Evaluation of Nuclear DNA from Rootless Hairs for Forensic Purposes
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PROVIDER: PRJNA854257 | ENA |
REPOSITORIES: ENA
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Project description:Evaluation of Nuclear DNA from Rootless Hairs for Forensic Purposes
| PRJNA854258 | ENA
Project description:Soil metagenomes profiling for forensic purposes
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Project description:Characterization of hair proteome in damaged single hairs after an explosive blast and evaluation of success rates in genetically variant peptide marker detection for protein-based human identification.
2020-05-14 | PXD017427 | Pride
Project description:Forensic body fluid identification is important for crime scene reconstruction. We used Illumina HumanMethylation 450K bead array containing over the 450,000 CpG sites in 16 body fluid samples to find novel DNA methylation marker for forensic body fluid identification. Examination of genome-wide DNA methylation profiling in 16 body fluid samples
2014-07-31 | E-GEOD-55734 | biostudies-arrayexpress
Project description:Forensic body fluid identification is important for crime scene reconstruction. We used Illumina HumanMethylation 450K bead array containing over the 450,000 CpG sites in 16 body fluid samples to find novel DNA methylation marker for forensic body fluid identification.
2014-07-31 | GSE55734 | GEO
Project description:Root hairs are frequently reported to be plastic in response to nutrient supply, but relatively little is known about their development in response to magnesium (Mg) availability, and evidence is scarce about the signals involved in this process. Here, we showed that both density and length of root hairs of Arabidopsis decreased logarithmically with increasing Mg supply in the media , which correlated with the initiation of new trichoblast files and likelihood of trichoblasts to form hairs. Low Mg resulted in greater concentrations of reactive oxygen species (ROS) and Ca2+ in the roots and displayed a stronger tip-focused gradient of ROS and cytosolic Ca2+ concentration ([Ca2+]c) during initiation and elongation of root hairs. This gradient could be eliminated by DPI or BAPTA. Application of either DPI or BAPTA to low Mg treatment blocked the enhanced development of root hairs. The opposite was true when the plants under high Mg were supplied with Ca2+ or PMS. Whole-genome transcriptome data revealed that the maximum differential expressed genes involved in ‘stress’, ‘oxidation reduction’, ‘ion transport and homeostasis’ and ‘cell wall organization’. A greater fraction of morphogenetic H-genes and root hair -specific genes as well as genes involved in ‘cell wall structure’ were up-regulated by 7-d treatment of 0.5 μM Mg but down-regulated by 7-d treatment of 10,000 μM Mg. It is concluded that a distinct and previously poorly characterized response of root hair development to Mg availability is presented in Arabidopsis where ROS and Ca2+ are the signaling molecules that control this response.
2012-12-14 | GSE42899 | GEO
Project description:Chromatin modifications, such as cytosine methylation of DNA, play a significant role in mediating gene expression in plants, which affects growth, development, and cell differentiation. Since root hairs are single cell extensions of the root epidermis and the primary organs for water uptake and nutrients, we sought to use root hairs as a single cell model system to measure the impact of environmental stress. We measured changes in cytosine DNA methylation in single cell root hairs as compared to multi-cellular stripped roots, as well as in response to heat stress. Differentially methylated regions (DMRs) in each methylation context showed very distinct methylation patterns between cell types and in response to heat stress. Intriguingly, at normal temperature, root hairs were more hypermethylated as compared to stripped roots. However, in response to heat stress, both root hairs and stripped roots showed more hypomethylation in each context, especially in the mCHH context. Moreover, expression analysis of mRNA from similar tissues and treatments identified some associations between DMRs, genes and transposons. Taken together, the data indicate that changes of dynamic DNA methylation directly or indirectly is associated with expression of genes and transposons either within the context of specific tissues/cells or stress (heat).
2017-08-01 | GSE90142 | GEO
Project description:Current molecular diagnostic techniques in forensic science are significantly hindered by DNA degradation, underscoring the urgent need for robust molecular tools with resistance to degradation. In our previous study using a murine traumatic brain injury (TBI) model, we were the first to propose the feasibility of using ATAC-seq (Assay for Transposase-Accessible Chromatin with high-throughput sequencing) to identify trauma-related chromatin changes under early postmortem degradation conditions (2 hours). However, its applicability to human forensic samples remains insufficiently evaluated. This study aims to systematically assess the utility of ATAC-seq in identifying chromatin accessibility changes induced by TBI in human samples, with a particular focus on its stability and reliability under late-stage postmortem degradation. Cortical brain tissues from three human TBI cases and three matched controls were collected and subjected to sampling at 0 and 24 hours postmortem. Standard ATAC-seq protocols were used for library construction and sequencing. Downstream analyses included quality control, differential accessibility analysis, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment, and transcription factor motif analysis. All 12 samples exhibited high-quality sequencing metrics. Numerous differentially accessible chromatin regions (peaks) were identified between TBI and control groups, demonstrating the sensitivity of ATAC-seq in detecting trauma-associated chromatin alterations. Notably, no significant differences were observed between samples degraded for 0 and 24 hours, indicating the method’s robustness to degradation. Enrichment analyses revealed that differential peaks were significantly associated with biological processes and pathways relevant to TBI pathology, including axon development, synaptic signaling, and neurotrophin signaling pathways. The SOX transcription factor family emerged as a dominant motif, consistent with known mechanisms of TBI pathophysiology. This study provides compelling evidence that trauma-induced chromatin accessibility changes remain stable even in degraded forensic brain tissues, including those subject to late postmortem intervals. The high sensitivity and specificity of ATAC-seq support its potential application in forensic pathology, offering both a theoretical foundation and empirical validation for its broader use in forensic diagnostics.
2026-06-04 | GSE298572 | GEO
Project description:Bone is a long-lasting biological tissue often used in forensic investigations as it retains vital biomolecular information commonly used for identification purposes. Bone proteins have attracted interest for their potential in estimating post-mortem interval (PMI) and age-at-death (AAD). However, the preservation of such proteins is highly dependent on intrinsic and extrinsic factors, and these have an impact in the potential application of molecular techniques to forensic sciences. The present study aims at investigating the effect that two commonly used types of burial practices (entombment and inhumation) have on bone protein survival. The sample consists in 14 exhumed individuals from cemeteries in south of Italy at with different AADs (29-85 yeas) and PMIs (1-37 years). LC-MS/MS analyses show that 16 proteins are better preserved in the entombed condition and four in the inhumated one, while no clear cluster separation is detected with principal component analysis. Besides the different burial environments, several potential protein markers are identified for PMI and AAD estimation. Overall, preliminary results show that the two burial environments seem to play a marginal role in the differential preservation of non-collagenous proteins and in the accumulation of post-translational modifications, confirming the potential of LC-MS/MS based proteomics in forensic sciences.
2022-03-25 | PXD029911 | Pride
Project description:We provide an atlas of gene and protein expression in Arabidopsis root hair cells, generated by paired-end RNA-seq and LC/MS-MS analysis from protoplasts that carry the root hair-specific pEXP7-GFP reporter construct. In total, transcripts from 23,234 genes were detected in root hairs; those related to cell wall biosynthesis and translation differed most dramatically in abundance when compared to non-GFP root protoplasts.
2012-12-04 | E-MTAB-4375 | biostudies-arrayexpress