may affect their income or production, growers are mainly affected by the low prices of their products and the lack of fix contracts. These socioeconomic stressors strongly condition their capacity to adapt to climate change, meaning that growers prioritize their immediate income problems, rather than future socioeconomic or climate threats. Therefore, growers undertake reactive adaptation to climate changing conditions, mainly based on ancient knowledge, whilst wineries combine both reactive and anticipatory adaptation practices. These circumstances should be addressed in order to allow better anticipatory adaptation to be implemented, thus avoiding future climate threats.

Networking of differentially expressed genes in human cancer cells resistant to methotrexate

BACKGROUND: The need for an integrated view of data obtained from high-throughput technologies gave rise to network analyses. These are especially useful to rationalize how external perturbations propagate through the expression of genes. To address this issue in the case of drug resistance, we constructed biological association networks of genes differentially expressed in cell lines resistant to methotrexate (MTX). METHODS: Seven cell lines representative of different types of cancer, including colon cancer (HT29 and Caco2), breast cancer (MCF-7 and MDA-MB-468), pancreatic cancer (MIA PaCa-2), erythroblastic leukemia (K562) and osteosarcoma (Saos-2), were used. The differential expression pattern between sensitive and MTX-resistant cells was determined by whole human genome microarrays and analyzed with the GeneSpring GX software package. Genes deregulated in common between the different cancer cell lines served to generate biological association networks using the Pathway Architect software. RESULTS: Dikkopf homolog-1 (DKK1) is a highly interconnected node in the network generated with genes in common between the two colon cancer cell lines, and functional validations of this target using small interfering RNAs (siRNAs) showed a chemosensitization toward MTX. Members of the UDP-glucuronosyltransferase 1A (UGT1A) family formed a network of genes differentially expressed in the two breast cancer cell lines. siRNA treatment against UGT1A also showed an increase in MTX sensitivity. Eukaryotic translation elongation factor 1 alpha 1 (EEF1A1) was overexpressed among the pancreatic cancer, leukemia and osteosarcoma cell lines, and siRNA treatment against EEF1A1 produced a chemosensitization toward MTX. CONCLUSIONS: Biological association networks identified DKK1, UGT1As and EEF1A1 as important gene nodes in MTX-resistance. Treatments using siRNA technology against these three genes showed chemosensitization toward MTX.

Ecology and life history affect different aspects of the population structure of 27 high-alpine plants.

A plant species' genetic population structure is the result of a complex combination of its life history, ecological preferences, position in the ecosystem and historical factors. As a result, many different statistical methods exist that measure different aspects of species' genetic structure. However, little is known about how these methods are interrelated and how they are related to a species' ecology and life history. In this study, we used the IntraBioDiv amplified fragment length polymorphisms data set from 27 high-alpine species to calculate eight genetic summary statistics that we jointly correlate to a set of six ecological and life-history traits. We found that there is a large amount of redundancy among the calculated summary statistics and that there is a significant association with the matrix of species traits. In a multivariate analysis, two main aspects of population structure were visible among the 27 species. The first aspect is related to the species' dispersal capacities and the second is most likely related to the species' postglacial recolonization of the Alps. Furthermore, we found that some summary statistics, most importantly Mantel's r and Jost's D, show different behaviour than expected based on theory. We therefore advise caution in drawing too strong conclusions from these statistics.

L'agrégation toxique des protéines: une forme de "delinquance moléculaire" activement combattue dans la cellule par les chaperones moléculaires et les protéases [The toxic aggregation of proteins: a kind of "molecular delinquency" actively fought in the cell by molecular chaperones and proteases]

Under various stresses, mutation-sensitised proteins may spontaneously convert into inactive, aggregation-prone structures, which may be cytotoxic and infectious. In the cell, this new kind of "molecular criminality" is actively fought against by a network of molecular chaperones that can specifically identify, isolate and unfold damaged (delinquent) proteins and favour their subsequent native refolding. Irreversibly damaged molecules unable to natively refold are preferentially "executed" and recycled by proteases. Failing that, they are "imprisoned" within compact amyloids, or "evicted" from the cell. Thus, striking parallels, although of questionable ethical value, exist between protein and human criminality, and between the cellular and social responses to these different types of criminality. Fundamental differences also exist. Whereas programmed death (apoptosis) is the preferred solution chosen by aged and aggregation-stressed cells, collective suicide is seldom an option chosen by lawless human societies. More significantly, there is no clear cellular equivalent for the role of the family and the education system, which are so essential to the proper shaping of functional individuals in the society, and give rise to humanism, that favours crime prevention, reeducation and reinsertion programs over capital punishment. To the cardiologist and transplantation surgeon, the interest of molecular chaperones, in particular of Hsp70, Hsp90 and Hsp27, lays in their ability to inhibit the signalling pathway of programmed cell death. Their induction before and during ischemia, by various treatments and drugs could significantly reduce damages from the post ischemic reperfusion of organs.

Concept of fat balance in human obesity revisited with particular reference to de novo lipogenesis.

The measurement of fat balance (fat input minus fat output) involves the accurate estimation of both metabolizable fat intake and total fat oxidation. This is possible mostly under laboratory conditions and not yet in free-living conditions. In the latter situation, net fat retention/mobilization can be estimated based on precise and accurate sequential body composition measurements. In case of positive balance, lipids stored in adipose tissue can originate from dietary (exogenous) lipids or from nonlipid precursors, mainly from carbohydrates (CHOs) but also from ethanol, through a process known as de novo lipogenesis (DNL). Basic equations are provided in this review to facilitate the interpretation of the different subcomponents of fat balance (endogenous vs exogenous) under different nutritional circumstances. One difficulty is methodological: total DNL is difficult to measure quantitatively in man; for example, indirect calorimetry only tracks net DNL, not total DNL. Although the numerous factors (mostly exogenous) influencing DNL have been studied, in particular the effect of CHO overfeeding, there is little information on the rate of DNL in habitual conditions of life, that is, large day-to-day fluctuations of CHO intakes, different types of CHO ingested with different glycemic indexes, alcohol combined with excess CHO intakes, etc. Three issues, which are still controversial today, will be addressed: (1) Is the increase of fat mass induced by CHO overfeeding explained by DNL only, or by decreased endogenous fat oxidation, or both? (2) Is DNL different in overweight and obese individuals as compared to their lean counterparts? (3) Does DNL occur both in the liver and in adipose tissue? Recent studies have demonstrated that acute CHO overfeeding influences adipose tissue lipogenic gene expression and that CHO may stimulate DNL in skeletal muscles, at least in vitro. The role of DNL and its importance in health and disease remain to be further clarified, in particular the putative effect of DNL on the control of energy intake and energy expenditure, as well as the occurrence of DNL in other tissues (such as in myocytes) in addition to hepatocytes and adipocytes.

Clinical management and burden of bipolar disorder: a multinational longitudinal study (WAVE-bd Study)

BACKGROUND: Studies in bipolar disorder (BD) to date are limited in their ability to provide a whole-disease perspective--their scope has generally been confined to a single disease phase and/or a specific treatment. Moreover, most clinical trials have focused on the manic phase of disease, and not on depression, which is associated with the greatest disease burden. There are few longitudinal studies covering both types of patients with BD (I and II) and the whole course of the disease, regardless of patients' symptomatology. Therefore, the Wide AmbispectiVE study of the clinical management and burden of Bipolar Disorder (WAVE-bd) (NCT01062607) aims to provide reliable information on the management of patients with BD in daily clinical practice. It also seeks to determine factors influencing clinical outcomes and resource use in relation to the management of BD. METHODS: WAVE-bd is a multinational, multicentre, non-interventional, longitudinal study. Approximately 3000 patients diagnosed with BD type I or II with at least one mood event in the preceding 12 months were recruited at centres in Austria, Belgium, Brazil, France, Germany, Portugal, Romania, Turkey, Ukraine and Venezuela. Site selection methodology aimed to provide a balanced cross-section of patients cared for by different types of providers of medical aid (e.g. academic hospitals, private practices) in each country. Target recruitment percentages were derived either from scientific publications or from expert panels in each participating country. The minimum follow-up period will be 12 months, with a maximum of 27 months, taking into account the retrospective and the prospective parts of the study. Data on demographics, diagnosis, medical history, clinical management, clinical and functional outcomes (CGI-BP and FAST scales), adherence to treatment (DAI-10 scale and Medication Possession Ratio), quality of life (EQ-5D scale), healthcare resources, and caregiver burden (BAS scale) will be collected. Descriptive analysis with common statistics will be performed. DISCUSSION: This study will provide detailed descriptions of the management of BD in different countries, particularly in terms of clinical outcomes and resources used. Thus, it should provide psychiatrists with reliable and up-to-date information about those factors associated with different management patterns of BD. TRIAL REGISTRATION NO: ClinicalTrials.gov: NCT01062607.

Evaluation of the Need for Longitudinal Median Joints in Bridge Decks on Dual Structures, TR-661, 2015

The primary objective of this project was to determine the effect of bridge width on deck cracking in bridges. Other parameters, such as bridge skew, girder spacing and type, abutment type, pier type, and number of bridge spans, were also studied. To achieve the above objectives, one bridge was selected for live-load and long-term testing. The data obtained from both field tests were used to calibrate a three-dimensional (3D) finite element model (FEM). Three different types of loading—live loading, thermal loading, and shrinkage loading—were applied. The predicted crack pattern from the FEM was compared to the crack pattern from bridge inspection results. A parametric study was conducted using the calibrated FEM. The general conclusions/recommendations are as follows: -- Longitudinal and diagonal cracking in the deck near the abutment on an integral abutment bridge is due to the temperature differences between the abutment and the deck. Although not likely to induce cracking, shrinkage of the deck concrete may further exacerbate cracks developed from thermal effects. -- Based upon a limited review of bridges in the Iowa DOT inventory, it appears that, regardless of bridge width, longitudinal and diagonal cracks are prevalent in integral abutment bridges but not in bridges with stub abutments. -- The parametric study results show that bridge width and skew have minimal effect on the strain in the deck bridge resulting from restrained thermal expansion. -- Pier type, girder type, girder spacing, and number of spans also appear to have no influence on the level of restrained thermal expansion strain in the deck near the abutment.

Silver-base metal epithermal vein and listwaenite types of deposit Crnac, Rogozna Mts., Kosovo. Part I: Ore mineral geochemistry and sulfur isotope study

Pb-Zn-Ag vein and listwaenite types of mineralization in Crnac deposit, Western Vardar zone, were deposited within several stages: (i) the pre-ore stage comprises pyrite, arsenopyrite, pyrrhotite, quartz, kaolinite and is followed by magnetite-pyrite; (ii) the syn-ore stage is composed of galena, sphalerite, tetrahedrite and stefanite; and (iii) the post-ore stage is composed of carbonates, pyrite, arsenopyrite and minor galena. The vein type mineralization is hosted by Jurassic amphibolites and veins terminate within overlying serpentinites. Mineralized listwaenites are developed along the serpentinite-amphibolite interface. The reserves are estimated to 1.7 Mt of ore containing in average 7.6% lead, 2.9% zinc, and 102 g/t silver. Sulfides from the pre- and syn-mineralization assemblage of the vein- and listwaenite-types of mineralization from the Crnac Pb-Zn-Ag deposit have been analyzed using microprobe, crush-leachates and sulfur isotopes. The pre-ore assemblage precipitated under high sulfur fugacities (f(S(2)) = 10(-8)-10(-6) bar) from temperatures ranging between 350 degrees C and 380 degrees C. Most likely water-rock reactions, boiling and/or increase of pH caused an increase of delta(34)S of pyrite toward upper levels within the deposit. The decomposition of pre-ore pyrrhotite to a pyrite-magnetite mixture occurred at a fugacity of sulfur from f(S(2)) = 8.7 x 10(-10) to 9.6 x 10(-9) bar and fugacity of oxygen from f(O(2)) = 2.4 x 10(-30) to 3.1 x 10(-28) bars, indicating a contribution of an oxidizing fluid, i.e. meteoric water during pre-ore stages of hydrothermal activity. The crystallization temperatures obtained by the sphalerite-galena isotope geothermometer range from 230 to 310 degrees C. The delta(34)S values of pre- and syn-ore sulfides (pyrite, galena, sphalerite, delta(34)S = 0.3-5.9 parts per thousand) point to magmatic sulfur. Values of delta(34)S of galena and sphalerite are decreasing upwards due to precipitation of early formed sulfide minerals. Post-ore assemblage precipitated at temperature below 190 degrees C. Based on data presented above, we assume two fluid sources: (i) a magmatic source, supported by sulfur isotopic compositions within pre- and syn-ore minerals and a high mol% of fluorine found within pre- and syn-ore leachates, and (ii) a meteoric source, deduced by coincident pyrite-magnetite intergrowth, sulfur isotopic trends within syn-ore minerals and decrease of crystallization temperatures from the pre-ore stage (380-350 degrees C), towards the syn-ore (310-215 degrees C) and post-ore stages (<190 degrees C). Post-ore fluids are Na-Ca-Mg-K-Li chlorine rich and were modified via water-rock reactions. Simple mineral assemblage and sphalerite composition range from 1.5 to 10.1 mol% of FeS catalog Crnac to a group of intermediate sulfidation epithermal deposit. (C) 2011 Elsevier B.V. All rights reserved.

Dynamic Modelling of Material Flows and Sustainable Resource Use: Case Studies in Regional Metabolism and Space Life Support Systems

Sustainable resource use is one of the most important environmental issues of our times. It is closely related to discussions on the 'peaking' of various natural resources serving as energy sources, agricultural nutrients, or metals indispensable in high-technology applications. Although the peaking theory remains controversial, it is commonly recognized that a more sustainable use of resources would alleviate negative environmental impacts related to resource use. In this thesis, sustainable resource use is analysed from a practical standpoint, through several different case studies. Four of these case studies relate to resource metabolism in the Canton of Geneva in Switzerland: the aim was to model the evolution of chosen resource stocks and flows in the coming decades. The studied resources were copper (a bulk metal), phosphorus (a vital agricultural nutrient), and wood (a renewable resource). In addition, the case of lithium (a critical metal) was analysed briefly in a qualitative manner and in an electric mobility perspective. In addition to the Geneva case studies, this thesis includes a case study on the sustainability of space life support systems. Space life support systems are systems whose aim is to provide the crew of a spacecraft with the necessary metabolic consumables over the course of a mission. Sustainability was again analysed from a resource use perspective. In this case study, the functioning of two different types of life support systems, ARES and BIORAT, were evaluated and compared; these systems represent, respectively, physico-chemical and biological life support systems. Space life support systems could in fact be used as a kind of 'laboratory of sustainability' given that they represent closed and relatively simple systems compared to complex and open terrestrial systems such as the Canton of Geneva. The chosen analysis method used in the Geneva case studies was dynamic material flow analysis: dynamic material flow models were constructed for the resources copper, phosphorus, and wood. Besides a baseline scenario, various alternative scenarios (notably involving increased recycling) were also examined. In the case of space life support systems, the methodology of material flow analysis was also employed, but as the data available on the dynamic behaviour of the systems was insufficient, only static simulations could be performed. The results of the case studies in the Canton of Geneva show the following: were resource use to follow population growth, resource consumption would be multiplied by nearly 1.2 by 2030 and by 1.5 by 2080. A complete transition to electric mobility would be expected to only slightly (+5%) increase the copper consumption per capita while the lithium demand in cars would increase 350 fold. For example, phosphorus imports could be decreased by recycling sewage sludge or human urine; however, the health and environmental impacts of these options have yet to be studied. Increasing the wood production in the Canton would not significantly decrease the dependence on wood imports as the Canton's production represents only 5% of total consumption. In the comparison of space life support systems ARES and BIORAT, BIORAT outperforms ARES in resource use but not in energy use. However, as the systems are dimensioned very differently, it remains questionable whether they can be compared outright. In conclusion, the use of dynamic material flow analysis can provide useful information for policy makers and strategic decision-making; however, uncertainty in reference data greatly influences the precision of the results. Space life support systems constitute an extreme case of resource-using systems; nevertheless, it is not clear how their example could be of immediate use to terrestrial systems.

Anorectal anomalies associated with or as part of other anomalies.

Anorectal anomalies occurring with other anomalies or as part of syndromes were analyzed to determine how their epidemiological characteristics differed from those of isolated anal anomalies. Almost 15% of cases were chromosomal, monogenic or teratogenic syndromes, whereas the rest were of unknown cause including sequences (9.3%), VACTERL associations (15.4%) and multiple congenital anomalies (MCA) (60.2%). Almost half of babies with MCA had one or two VACTERL anomalies with distribution frequencies that did not differ significantly from those in babies with the full VACTERL association. There were considerable differences in the frequency of the VACTERL association among babies with different types of anorectal anomaly. Babies with anal anomalies occurring with sequences, VACTERL or MCA showed the same sex differences as babies with isolated anal anomalies, namely male predominance in anal atresia without fistula or cloaca, no sex difference in anal atresia with fistula, and female predominance in ectopic anus and congenital anal fistula. These anomalies, however, were associated with significantly lower mean gestational lengths and birth weights, and higher frequencies of fetal death and pregnancy termination than babies with isolated anal anomalies. Twins were more frequent in sequences, VACTERL and MCA than in isolated anomalies, monogenic syndromes or chromosome anomalies. Five cases were conjoined twins, representing 15% of all cases of twin pregnancies with an anal anomaly. Indeterminate sex was more frequent in babies with anal atresias without fistula than in those with fistula. Anal anomalies are defects of blastogenesis attributable to disorders in expression of pattern determining genes. The differential sex involvement in different types of anal anomaly may be manifestations of expression of the HY/SRY genes during blastogenesis or of X-linkage.

Analysis of the antibiotic prophylaxis prescribed by Spanish oral surgeons

Aim: To identify prophylactic antibiotic prescription practices among Spanish dentists with preferential dedication to Oral Surgery in different types of tooth extraction surgeries. Method: Members of the Spanish Oral Surgery Society were surveyed on antibiotic prophylaxis use in 4 different tooth extraction modalities scaled according to their surgical invasiveness. Results: Sixty-nine of the 105 distributed questionnaires were returned completed. Thirteen percent of the surveyed surgeons would prescribe antibiotics to prevent postoperative wound infection when confronted with conventional tooth extraction lasting less than 5 minutes. In the case of surgery lasting more than 5 minutes, the percentage of participants that would prescribe antibiotics increased to 39%. When a mucoperiosteal flap was elevated or an ostectomy was performed, 87% and 100%, respectively, would prescribe antibiotic prophylaxis. Amoxicillin and its combination with clavulanic acid were the most commonly prescribed antibiotics. All participants would prescribe the antibiotic orally, starting after surgery and with a duration that ranged from 2-8 days. Conclusions: The results obtained suggest that antibiotic prophylaxis for preventing local odontogenic infection is not being correctly implemented in Spain. This can generate new bacterial resistances, facilitate adverse drug reactions and favor opportunistic infections. Better designed studies are needed in order to clarify the role of antibiotics in the prevention of postsurgical wound infection

Impact of Left-Turn Phasing on Older and Younger Drivers at High-Speed Signalized Intersections, 2004

Several recent studies have demonstrated differences in safety between different types of left-turn phasing—protected, permitted, and protected/permitted phasing. The issue in question is whether older and younger drivers are more affected by a particular type of left-turn phasing at high-speed signalized intersections and whether they are more likely to contribute to a left-turn related crash under a specific type of left-turn phasing. This study evaluated the impact of different types of left-turn phasing on older and younger drivers at high-speed signalized intersections in Iowa. High-speed signalized intersections were of interest since oncoming speeds and appropriate gaps may be more difficult to judge for older drivers and those with less experience. A total of 101 intersections from various urban locations in Iowa with at least one intersecting roadway with a posted speed limit of 45 mph or higher were evaluated. Left-turn related crashes from 2001 to 2003 were evaluated. Left-turn crash rate and severity for young drivers (14- to 24-year-old), middle-age drivers (25- to 64-year-old), and older drivers (65 years and older) were calculated. Poisson regression was used to analyze left-turn crash rates by age group and type of phasing. Overall, left-turn crash rates indicated that protected phasing is much safer than protected/permitted and permitted phasing. Protected/permitted phasing had the highest left-turn crash rates overall.