On the reproducibility and repeatability of laser absorption spectroscopy measurements for δ2H and δ18O isotopic analysis

The aim of this study was to analyse the reproducibility of off-axis integrated cavity output spectroscopy (OA-ICOS)-derived δ2H and δ18O measurements on a set of 35 water samples by comparing the performance of four laser spectroscopes with the performance of a conventional mass spectrometer under typical laboratory conditions. All samples were analysed using three different schemes of standard/sample combinations and related data processing to assess the improvement of results compared with mass spectrometry. The repeatability of the four OA-ICOS instruments was further investigated by multiple analyses of a sample subset to evaluate the stability of δ2H and δ18O measurements. Results demonstrated an overall agreement between OA-ICOS-based and mass spectrometry-based measurements for the entire dataset. However, a certain degree of variability existed in precision and accuracy between the four instruments. There was no evident bias or systematic deviations from the mass spectrometer values, but random errors, which were apparently not related to external factors, significantly affected the final results. Our investigation revealed that analytical precision ranged ±from ±0.56‰ to ±1.80‰ for δ2H and from ±0.10‰ to ±0.27‰ for δ18O measurements, with a marked variability among the four instruments. The overall capability of laser instruments to reproduce stable results with repeated measurements of the same sample was acceptable, and there were general differences within the range of the analytical precision for each spectroscope. Hence, averaging the measurements of three identical samples led to a higher degree of accuracy and eliminated the potential for random deviations

Soil moisture and matric potential-an open field comparison of sensor systems

Soil water content and matric potential are central hydrological state variables. A large variety of automated probes and sensor systems for state monitoring exist and are frequently applied. Most applications solely rely on the calibration by the manufacturers. Until now, there has been no commonly agreed-upon calibration procedure. Moreover, several opinions about the capabilities and reliabilities of specific sensing methods or sensor systems exist and compete. A consortium of several institutions conducted a comparison study of currently available sensor systems for soil water content and matric potential under field conditions. All probes were installed at 0.2mb.s. (metres below surface), following best-practice procedures. We present the set-up and the recorded data of 58 probes of 15 different systems measuring soil moisture and 50 further probes of 14 different systems for matric potential. We briefly discuss the limited coherence of the measurements in a cross-correlation analysis. The measuring campaign was conducted during the growing period of 2016. The monitoring data, results from pedophysical analyses of the soil and laboratory reference measurements for calibration are published in Jackisch et al. (2018, https://doi.org/10.1594/PANGAEA.892319)

Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues

<p>Abstract</p> <p>Background</p> <p>Breast carcinomas represent a heterogeneous group of tumors diverse in behavior, outcome, and response to therapy. Identification of proteins resembling the tumor biology can improve the diagnosis, prediction, treatment selection, and targeting of therapy. Since the beginning of the post-genomic era, the focus of molecular biology gradually moved from genomes to proteins and proteomes and to their functionality. Proteomics can potentially capture dynamic changes in protein expression integrating both genetic and epigenetic influences.</p> <p>Methods</p> <p>We prepared primary cultures of epithelial cells from 23 breast cancer tissue samples and performed comparative proteomic analysis. Seven patients developed distant metastases within three-year follow-up. These samples were included into a metastase-positive group, the others formed a metastase-negative group. Two-dimensional electrophoretical (2-DE) gels in pH range 4–7 were prepared. Spot densities in 2-DE protein maps were subjected to statistical analyses (R/maanova package) and data-mining analysis (GUHA). For identification of proteins in selected spots, liquid chromatography-tandem mass spectrometry (LC-MS/MS) was employed.</p> <p>Results</p> <p>Three protein spots were significantly altered between the metastatic and non-metastatic groups. The correlations were proven at the 0.05 significance level. Nucleophosmin was increased in the group with metastases. The levels of 2,3-trans-enoyl-CoA isomerase and glutathione peroxidase 1 were decreased.</p> <p>Conclusion</p> <p>We have performed an extensive proteomic study of mammary epithelial cells from breast cancer patients. We have found differentially expressed proteins between the samples from metastase-positive and metastase-negative patient groups.</p

Monitoring molecular chirality exchange by photon echoes

We construct pulse polarization configurations in heterodyne four wave mixing for monitoring ultrafast(picosecond)exchange rates between optical isomers with axial chirality.This information is not available from linear circular dichroism,since enantiomers may not be isolated and racemate shows no chiral signal

Far from home: genetic variability of Knipowitschia sp. from Italy revealed unexpected species in coastal lagoons of the Tyrrhenian coast

Coastal lagoons are resilient and productive ecosystems that support high biological and habitat diversity, but are increasingly affected by several threats due to human exploitation. Many resident species of these environments show a restricted geographical range and a strict association with specific habitats, thus they could represent ecological indicators of these ecosystems. Data on the genetic variability distribution in populations of these species are crucial to identify the presence of different evolutionary units across their geographical distribution ranges and to plan actions for their management and conservation. In this context, the assessment of the genetic variability and structure of Italian specimens of the Adriatic dwarf goby Knipowitschia panizzae, a brackish species endemic in the Adriatic Sea, and included among the species of Community interest in Annex II of Habitats Directive, was carried out. To this purpose, goby samples were collected both from Italian sites where the species is native (Adriatic) and non-native (Tyrrhenian), probably introduced due to the practice of stocking lakes and coastal lagoons with juvenile of euryhaline species to sustain local fisheries. Results show the presence of high values of haplotype diversity, and no shared haplotypes between fish from sites where the species is native or introduced. Moreover, in Tyrrhenian Italian lagoons we identified an allochthonous species of Knipowitschia, previously undetected in Italy: the Corfu dwarf goby K. goerneri. This species was originally described as endemic to the Korission Lagoon catchment on Corfu Island, but recently found also in Butrinti lagoon in Albania. The presence of this species, that almost totally replaced Adriatic dwarf goby in the Tyrrhenian lagoons under study, can be ascribed to the stockings of wild fry of commercially important species originating from Balkan countries

Adding nuclear rhodopsin data where mitochondrial COI indicates discrepancies – can this marker help to explain conflicts in cyprinids?

DNA barcoding is a fast and reliable tool for species identification, and has been successfully applied to a wide range of freshwater fishes. The limitations reported were mainly attributed to effects of geographic scale, taxon-sampling, incomplete lineage sorting, or mitochondrial introgression. However, the metrics for the success of assigning unknown samples to species or genera also depend on a suited taxonomic framework. A simultaneous use of the mitochondrial COI and the nuclear RHO gene turned out to be advantageous for the barcode efficiency in a few previous studies. Here, we examine 14 cyprinid fish genera, with a total of 74 species, where standard DNA barcoding failed to identify closely related species unambiguously. Eight of the genera (Acanthobrama, Alburnus, Chondrostoma, Gobio, Mirogrex, Phoxinus, Scardinius, and Squalius) contain species that exhibit very low interspecific divergence, or haplotype sharing (12 species pairs) with presumed introgression based on mtCOI data. We aimed to test the utility of the nuclear rhodopsin marker to uncover reasons for the high similarity and haplotype sharing in these different groups. The included labeonine species belonging to Crossocheilus, Hemigrammocapoeta, Tylognathus and Typhlogarra were found to be nested within the genus Garra based on mtCOI. This specific taxonomic uncertainty was also addressed by the use of the additional nuclear marker. As a measure of the delineation success we computed barcode gaps, which were present in 75% of the species based on mtCOI, but in only 39% based on nuclear rhodopsin sequences. Most cases where standard barcodes failed to offer unambiguous species identifications could not be resolved by adding the nuclear marker. However, in the labeonine cyprinids included, nuclear rhodopsin data generally supported the lineages as defined by the mitochondrial marker. This suggests that mitochondrial patterns were not mislead by introgression, but are caused by an inadequate taxonomy. Our findings support the transfer of the studied species of Crossocheilus, Hemigrammocapoeta, Tylognathus and Typhlogarra to Garra

A global assessment of freshwater fish introductions in mediterranean-climate regions

Mediterranean-climate regions (med-regions) are global hotspots of endemism facing mounting environmental threats associated with human-related activities, including the ecological impacts associated with non-native species introductions. We review freshwater fish introductions across med-regions to evaluate the influences of non-native fishes on the biogeography of taxonomic and functional diversity. Our synthesis revealed that 136 freshwater fish species (26 families, 13 orders) have been introduced into med-regions globally. These introductions, and local extirpations, have increased taxonomic and functional faunal similarity among regions by an average of 7.5% (4.6-11.4%; Jaccard) and 7.2% (1.4-14.0%; Bray-Curtis), respectively. Faunal homogenisation was highest in Chile and the western Med Basin, whereas sw Cape and the Aegean Sea drainages showed slight differentiation (decrease in faunal similarity) over time. At present, fish faunas of different med-regions have widespread species in common (e.g. Gambusia holbrooki, Cyprinus carpio, Oncorhynchus mykiss, Carassius auratus, and Micropterus salmoides) which are typically large-bodied, non-migratory, have higher physiological tolerance, and display fast population growth rates. Our findings suggest that intentional and accidental introductions of freshwater fish have dissolved dispersal barriers and significantly changed the present-day biogeography of med-regions across the globe. Conservation challenges in med-regions include understanding the ecosystem consequences of non-native species introductions at macro-ecological scales