Environmental DNA from peck marks enables non-invasive species monitoring of woodpeckers
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB85455 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR14231534_1.fastq.gz | Fastqsanger.gz | |||
| ERR14231534_2.fastq.gz | Fastqsanger.gz | |||
| ERR14231535_1.fastq.gz | Fastqsanger.gz | |||
| ERR14231535_2.fastq.gz | Fastqsanger.gz | |||
| ERR14231536_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 46 |
Similar Datasets
Project description:One of the most ambitious endeavors in the field of diabetes technology is non-invasive glucose sensing. In the past decades, a number of different technologies have been assessed, but none of these have found its entry into general clinical use. We report on the development of a table-top confocal Raman spectrometer that was used in the home of patients with diabetes and operated for extended periods of time unsupervised and without recalibration. The system is based on measurement of glucose levels at a 'critical depth' in the skin, specifically in the interstitial fluid located below the stratum corneum but above the underlying adipose tissue layer. The region chosen for routine glucose measurements was the base of the thumb (the thenar). In a small clinical study, 35 patients with diabetes analyzed their interstitial fluid glucose for a period of 60 days using the new critical-depth Raman (CD-Raman) method and levels were correlated to reference capillary blood glucose values using a standard finger-stick and test strip product. The calibration of the CD-Raman system was stable for > 10 days. Measurement performance for glucose levels present at, or below, a depth of ~250μm below the skin surface was comparable to that reported for currently available invasive continuous glucose monitors. In summary, using the CD-Raman technology we have demonstrated the first successful use of a non-invasive glucose monitor in the home.
| S-EPMC5947912 | biostudies-literature
Project description:Marine invasive species monitoring in Sweden
| PRJEB60147 | ENA
Project description:Genetic tagging from scats is one of the minimally invasive sampling (MIS) monitoring approaches commonly used to guide management decisions and evaluate conservation efforts. Microsatellite markers have traditionally been used but are prone to genotyping errors. Here, we present a novel method for individual identification in the Threatened ghost bat Macroderma gigas using custom-designed Single Nucleotide Polymorphism (SNP) arrays on the MassARRAY system. We identified 611 informative SNPs from DArTseq data from which three SNP panels (44-50 SNPs per panel) were designed. We applied SNP genotyping and molecular sexing to 209 M. gigas scats collected from seven caves in the Pilbara, Western Australia, employing a two-step genotyping protocol and identifying unique genotypes using a custom-made R package, ScatMatch. Following data cleaning, the average amplification rate was 0.90 ± 0.01 and SNP genotyping errors were low (allelic dropout 0.003 ± 0.000) allowing clustering of scats based on one or fewer allelic mismatches. We identified 19 unique bats (9 confirmed/likely males and 10 confirmed/likely females) from a maternity and multiple transitory roosts, with two male bats detected using roosts, 9 km and 47 m apart. The accuracy of our SNP panels enabled a high level of confidence in the identification of individual bats. Targeted SNP genotyping is a valuable tool for monitoring and tracking of non-model species through a minimally invasive sampling approach.
| S-EPMC10803360 | biostudies-literature
Project description:Bioluminescence generated by luciferase and luciferin has been extensively used in biological research. However, detecting signals from deep tissues in vivo poses a challenge to traditional methods. To overcome this, the Akaluc and AkaLumine bioluminescent systems were developed, resulting in improved signal detection. We evaluate the potential of Akaluc/AkaLumine in Drosophila melanogaster to establish a highly sensitive, non-invasive, and temporal detection method for gene expression. Our results show that oral administration of AkaLumine to flies expressing Akaluc provided a higher luminescence signal than Luc/D-luciferin, with no observed harmful effects on flies. The Akaluc/AkaLumine system allows for monitoring of dynamic temporal changes in gene expression. Additionally, using the Akaluc fusion gene allows for mRNA splicing monitoring. Our findings indicate that the Akaluc/AkaLumine system is a powerful bioluminescence tool for analyzing gene expression in deep tissues and small numbers of cells in Drosophila.
| S-EPMC10721803 | biostudies-literature
Project description:BackgroundPlasma-derived tumour-specific cell-free nucleic acids are increasingly utilized as a minimally invasive, real-time biomarker approach in many solid tumours. Circulating tumour DNA of melanoma-specific mutations is currently the best studied liquid biopsy biomarker for melanoma. However, the combination of hotspot genetic alterations covers only around 80% of all melanoma patients. Therefore, alternative approaches are needed to enable the follow-up of all genotypes, including wild-type.MethodsWe identified KPNA2, DTL, BACE2 and DTYMK messenger RNA (mRNA) upregulated in melanoma versus nevi tissues by unsupervised data mining (N = 175 melanoma, N = 20 normal skin, N = 6 benign nevi) and experimentally confirmed differential mRNA expression in vitro (N = 18 melanoma, N = 8 benign nevi). Circulating cell-free RNA (cfRNA) was analysed in 361 plasma samples (collected before and during therapy) from 100 melanoma patients and 18 healthy donors. Absolute cfRNA copies were quantified on droplet digital PCR.ResultsKPNA2, DTL, BACE2 and DTYMK cfRNA demonstrated high diagnostic accuracy between melanoma patients' and healthy donors' plasma (AUC > 86%, p < .0001). cfRNA copies increased proportionally with increasing tumour burden independently of demographic variables and even remained elevated in individuals with radiological absence of disease. Re-analysis of single-cell transcriptomes revealed a pan-tumour origin of cfRNA, including endothelial, cancer-associated fibroblasts, macrophages and B cells beyond melanoma cells as cellular sources. Low baseline cfRNA levels were associated with significantly longer progression-free survival (PFS) (KPNA2 HR = .54, p = .0362; DTL HR = .60, p = .0349) and overall survival (KPNA2 HR = .52, p = .0237; BACE2 HR = .55, p = .0419; DTYMK HR = .43, p = .0393). Lastly, we found that cfRNA copies significantly increased during therapy in non-responders compared to responders regardless of therapy and mutational subtypes and that the increase of KPNA2 (HR = 1.73, p = .0441) and DTYMK (HR = 1.82, p = .018) cfRNA during therapy was predictive of shorter PFS.ConclusionsIn sum, we identified a new panel of cfRNAs for a pan-tumour liquid biopsy approach and demonstrated its utility as a prognostic, therapy-monitoring tool independent of the melanoma mutational genotype.
| S-EPMC9626658 | biostudies-literature
Project description:Knowledge of atrial wall thickness (AWT) has the potential to provide important information for patient stratification and the planning of interventions in atrial arrhythmias. To date, information about AWT has only been acquired in post-mortem or poor-contrast computed tomography (CT) studies, providing limited coverage and highly variable estimates of AWT. We present a novel contrast agent-free MRI sequence for imaging AWT and use it to create personalized AWT maps and a biatrial atlas. A novel black-blood phase-sensitive inversion recovery protocol was used to image ten volunteers and, as proof of concept, two atrial fibrillation patients. Both atria were manually segmented to create subject-specific AWT maps using an average of nearest neighbors approach. These were then registered non-linearly to generate an AWT atlas. AWT was 2.4 ± 0.7 and 2.7 ± 0.7 mm in the left and right atria, respectively, in good agreement with post-mortem and CT data, where available. AWT was 2.6 ± 0.7 mm in the left atrium of a patient without structural heart disease, similar to that of volunteers. In a patient with structural heart disease, the AWT was increased to 3.1 ± 1.3 mm. We successfully designed an MRI protocol to non-invasively measure AWT and create the first whole-atria AWT atlas. The atlas can be used as a reference to study alterations in thickness caused by atrial pathology. The protocol can be used to acquire personalized AWT maps in a clinical setting and assist in the treatment of atrial arrhythmias.
| S-EPMC5549842 | biostudies-other
Project description:Circulatory monitoring is currently limited to heart rate and blood pressure assessment in the majority of neonatal units globally. Non-invasive cardiac output monitoring (NiCO) in term and preterm neonates is increasing, where it has the potential to enhance our understanding and management of overall circulatory status. In this narrative review, we summarized 33 studies including almost 2,000 term and preterm neonates. The majority of studies evaluated interchangeability with echocardiography. Studies were performed in various clinical settings including the delivery room, patent ductus arteriosus assessment, patient positioning, red blood cell transfusion, and therapeutic hypothermia for hypoxic ischemic encephalopathy. This review presents an overview of NiCO in neonatal care, focusing on technical and practical aspects as well as current available evidence. We discuss potential goals for future research.
| S-EPMC7880199 | biostudies-literature
Project description:Protein acetylation is a key recurring co- and posttranslational modification. How different types of acetylation respond to the same environmental stress is unknown. A member of the newly discovered family of plastid acetyltransferases (GNAT2), which is featuring both lysine- and N-terminal acetyltransferase activity, was used in this study to obtain a holistic multi-omics acetylation-dependent view of the acclimation of plants to short-term light changes. Characterization of the N-terminal acetylome reveals that both its yield and coverage remain unchanged between WT and gnat2 knockout mutant lines when they are subjected for two hours to high-light or dark conditions. Similarly, no differences in their transcriptome or adenylate energy charge oscillations were observed under the tested light conditions between the genotypes. However, the GNAT2-associated lysine acetylome turned out to be sensitive to light changes. Our data suggests that the lysine acetylome marks on proteins change more rapidly allowing the acclimation to the environmental condition, while N-terminal acetylation changes are associated to long term responses. Taken together, our data reveals unique strategies of plant acclimation to the different treatments involving lysine but not N-terminal acetylation activities for the responses to environmental changes.
2024-08-19 | PXD040517 | JPOST Repository
Project description:Despite advances in genomic sequencing and bioinformatics, conservation genomics is still often hindered by a reliance on non-invasive samples. The presence of exogenous DNA and the low quantity and poor quality of DNA in non-invasive samples have been a roadblock to sequencing, thereby limiting the potential for genomic monitoring of endangered species. Recent molecular advances, such as host DNA enrichment, hold promise for facilitating sequencing from non-invasive samples. We used the FecalSeq method to enrich DNA extracted from wild-collected fecal pellets of the imperiled New England cottontail and identified SNPs from 3RAD Sequencing. We obtained SNPs from rabbit pellets, including pellets that were collected in poor environmental conditions and samples that performed poorly with microsatellites. Measures of sequencing success improved with greater amounts of starting DNA and 32% of samples generated SNP genotypes that passed quality control filtering. Genotyping error rates were high, however, and the approach was unable to consistently distinguish unique individuals or matching genotypes, while it was suitable for recovering the expected population structure. Pairing FecalSeq enrichment with RADseq is a promising low-cost method for monitoring wild populations using non-invasive samples in an environmental context, but it may be better suited for informing conservation through population genomics.
| S-EPMC11289273 | biostudies-literature
Project description:Oncosurgeries may incur massive blood loss demanding frequent blood sampling to assess blood loss and the need for intraoperative blood transfusions. Accuracy of non-invasive spectrophotometric haemoglobin (hereafter to be referred as SpHb) monitoring has been studied in various perioperative settings. The intraoperative use of Radical-7®, Masimo Corp., (Radical-7®) for SpHb monitoring may be useful during cancer surgery. The aim of this study is to evaluate the intraoperative utility of SpHb monitoring by the Radical-7® to guide intraoperative transfusion in oncosurgeries.Fifty adult patients, undergoing oncosurgery with anticipated blood loss of more than 20% of blood volume, were selected. Continuous SpHb monitoring was performed intraoperatively and blood transfusion was based on SpHb values. Simultaneous laboratory haemoglobin (LabHb) samples were taken for validation. The accuracy of intraoperative blood transfusions based on SpHb was analysed using Error Grid Analysis. Paired measurements of SpHb and LabHb were compared using Bland-Altman plot analysis.There were 66 paired data points for blood transfusion from fifty patients with a correlation of 73% (P < 0.001) between SpHb and LabHb. In the Bland-Altman analysis, the bias was - 0.313 g/dl with ~ 95% of values within the limits of agreement of 1.81 g/dl to -2.44 g/dl. In the Error Grid Analysis, most data points were in the least error zone (Zone A).The Radical-7® has the advantage of providing SpHb value continuously to take prompt decision regarding blood transfusion intraoperatively.
| S-EPMC5530738 | biostudies-other