Assessing the effects of forest-to-bog restoration in the hyporheic zone at known Atlantic salmon (Salmo salar) spawning sites

In the UK, large areas of blanket bogs were afforested with non-native conifers between the 1960s and the 1980s. Following recognition of the detrimental effects of such practice on biodiversity and carbon stocks, large-scale restoration trials started in the late 1990s and are further supported by recent changes in policy. The removal of forestry from peatlands is likely to be a widespread land-use change in the coming decades and could affect adjacent freshwater systems. This study aimed to investigate whether forestry removal with drain blocking affected nearby spawning sites used by Atlantic salmon (Salmo salar). We analysed the chemistry of hyporheic (beneath and just above the streambed) and surface water, and measured sediment deposition upstream of, within and downstream of a forestry block in the north of Scotland, during and after restoration management operations. We found no immediate effect of management except on potassium and zinc concentrations, which increased after restoration. The general lack of effect is attributed to catchment properties, including the small proportion of catchment (< 5 %) affected by management, and to dilution effects related to heavy precipitation during the intervention phase. We suggest that longer-term monitoring should be implemented as the sizes of areas undergoing restoration management increases

Acetylcholinesterase sensors based on gold electrodes modified with dendrimer and polyaniline: A comparative research

Potentiometric and amperometric enzyme sensors based on modified gold electrodes have been developed and compared in pesticide determination. PAMAM dendrimer (generation G4) stabilized with 1-hexadecanethiol was used for the immobilization of acetylcholinesterase from electric eel and choline oxidase from Alcaligenes species in the assembly of amperometric sensor. Polyaniline-doped with camphorsulfonic acid was used to obtain potentiometric response. Trichlorfon, carbofuran and eserine suppress the biosensor response due to their inhibitory effect. The detection limits of 0.003 and 200 nmol l-1 (trichlorfon), 0.04 and 6 nmol l-1 (carbofuran) and 0.1 and 700 nmol l-1 were obtained for amperometric and potentiometric sensors, respectively. The difference in the biosensor behavior and the high sensitivity of the dendrimer modified sensor to the inhibitors is due to the specific organization of protein layer at charged surface of the modifier macromolecules. © 2004 Elsevier B.V. All rights reserved

Metabolism of aceclofenac in cattle to vulture-killing diclofenac

The non-steroidal anti-inflammatory drug (NSAID) diclofenac is highly toxic to Gyps vultures and its recent widespread use in South Asia caused catastrophic declines in at least three scavenging raptors. The manufacture of veterinary formulations of diclofenac has since been banned across the region with mixed success. However, at least 12 other NSAIDs are available for veterinary use in South Asia. Aceclofenac is one of these compounds and it is known to metabolise into diclofenac in some mammal species. The metabolic pathway of aceclofenac in cattle, the primary food of vultures in South Asia, is unknown. In this study, we give six cattle the recommended dose of aceclofenac (2 mg/kg), collect blood along a time series and undertake a pharmacokinetic analysis of aceclofenac and diclofenac-metabolites in their plasma using liquid chromatography with mass spectrometry. We found that nearly all of the aceclofenac administered to the cattle was very rapidly metabolised into diclofenac. Therefore, treating livestock with pure diclofenac or aceclofenac poses the same risk to vultures. This fact, coupled with the risk that aceclofenac may replace diclofenac in the veterinary market, fortifies the need for an immediate ban on all aceclofenac formulations that can be used to treat livestock. Without such a ban, the recovery of vultures across South Asia will not be successful.This study was largely funded by the RSPB Centre for Conversation Science. In addition, SAC Consulting: Veterinary Services receives funding from the Scottish Government through the Veterinary and Advisory Services (VAS) programme.http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1523-17392017-10-31hb2016Paraclinical Science

Biopolymer-based structuring of liquid oil into soft solids and oleogels using water-continuous emulsions as templates

Physical trapping of a hydrophobic liquid oil in a matrix of water-soluble biopolymers was achieved using a facile two-step process by first formulating a surfactant-free oil-in-water emulsion stabilized by biopolymers (a protein and a polysaccharide) followed by complete removal of the water phase (by either high- or low-temperature drying of the emulsion) resulting in structured solid systems containing a high concentration of liquid oil (above 97 wt %). The microstructure of these systems was revealed by confocal and cryo-scanning electron microscopy, and the effect of biopolymer concentrations on the consistency of emulsions as well as the dried product was evaluated using a combination of small-amplitude oscillatory shear rheometry and large deformation fracture studies. The oleogel prepared by shearing the dried product showed a high gel strength as well as a certain degree of thixotropic recovery even at high temperatures. Moreover, the reversibility of the process was demonstrated by shearing the dried product in the presence of water to obtain reconstituted emulsions with rheological properties comparable to those of the fresh emulsion

The proposal of a GSSP for the Berriasian Stage (Cretaceous System): Part 1.

Here in the first part of this publication we discuss the possibilities for the selection of a GSSP for the Berriasian Stage of the Cretaceous System, based on the established methods for correlation in the Tithonian/Berriasian interval. This will be followed, in the second part, by an account of the stratigraphic evidence that justifies the locality of Tré Maroua (Hautes-Alpes, SE France) as the proposed GSSP. Here we discuss the possibilities for correlation in the historical J/K boundary interval, and the evolution of thinking on the positioning of the boundary over recent generations, and in relation to research in the last ten years. The Tithonian/Berriasian boundary level is accepted as occurring within magnetosubzone M19n.2n. The detailed distribution of calpionellids has been recorded at numerous sites, tied to magnetostratigraphy, and the base of the calpionellid Alpina Zone is taken to define the base of the Berriasian Stage. This is at a level just below the distinctive reversed magnetic subzone M19n.1r (the so-called Brodno reversal). We discuss a wide range of magnetostratigraphic and biostratigraphic data from key localities globally, in the type Berriasian areas of France and wider regions (Le Chouet, Saint Bertrand, Puerto Escaño, Rio Argos, Bosso, Brodno, Kurovice, Theodosia etc.). The characteristic datums that typify the J/K boundary interval in Tethys and its extensions are detailed, and the correlative viability of various fossil groups is discussed. The boundary level is correlated to well-known J/K sections globally, and a series of secondary markers and proxies are indicated which assist wider correlation. Particularly significant are the primary basal Berriasian marker, the base of the Alpina Subzone (marked by dominance of small Calpionella alpina, Crassicollaria parvula and Tintinopsella carpathica) and secondary markers bracketing the base of the Calpionella Zone, notably the FOs of the calcareous nannofossil species Nannoconus wintereri (just below the boundary) and the FO of Nannoconus steinmannii minor (just above). Notable proxies for the boundary are: 1) the base of the Arctoteuthis tehamaensis Zone in boreal and subboreal regions, 2) the dated base of the Alpina Subzone at 140.22 ± 0.14 Ma, which also gives a precise age estimate for the system boundary; and 3) the base of radiolarian “unitary zone” 14, which is situated just above the base of the Alpina Subzone

Short amplicon reverse transcription-polymerase chain reaction detects aberrant splicing in genes with low expression in blood missed by ribonucleic acid sequencing analysis for clinical diagnosis.

Use of blood RNA sequencing (RNA-seq) as a splicing analysis tool for clinical interpretation of variants of uncertain significance (VUSs) found via whole-genome and exome sequencing can be difficult for genes that have low expression in the blood due to insufficient read count coverage aligned to specific genes of interest. Here, we present a short amplicon reverse transcription-polymerase chain reaction(RT-PCR) for the detection of genes with low blood expression. Short amplicon RT-PCR, is designed to span three exons where an exon harboring a variant is flanked by one upstream and one downstream exon. We tested short amplicon RT-PCRs for genes that have median transcripts per million (TPM) values less than one according to the genotype-tissue expression database. Median TPM values of genes analyzed in this study are SYN1 = 0.8549, COL1A1 = 0.6275, TCF4 = 0.4009, DSP = .2894, TTN = 0.2851, COL5A2 = 0.1036, TERT = 0.04452, NTRK2 = 0.0344, ABCA4 = 0.00744, PRPH = 0, and WT1 = 0. All these genes show insufficient exon-spanning read coverage in our RNA-seq data to allow splicing analysis. We successfully detected all genes tested except PRPH and WT1. Aberrant splicing was detected in SYN1, TCF4, NTRK2, TTN, and TERT VUSs. Therefore, our results show short amplicon RT-PCR is a useful alternative for the analysis of splicing events in genes with low TPM in blood RNA for clinical diagnostics

Test-retest reliability and predictive validity of a juvenile guide dog behavior test

The ability to measure stable and consistent behavioral traits in dogs would facilitate selection and assessment of working dogs, such as guide dogs. Ideally, these measures should predict suitability for the working role from a young age. This study assessed test-retest reliability of a juvenile guide dog behavior test and predictive validity using qualification or withdrawal from guide dog training. Ninety-three guide dog puppies (52 female; 41 male) were tested at 5 (mean 4.78; ±0.73 SD) and 8 (mean 7.98; ±0.78 SD) months of age. The dogs were exposed to a sequence of 11 stimuli designed to assess the dogs’ reactions to meeting a stranger, obedience commands, body sensitivity, scavenging, and “animal” and human distractions. The behavior of dogs was digitally recorded and analyzed using an ethogram incorporating both frequency of behavior and specific reactions to stimuli. Test-retest reliability indicated interindividual consistency in many of the behavioral measures such as jumping, barking, and “low” greeting posture, as defined in our ethogram. Behavior measures that did not show interindividual consistency between tests included obedience responses, lip licking, body shaking, and scratching. Binary logistic regression models revealed 7 behavioral measures at 5 months and 5 measures at 8 months that were significantly associated with qualification or withdrawal. Uncorrelated measures and principal component scores of correlated measures were combined in a logistic regression model that showed great potential for predicting the probability of a dog qualifying or being withdrawn from guide dog training

PDBe-KB: collaboratively defining the biological context of structural data

The Protein Data Bank in Europe - Knowledge Base (PDBe-KB, https://pdbe-kb.org) is an open collaboration between world-leading specialist data resources contributing functional and biophysical annotations derived from or relevant to the Protein Data Bank (PDB). The goal of PDBe-KB is to place macromolecular structure data in their biological context by developing standardised data exchange formats and integrating functional annotations from the contributing partner resources into a knowledge graph that can provide valuable biological insights. Since we described PDBe-KB in 2019, there have been significant improvements in the variety of available annotation data sets and user functionality. Here, we provide an overview of the consortium, highlighting the addition of annotations such as predicted covalent binders, phosphorylation sites, effects of mutations on the protein structure and energetic local frustration. In addition, we describe a library of reusable web-based visualisation components and introduce new features such as a bulk download data service and a novel superposition service that generates clusters of superposed protein chains weekly for the whole PDB archive

Salivary Gland Transcriptomes and Proteomes of Phlebotomus tobbi and Phlebotomus sergenti, Vectors of Leishmaniasis

Phlebotomine female sand flies require a blood meal for egg development, and it is during the blood feeding that pathogens can be transmitted to a host. Leishmania parasites are among these pathogens and can cause disfiguring cutaneous or even possibly fatal visceral disease. The Leishmania parasites are deposited into the bite wound along with the sand fly saliva. The components of the saliva have many pharmacologic and immune functions important in blood feeding and disease establishment. In this article, the authors identify and investigate the protein components of saliva of two important vectors of leishmaniasis, Phlebotomus tobbi and P. sergenti, by sequencing the transcriptomes of the salivary glands. We then compared the predicted protein sequences of these salivary proteins to those of other bloodsucking insects to elucidate the similarity in composition, structure, and enzymatic activity. Finally, this descriptive analysis of P. tobbi and P. sergenti transcriptomes can aid future research in identifying molecules for epidemiologic assays and in investigating sand fly-host interactions

Loss of Nrf2 abrogates the protective effect of Keap1 down regulation in a preclinical model of cutaneous squamous cell carcinoma

Cutaneous squamous cell carcinomas (cSCC) are the most common and highly mutated human malignancies, challenging identification of driver mutations and targeted therapies. Transcription factor NF-E2 p45-related factor 2 (Nrf2) orchestrates a cytoprotective inducible program, which counteracts the damaging effects of solar UV radiation, the main etiological factor in cSCC development. Downregulation of Kelch-like ECH-associated protein 1 (Keap1), a Cullin-3/Rbx1 ubiquitin ligase substrate adaptor protein, which mediates the ubiquitination and proteasomal degradation of Nrf2, has a strong protective effect in a preclinical model of cSCC. However, in addition to Nrf2, Keap1 affects ubiquitination of other proteins in the carcinogenesis process, including proteins involved in inflammation and DNA damage repair. Here, we generated Keap1(flox/flox) SKH-1 hairless mice in which Nrf2 is disrupted (Keap1(flox/flox)/Nrf2(−/−)) and subjected them chronically to solar-simulated UV radiation. We found that the incidence, multiplicity and burden of cSCC that form in Keap1(flox/flox)/Nrf2(−/−) mice are much greater than in their Keap1(flox/flox)/Nrf2(+/+) counterparts, establishing Nrf2 activation as the protection mediator. Our findings further imply that inhibition of Nrf2 globally, a strategy proposed for cancer treatment, is unlikely to be beneficial