Transcriptomics in ecotoxicology

The emergence of analytical tools for high-throughput screening of biomolecules has revolutionized the way in which toxicologists explore the impact of chemicals or other stressors on organisms. One of the most developed and routinely applied high-throughput analysis approaches is transcriptomics, also often referred to as gene expression profiling. The transcriptome represents all RNA molecules, including the messenger RNA (mRNA), which constitutes the building blocks for translating DNA into amino acids to form proteins. The entirety of mRNA is a mirror of the genes that are actively expressed in a cell or an organism at a given time. This in turn allows one to deduce how organisms respond to changes in the external environment. In this article we explore how transcriptomics is currently applied in ecotoxicology and highlight challenges and trends. Figure The transcriptome (RNA) is a mirror of the genes that are actively expressed in a cell or organism at a given time, providing information on how organisms respond to chemicals or other stressors in the environmen

Characterization of singlet oxygen-accumulating mutants isolated in a screen for altered oxidative stress response in Chlamydomonas reinhardtii

<p>Abstract</p> <p>Background</p> <p>When photosynthetic organisms are exposed to harsh environmental conditions such as high light intensities or cold stress, the production of reactive oxygen species like singlet oxygen is stimulated in the chloroplast. In <it>Chlamydomonas reinhardtii </it>singlet oxygen was shown to act as a specific signal inducing the expression of the nuclear glutathione peroxidase gene <it>GPXH/GPX5 </it>during high light stress, but little is known about the cellular mechanisms involved in this response. To investigate components affecting singlet oxygen signaling in <it>C. reinhardtii</it>, a mutant screen was performed.</p> <p>Results</p> <p>Mutants with altered <it>GPXH </it>response were isolated from UV-mutagenized cells containing a <it>GPXH</it>-arylsulfatase reporter gene construct. Out of 5500 clones tested, no mutant deficient in <it>GPXH </it>induction was isolated, whereas several clones showed constitutive high <it>GPXH </it>expression under normal light conditions. Many of these <it>GPXH </it>overexpressor (<it>gox</it>) mutants exhibited higher resistance to oxidative stress conditions whereas others were sensitive to high light intensities. Interestingly, most <it>gox </it>mutants produced increased singlet oxygen levels correlating with high <it>GPXH </it>expression. Furthermore, different patterns of altered photoprotective parameters like non-photochemical quenching, carotenoid contents and α-tocopherol levels were detected in the various <it>gox </it>mutants.</p> <p>Conclusions</p> <p>Screening for mutants with altered <it>GPXH </it>expression resulted in the isolation of many <it>gox </it>mutants with increased singlet oxygen production, showing the relevance of controlling the production of this ROS in photosynthetic organisms. Phenotypic characterization of these <it>gox </it>mutants indicated that the mutations might lead to either stimulated triplet chlorophyll and singlet oxygen formation or reduced detoxification of singlet oxygen in the chloroplast. Furthermore, changes in multiple protection mechanisms might be responsible for high singlet oxygen formation and <it>GPXH </it>expression, which could either result from mutations in multiple loci or in a single gene encoding for a global regulator of cellular photoprotection mechanisms.</p

Character Queries: A Transformer-based Approach to On-Line Handwritten Character Segmentation

On-line handwritten character segmentation is often associated with handwriting recognition and even though recognition models include mechanisms to locate relevant positions during the recognition process, it is typically insufficient to produce a precise segmentation. Decoupling the segmentation from the recognition unlocks the potential to further utilize the result of the recognition. We specifically focus on the scenario where the transcription is known beforehand, in which case the character segmentation becomes an assignment problem between sampling points of the stylus trajectory and characters in the text. Inspired by the $k$-means clustering algorithm, we view it from the perspective of cluster assignment and present a Transformer-based architecture where each cluster is formed based on a learned character query in the Transformer decoder block. In order to assess the quality of our approach, we create character segmentation ground truths for two popular on-line handwriting datasets, IAM-OnDB and HANDS-VNOnDB, and evaluate multiple methods on them, demonstrating that our approach achieves the overall best results.Comment: ICDAR 2023 Best Student Paper Award. Code available at https://github.com/jungomi/character-querie

Transcriptomics in ecotoxicology

The emergence of analytical tools for high-throughput screening of biomolecules has revolutionized the way in which toxicologists explore the impact of chemicals or other stressors on organisms. One of the most developed and routinely applied high-throughput analysis approaches is transcriptomics, also often referred to as gene expression profiling. The transcriptome represents all RNA molecules, including the messenger RNA (mRNA), which constitutes the building blocks for translating DNA into amino acids to form proteins. The entirety of mRNA is a mirror of the genes that are actively expressed in a cell or an organism at a given time. This in turn allows one to deduce how organisms respond to changes in the external environment. In this article we explore how transcriptomics is currently applied in ecotoxicology and highlight challenges and trends

Function and regulation of the glutathione peroxidase homologous gene GPXH

When exposed to strong sunlight, photosynthetic organisms encounter photooxidative stress by the increased production of reactive oxygen species causing harmful damages to proteins and membranes. Consequently, a fast and specific induction of defense mechanisms is required to protect the organism from cell death. In Chlamydomonas reinhardtii, the glutathione peroxidase homologous gene GPXH/GPX5 was shown to be specifically upregulated by singlet oxygen formed during high light conditions presumably to prevent the accumulation of lipid hydroperoxides and membrane damage. We now showed that the GPXH protein is a thioredoxin-dependent peroxidase catalyzing the reduction of hydrogen peroxide and organic hydroperoxides. Furthermore, the GPXH gene seems to encode a dual-targeted protein, predicted to be localized both in the chloroplast and the cytoplasm, which is active with either plastidic TRXy or cytosolic TRXh1. Putative dual-targeting is achieved by alternative transcription and translation start sites expressed independently from either a TATA-box or an Initiator core promoter. Expression of both transcripts was upregulated by photooxidative stress even though with different strengths. The induction required the presence of the core promoter sequences and multiple upstream regulatory elements including a Sp1-like element and an earlier identified CRE/AP-1 homologous sequence. This element was further characterized by mutation analysis but could not be confirmed to be a consensus CRE or AP1 element. Instead, it rather seems to be another member of the large group of TGAC-transcription factor binding sites found to be involved in the response of different genes to oxidative stres

Transcatheter closure of atrial septal defects within the oval fossa: medium-term results in children using the ‘ASDOS'-technique

Abstract Objectives The purpose of this study was to evaluate the safety and efficacy of the ASDOS-tech-nique (Sulzer-Osypka GmbH, Germany) for transcatheter closure of atrial septal defects within the oval fossa. Background Although several attempts have been made to occlude defects within the oval fossa by transcatheter techniques, none of these has gained general acceptance. Methods Patients with a defect in the oval fossa measuring equal to or less than 20 mm diameter, with a residual septal rim of 5mm or greater, body weight greater than 10 kg, with clinical indications for surgical closure were considered for transcatheter closure. Follow-up investigations were performed at discharge, after 1, 3, 6 and 9 months, as well as after 1 and 2 years. Results Of 78 patients considered for closure, a device was inserted in 41 patients (53%), with success being achieved in 40 patients (98%). The ages ranged from 1.1 to 15 years (7.8 ± 1.92 years), the 'stretched' diameter of the defect from 10 to 20 mm (14.7 ± 2.60 mm), and the diameters of the inserted devices from 25 to 45 mm (33.2 ± 5.43 mm). Transient impairment of atrioventricular conduction occured in 4 patients. During the follow-up of 23.0 ± 5.6 months elective surgical closure of a residual shunt was performed 26 months after insertion of the devcie in one patient. None of the other patients required surgery, hospitalisation or medical treatment, and none is requiring further treatment of the defect within the oval fossa. Fracture of one arm of the device occurred in 4 patients, but the fractured arms are in an unchanged and stable position after a period of at least 19 months. Conclusions Our medium-term data show that transcatheter closure in children of defects within the oval fossa can be performed with a high efficacy and safety using the ASDOS-devic

Use of a hydrophilic coating wire reduces significantly the rate of central vein punctures and the incidence of pneumothorax in totally implantable access port (TIAP) surgery

Background: Insertion of a Totally Implantable Access Port (TIAP) can be performed either via Central Vein Puncture (CVP) or Brachiocephalic Vein Cut-down (venous section-VS). The primary success rate of TIAP implantation using VS rarely ever achieves 100%. The objective of this study was to describe a modified VS approach using a hydrophilic coated wire (TVS). Methods: From 01.01.2015 to 31.12.2015, all patients receiving TIAP implantations were screened. During this time, all patients in whom the primary VS procedure was found to be unsuccessful were analysed. Results: In 2015, 1152 patients had TIAP implantations performed by 24 different surgeons. Of these, 277 patients needed a second line rescue strategy either by CVP (n= 69) or TVS (n= 208). There were no statistically significant differences regarding demographics or indication for TIAP implantation between CVP and TVS. The operation time and the qualification of the operating surgeon between CVP and TVS did not differ significantly. After the introduction of the guidewire with a hydrophilic coated wire, the need for CVP decreased significantly from 12.7% to 8.8% (p< 0.0001). In patients receiving CVP as a second line rescue strategy, the incidence of pneumothorax (n= 3 patients (4.3%)) was significantly higher compared to patients with TVS as a second line rescue strategy (n= 1 patient (0.48%),p=0.02). Conclusion: The use of a hydrophilic coated wire significantly decreased the number of CVP and the incidence of pneumothorax. TVS is a safe and successful second-line rescue strategy

18F-Fluoride PET/CT for detection of sacroiliitis in ankylosing spondylitis

Purpose: The aim of this study was to evaluate the performance of 18F-fluoride-PET/CT (PET/CT) for the diagnosis of sacroiliac joint (SIJ) arthritis in patients with active ankylosing spondylitis (AS). Methods: Included in the study were 15 patients with AS according to the modified New York criteria (AS group) and with active disease and 13 patients with mechanical low back pain (MLBP; control group) who were investigated with whole-body 18F-fluoride PET/CT. The ratio of the uptake in the SIJ and that in the sacrum (SIJ/S) was calculated for every joint. Results: The mean SIJ/S ratio of 30 quantified joints in the AS group was 1.66 (range 1.10-3.07) with PET/CT, and the mean SIJ/S ratio of 26 quantified joints in the MLBP group was 1.12 (range 0.71-1.52). The area under the receiver operating characteristic curve for SIJ arthritis was 0.84. With plain radiography as a the gold standard and taking an SIJ/S ratio of >1.3 as the threshold, the sensitivity, specificity and accuracy on a per patient basis were 80%, 77% and 79%, respectively. On a per SIJ basis, the greatest sensitivity (94%) was found in grade 3 sacroiliitis (n = 16). Conclusion: Our results suggest that quantitative 18F-fluoride PET/CT may play a role in the diagnosis of sacroiliitis in active AS and is an alternative to conventional bone scintigraphy in times of molybdenum shortag

Challenges and pitfalls of experimental bariatric procedures in rats

Introduction: The impact of Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG) on obesity and obesity-related diseases is unquestionable. Up to now, the technical descriptions of these techniques in animals/rats have not been very comprehensive. Methods: For SG and RYGB, operating time, learning curve, and intraoperative mortality in relation to weight of the rat and type of anesthesia were recorded. Furthermore, a review of the literature on experimental approaches towards SG and RYGB in rats was carried out, merging in a detailed technical description for both procedures. Results: The data presented here revealed that the mean operating time for SG (69.4 +/- 22.2 min (SD)) was shorter than for RYGB (123.0 +/- 20.7 min). There is a learning curve for both procedures, resulting in a reduced operating time of up to 60% in SG and 35% in RYGB (p < 0.05; t-test). However, with increased weight, operating time increases to about 80 min for SG and about 120 min for RYGB. Obese rats have an increased intraoperative mortality rate of up to 50%. After gaseous anesthesia the mortality can be even higher. The literature search revealed 40 papers dealing with SG and RYGB in rats. 18 articles (45%) contained neither photographs nor illustrations; 14 articles (35%) did not mention the applied type of anesthesia. The mortality rate was described in 15 papers (37.5%). Conclusion: Experimental obesity surgery in rats is challenging. Because of the high mortality in obese rats operated under gaseous anesthesia, exercises to establish the techniques should be performed in small rats using intraperitoneal anesthesia. Copyright (C) 2012 S. Karger GmbH, Freibur

Semantic segmentation of surgical hyperspectral images under geometric domain shifts

Robust semantic segmentation of intraoperative image data could pave the way for automatic surgical scene understanding and autonomous robotic surgery. Geometric domain shifts, however, although common in real-world open surgeries due to variations in surgical procedures or situs occlusions, remain a topic largely unaddressed in the field. To address this gap in the literature, we (1) present the first analysis of state-of-the-art (SOA) semantic segmentation networks in the presence of geometric out-of-distribution (OOD) data, and (2) address generalizability with a dedicated augmentation technique termed "Organ Transplantation" that we adapted from the general computer vision community. According to a comprehensive validation on six different OOD data sets comprising 600 RGB and hyperspectral imaging (HSI) cubes from 33 pigs semantically annotated with 19 classes, we demonstrate a large performance drop of SOA organ segmentation networks applied to geometric OOD data. Surprisingly, this holds true not only for conventional RGB data (drop of Dice similarity coefficient (DSC) by 46 %) but also for HSI data (drop by 45 %), despite the latter's rich information content per pixel. Using our augmentation scheme improves on the SOA DSC by up to 67 % (RGB) and 90 % (HSI) and renders performance on par with in-distribution performance on real OOD test data. The simplicity and effectiveness of our augmentation scheme makes it a valuable network-independent tool for addressing geometric domain shifts in semantic scene segmentation of intraoperative data. Our code and pre-trained models are available at https://github.com/IMSY-DKFZ/htc.Comment: The first two authors (Jan Sellner and Silvia Seidlitz) contributed equally to this pape