Deformation Sequence and Paleofluids in Carbonate Buckle Folds Under Transpression (Pag Anticline, External Dinarides, Croatia)

Contractional deformation structures at the front of transpressional orogens display complex three-dimensional geometries deviating from the interpretative templates commonly applied in thrust belts. Accordingly, detailed constraints on deformation patterns and associated paleofluid circulation are desirable, especially for fracture geometry and permeability predictive purposes. The Pag anticline, which is located in the Dinaric fold and thrust belt, provides an appropriate field site for studying fold- and fault-related deformation structures in a transpressive setting. We performed a multiscale structural analysis together with petrographic and stable isotope characterization of the deformation-related calcite cements. Structural mapping suggests that the Pag anticline is a detachment fold developed mainly by buckling, since large-scale thrust faults are absent. Fold tightening in a transpressive setting produced a complex deformational structure including two sets of N-S right-lateral and E-W left-lateral late-stage strike-slip fault sets trending oblique to the NW-SE fold axis. The pre-folding deformation pattern includes incipient normal faults likely related to the forebulge stage, veins and stylolites coherent with NE-SW layer parallel shortening contraction in a strike-slip regime, and metric to decametric scale conjugate thrusts coherent with layer parallel shortening in a compressive regime. Buckle folding preceded propagation of a series of accommodation structures during fold tightening. Petrographic and isotopic data indicate meteoric alteration of the Cretaceous platform carbonates in the prefolding stage, likely due to forebulge subaerial exposure. Layer parallel shortening and early syn-folding veins involved formational fluids resulting from mixed marine and meteoric fluids during folding at shallow burial conditions. Eventually, meteoric fluid infiltrated again along strike-slip faults, acting as cross-formational conduits in the postfolding stage

Multidisciplinary investigations of a karst reservoir for managed aquifer recharge applications on the island of Vis (Croatia)

Managed aquifer recharge (MAR) refers to a suite of methods by which excess surface water or non-conventional water is stored underground for subsequent recovery or environmental purposes. MAR solutions have been largely used in unconsolidated aquifers, while their application in karst aquifers is rare. This research presents the first results of a MAR viability study on the island of Vis, a small karstic island in the Adriatic Sea. Favorable geological and hydrogeological conditions enable the formation of karst aquifers, making the island autonomous in terms of water supply. The island's main aquifer, exploited in the Korita well field, is protected from seawater intrusion by several hydrogeological barriers. However, climate change and high seasonal pressures related to tourism pose a threat to the future availability of freshwater. Multidisciplinary field and laboratory investigations were carried out to detail the geological and hydrogeological setting of the island and its groundwater resource. Field analyses consisted of groundwater monitoring and sampling, geophysical investigations (i.e., electrical resistivity tomography), and structural measurements. Laboratory analyses included measurements of principal cations and anions and tritium activity. Despite low precipitation during the observation period (September 2019 - December 2020), the groundwater resource at the Korita site showed stable trends of physico-chemical parameters with a good storage potential and a long-term reserve. Geophysical investigations evidenced a relatively homogeneous sequence of the rock mass at a larger scale, while structural analyses indicated the occurrence of E-W karstified and open fractures that could represent a preferential flow path in the carbonate aquifer. A MAR solution for the Vis island was proposed combining an infiltration pond scheme with the direct injection of the accumulated waters into the aquifer using available wells. The potential water source could be represented by the runoff collected in an old artificial channel and the associated pond system in Korita

Markers for the identification of late breast cancer recurrence

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited

Frictional Melting in Hydrothermal Fluid-Rich Faults: Field and Experimental Evidence From the Bolfin Fault Zone (Chile)

Tectonic pseudotachylytes are thought to be unique to certain water-deficient seismogenic environments and their presence is considered to be rare in the geological record. Here, we present field and experimental evidence that frictional melting can occur in hydrothermal fluid-rich faults hosted in the continental crust. Pseudotachylytes were found in the >40 km-long Bolf\uedn Fault Zone of the Atacama Fault System, within two ca. 1 m-thick (ultra)cataclastic strands hosted in a damage-zone made of chlorite-epidote-rich hydrothermally altered tonalite. This alteration state indicates that hydrothermal fluids were active during the fault development. Pseudotachylytes, characterized by presenting amygdales, cut and are cut by chlorite-, epidote- and calcite-bearing veins. In turn, crosscutting relationship with the hydrothermal veins indicates pseudotachylytes were formed during this period of fluid activity. Rotary shear experiments conducted on bare surfaces of hydrothermally altered rocks at seismic slip velocities (3\ua0m s 121) resulted in the production of vesiculated pseudotachylytes both at dry and water-pressurized conditions, with melt lubrication as the primary mechanism for fault dynamic weakening. The presented evidence challenges the common hypothesis that pseudotachylytes are limited to fluid-deficient environments, and gives insights into the ancient seismic activity of the system. Both field observations and experimental evidence, indicate that pseudotachylytes may easily be produced in hydrothermal environments, and could be a common co-seismic fault product. Consequently, melt lubrication could be considered one of the most efficient seismic dynamic weakening mechanisms in crystalline basement rocks of the continental crust

Métodos y progreso de la conservación de los recursos genéticos de los olmos en Europa

The progress made in the conservation of European elm genetic resources since the 1st International Elm Conference is reviewed, and the complementarity of in situ and ex situ methods is discussed. The financial support of the European Union to RESGEN project CT96-78 has permitted to co-ordinate and rationalize the ex situ conservation of elms. The project, which involved 17 partner institutes in nine west European countries, aimed at a better evaluation, conservation and utilisation of the existing collections of native elm clones. Main achievements are: establishing a common database of about 2,000 clones; characterizing over 500 clones through RAPDs and chloroplast DNA PCR-RFLPs molecular markers; completing and rationalizing the existing collections; establishing a long-term core collection of 850 clones; cryo-preserving a subset of 444 clones; and identifying clones of interest for breeding and prudent use in the reconstruction of countryside hedges. The «Noble Hardwoods» network of the pan-European programme EUFORGEN groups members representative of 31 countries, and promotes the dynamic conservation of the genetic resources of several genera of broadleaf forest trees, including Ulmus spp. Strategies for the conservation of the adaptive potential of elm resources were defined and will be disseminated among foresters and conservationists through «Guidelines» leaflets. Some countries have already started implementing conservation measures for U. laevis, associating in situ preservation and the establishment of seed orchards. Others are undertaking inventories, or acquiring genetic knowledge on target populations.Se discute el progreso realizado en la conservación de los olmos europeos desde la primera conferencia Internacional del Olmo y los métodos complementarios de conservación in situ y ex situ. El apoyo financiero de la Unión Europea al proyecto RESGEN CT96-78 ha permitido coordinar y racionalizar la conservación ex situ de los olmos. El proyecto, en el cual están involucrados 17 instituciones participantes en nueve países de Europa Occidental, tiene por objetivo una mejor evaluación, conservación y utilización de las colecciones actualmente existentes de clones nativos de olmo. Los principales logros son: el establecimiento de una base de datos común de aproximadamente 2.000 clones; la caracterización de más de 500 clones usando RAPD y marcadores moleculares PCR-RFLP de ADN cloroplástico; la finalización y racionalización de las colecciones existentes; el establecimiento a largo plazo de una colección central con 850 clones; la criopreservación de un conjunto de 444 clones; y la identificación de clones de interés para la mejora y para su uso en la restauración de setos en campo. La red «Noble Hardwoods» del programa pan-europeo EUFORGEN agrupa a miembros representantes de 31 países, y promueve la conservación dinámica de los recursos genéticos de varios géneros de árboles planifolios, incluido Ulmus spp.. Las estrategias para la conservación del potencial adaptativo de los recursos de los olmos se definieron y se dieron a conocer entre forestales y conservacionistas a través de folletos guía. Algunos países han comenzado ya a implementar medidas de conservación para U. laevis mediante el uso de la preservación in situ y el establecimiento de huertos semilleros. Otros están elaborando inventarios, o adquiriendo información genética de poblaciones de interés

Multigene prognostic tests in breast cancer: past, present, future

There is growing consensus that multigene prognostic tests provide useful complementary information to tumor size and grade in estrogen receptor (ER)-positive breast cancers. The tests primarily rely on quantification of ER and proliferation-related genes and combine these into multivariate prediction models. Since ER-negative cancers tend to have higher proliferation rates, the prognostic value of current multigene tests in these cancers is limited. First-generation prognostic signatures (Oncotype DX, MammaPrint, Genomic Grade Index) are substantially more accurate to predict recurrence within the first 5 years than in later years. This has become a limitation with the availability of effective extended adjuvant endocrine therapies. Newer tests (Prosigna, EndoPredict, Breast Cancer Index) appear to possess better prognostic value for late recurrences while also remaining predictive of early relapse. Some clinical prediction problems are more difficult to solve than others: there are no clinically useful prognostic signatures for ER-negative cancers, and drug-specific treatment response predictors also remain elusive. Emerging areas of research involve the development of immune gene signatures that carry modest but significant prognostic value independent of proliferation and ER status and represent candidate predictive markers for immune-targeted therapies. Overall metrics of tumor heterogeneity and genome integrity (for example, homologue recombination deficiency score) are emerging as potential new predictive markers for platinum agents. The recent expansion of high-throughput technology platforms including low-cost sequencing of circulating and tumor-derived DNA and RNA and rapid reliable quantification of microRNA offers new opportunities to build extended prediction models across multiplatform data

A Reliable Method for the Selection of Exploitable Melanoma Archival Paraffin Embedded Tissues for Transcript Biomarker Profiling

The source tissue for biomarkers mRNA expression profiling of tumors has traditionally been fresh-frozen tissue. The adaptation of formalin-fixed, paraffin-embedded (FFPE) tissues for routine mRNA profiling would however be invaluable in view of their abundance and the clinical information related to them. However, their use in the clinic remains a challenge due to the poor quality of RNA extracted from such tissues. Here, we developed a method for the selection of melanoma archival paraffin-embedded tissues that can be reliably used for transcript biomarker profiling. For that, we used qRT-PCR to conduct a comparative study in matched pairs of frozen and FFPE melanoma tissues of the expression of 25 genes involved in angiogenesis/tumor invasion and 15 housekeeping genes. A classification method was developed that can select the samples with a good frozen/FFPE correlation and identify those that should be discarded on the basis of paraffin data for four reference genes only. We propose therefore a simple and inexpensive assay which improves reliability of mRNA profiling in FFPE samples by allowing the identification and analysis of “good” samples only. This assay which can be extended to other genes would however need validation at the clinical level and on independent tumor series

Gene Expression Profiles from Formalin Fixed Paraffin Embedded Breast Cancer Tissue Are Largely Comparable to Fresh Frozen Matched Tissue

BACKGROUND AND METHODS: Formalin Fixed Paraffin Embedded (FFPE) samples represent a valuable resource for cancer research. However, the discovery and development of new cancer biomarkers often requires fresh frozen (FF) samples. Recently, the Whole Genome (WG) DASL (cDNA-mediated Annealing, Selection, extension and Ligation) assay was specifically developed to profile FFPE tissue. However, a thorough comparison of data generated from FFPE RNA and Fresh Frozen (FF) RNA using this platform is lacking. To this end we profiled, in duplicate, 20 FFPE tissues and 20 matched FF tissues and evaluated the concordance of the DASL results from FFPE and matched FF material. METHODOLOGY AND PRINCIPAL FINDINGS: We show that after proper normalization, all FFPE and FF pairs exhibit a high level of similarity (Pearson correlation >0.7), significantly larger than the similarity between non-paired samples. Interestingly, the probes showing the highest correlation had a higher percentage G/C content and were enriched for cell cycle genes. Predictions of gene expression signatures developed on frozen material (Intrinsic subtype, Genomic Grade Index, 70 gene signature) showed a high level of concordance between FFPE and FF matched pairs. Interestingly, predictions based on a 60 gene DASL list (best match with the 70 gene signature) showed very high concordance with the MammaPrint® results. CONCLUSIONS AND SIGNIFICANCE: We demonstrate that data generated from FFPE material with the DASL assay, if properly processed, are comparable to data extracted from the FF counterpart. Specifically, gene expression profiles for a known set of prognostic genes for a specific disease are highly comparable between two conditions. This opens up the possibility of using both FFPE and FF material in gene expressions analyses, leading to a vast increase in the potential resources available for cancer research

Relative impact of key sources of systematic noise in Affymetrix and Illumina gene-expression microarray experiments

<p>Abstract</p> <p>Background</p> <p>Systematic processing noise, which includes batch effects, is very common in microarray experiments but is often ignored despite its potential to confound or compromise experimental results. Compromised results are most likely when re-analysing or integrating datasets from public repositories due to the different conditions under which each dataset is generated. To better understand the relative noise-contributions of various factors in experimental-design, we assessed several Illumina and Affymetrix datasets for technical variation between replicate hybridisations of Universal Human Reference (UHRR) and individual or pooled breast-tumour RNA.</p> <p>Results</p> <p>A varying degree of systematic noise was observed in each of the datasets, however in all cases the relative amount of variation between standard control RNA replicates was found to be greatest at earlier points in the sample-preparation workflow. For example, 40.6% of the total variation in reported expressions were attributed to replicate extractions, compared to 13.9% due to amplification/labelling and 10.8% between replicate hybridisations. Deliberate probe-wise batch-correction methods were effective in reducing the magnitude of this variation, although the level of improvement was dependent on the sources of noise included in the model. Systematic noise introduced at the chip, run, and experiment levels of a combined Illumina dataset were found to be highly dependant upon the experimental design. Both UHRR and pools of RNA, which were derived from the samples of interest, modelled technical variation well although the pools were significantly better correlated (4% average improvement) and better emulated the effects of systematic noise, over all probes, than the UHRRs. The effect of this noise was not uniform over all probes, with low GC-content probes found to be more vulnerable to batch variation than probes with a higher GC-content.</p> <p>Conclusions</p> <p>The magnitude of systematic processing noise in a microarray experiment is variable across probes and experiments, however it is generally the case that procedures earlier in the sample-preparation workflow are liable to introduce the most noise. Careful experimental design is important to protect against noise, detailed meta-data should always be provided, and diagnostic procedures should be routinely performed prior to downstream analyses for the detection of bias in microarray studies.</p

Chromosomal Aberrations in Bladder Cancer: Fresh versus Formalin Fixed Paraffin Embedded Tissue and Targeted FISH versus Wide Microarray-Based CGH Analysis

Bladder carcinogenesis is believed to follow two alternative pathways driven by the loss of chromosome 9 and the gain of chromosome 7, albeit other nonrandom copy number alterations (CNAs) were identified. However, confirmation studies are needed since many aspects of this model remain unclear and considerable heterogeneity among cases has emerged. One of the purposes of this study was to evaluate the performance of a targeted test (UroVysion assay) widely used for the detection of Transitional Cell Carcinoma (TCC) of the bladder, in two different types of material derived from the same tumor. We compared the results of UroVysion test performed on Freshly Isolated interphasic Nuclei (FIN) and on Formalin Fixed Paraffin Embedded (FFPE) tissues from 22 TCCs and we didn't find substantial differences. A second goal was to assess the concordance between array-CGH profiles and the targeted chromosomal profiles of UroVysion assay on an additional set of 10 TCCs, in order to evaluate whether UroVysion is an adequately sensitive method for the identification of selected aneuploidies and nonrandom CNAs in TCCs. Our results confirmed the importance of global genomic screening methods, that is array based CGH, to comprehensively determine the genomic profiles of large series of TCCs tumors. However, this technique has yet some limitations, such as not being able to detect low level mosaicism, or not detecting any change in the number of copies for a kind of compensatory effect due to the presence of high cellular heterogeneity. Thus, it is still advisable to use complementary techniques such as array-CGH and FISH, as the former is able to detect alterations at the genome level not excluding any chromosome, but the latter is able to maintain the individual data at the level of single cells, even if it focuses on few genomic regions