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PubMed2026

Genome-wide survey of spliceosomal snRNA transcripts across hundreds of human biosamples reveals abundant transcription but low maturation level of snRNA variants.

Small nuclear RNAs (snRNAs) are essential components of the spliceosome and are encoded by large, multicopy gene families. However, their genome-wide identification and quantification have remained challenging due to high sequence similarity among family members. To address this, we utilized RAMPAGE (Rapid Amplification of cDNA Ends) data from the ENCODE project to comprehensively profile nascent transcription of spliceosomal snRNAs across 115 human biosamples. We identified 74 expressed snRNA variants, characterized by canonical promoter features including bidirectional transcription flanking a positioned nucleosome, active histone modifications, and evolutionary conservation- features largely absent from unexpressed variants. These transcriptional events were corroborated by total RNA-seq and Bru-seq data, yet the majority of these variants showed extremely low levels in small RNA-seq, indicating post-transcriptional bottlenecks for snRNA processing and maturation. Our findings reveal new layers of regulation in snRNA variant expression and suggest that selective post-transcriptional processing plays a critical role in shaping the functional snRNA repertoire and its contribution to splicing regulation.

Journal Article↗

PubMed2025

ClarID: A Human-Readable and Compact Identifier Specification for Biomedical Metadata Integration.

BACKGROUND: In biomedical research, subjects and biospecimens are commonly tracked using simple IDs or UUIDs, which guarantee uniqueness but convey no embedded semantic information. Contextual metadata (such as tissue type, diagnosis, or assay) is often stored separately, making integration, cohort selection, and downstream analysis cumbersome. While structured barcoding systems exist in large consortia (e.g., TCGA, GTEx) or domain-specific contexts (e.g., SPREC, GOLD), no unified, extensible framework currently spans both subjects and biosamples in a human- and machine-readable way. METHODS: We developed ClarID, a domain-agnostic specification that supports two identifier formats: (i) a human-readable form (e.g., 'CNAG_Test-HomSap-00001-LIV-TUM-RNA-C22.0-TRT-P1W' that encodes key metadata such as project, species, subject_id, tissue, assay, disease, timepoint and duration (from that event); and (ii) a compact version named 'stub' (e.g., 'CT01001LTR0N401T1W') optimized for filenames, pipelines, and labeling.ClarID is implemented through an open-source command-line tool, ClarID-Tools, which processes tabular metadata files (CSV/TSV) and uses a YAML-based codebook to generate, decode, and validate identifiers, as well as to create and read QR codes. The tool supports bulk and single-sample processing and allows easy integration with institutional workflows. RESULTS: To demonstrate ClarID's utility, we applied it to datasets from the Genomic Data Commons (GDC), generating interpretable identifiers for more than 113,000 clinical records (subjects) and 4,255 biospecimen records. All materials, including pre-processing scripts, input and encoded data, are publicly available and fully reproducible via the accompanying GitHub repository and Google Colab. CONCLUSIONS: ClarID fills a critical gap between opaque accession numbers and rich metadata schemas by embedding key context directly into structured identifiers. It enhances traceability, facilitates downstream analysis, and remains adaptable to project-specific needs through a configurable codebook. The accompanying ClarID-Tools software is freely available, together with full documentation and reproducible pipelines, at https://github.com/CNAG-Biomedical-Informatics/clarid-tools.

Biosample identifiers↗

PubMed2006

Screening for in vivo metabolites of isovalertatin family oligosaccharides in rats by liquid chromatography coupled to electrospray ionization tandem mass spectrometry.

Liquid chromatography/electrospray ionization tandem mass spectrometry (LC/MS(n)) was used to identify trace levels of in vivo metabolites after the administration of isovalertatin M23 or isovalertatin D23 to rats. The biosamples of urine, feces, and ileum incubation were pre-treated by solid-phase extraction (SPE), and then chromatographed with a reversed-phase C8 column with acetonitrile/1.5 mM aqueous ammonia (18:82, v/v) as the mobile solvent. The parent drug and the possible metabolites were identified by two independent qualitative parameters, retention time and collision-induced dissociation product ions. Nine and seven metabolites were successfully characterized from biosamples after administration of isovalertatins M23 and D23, respectively, to rats. The metabolism seemed to take place in the rat intestinal tract, and metabolic pathways were identified including isovaleryl de-esterification and hydrolysis of alpha-glucose units located either at the reducing or the non-reducing terminus.

Amines↗

PubMed2005

Practical aspects of sharing controls between case-control studies.

PURPOSE: We discuss the practical advantages and challenges of sharing controls among two or more concurrently conducted case-control studies. METHODS: We conducted two case-control studies, one of breast cancer and the other of endometrial cancer, with overlapping, shared control groups. The studies had overlapping geographic areas, identical telephone questionnaires and biosample collection, and identical age and race eligibility. RESULTS: Sharing controls reduced the number of potential controls that had to be identified by random-digit dialing by 25% and the number of eligible controls that had to be interviewed by 32%. The cost savings were approximately 2,96,000 dollars, or 7% of the program project that funded the studies. CONCLUSIONS: The disadvantage of sharing controls was the complexity of the design and the additional investigator time required to plan, monitor, and adjust the design. In the situation presented here, the complexities would have been reduced greatly if we had not attempted to frequency match on age in both studies. Generally, sharing controls is likely to work well when strict frequency matching is not required and there is a large overlap of interview questions, other data to be collected, and eligibility criteria among the studies.

Aged↗

PubMed1997

Hydrofluorosis in water buffalo (Bubalus bubalis) in India.

The concentration of fluoride was determined in water, forage and urine and serum samples of buffaloes from the Unnao district of India. The water and forage samples contained 2.01 +/- 0.51 and 22.50 +/- 0.82 ppm of fluoride, respectively. The analysis of biosamples collected from the affected animals revealed higher levels of fluoride in serum (0.58 +/- 0.05 ppm) and urine (10.64 +/- 1.23 ppm). Clinical examination identified a 40.34% prevalence rate of clinical lesions suggestive of fluorosis in buffalo of this locality. Dental lesions were present invariably in all affected animals whereas lameness, painful bony exostosis and emaciation were recorded in 28.17%, 8.45% and 76.00% of the animals. Based on the clinical lesions and fluoride content in water, serum and urine, it was concluded that the problem of fluorosis in buffalo is attributable to drinking water containing toxic levels of fluoride.

Animal Feed↗

PubMed2019

Genome-wide analysis of polymerase III-transcribed Alu elements suggests cell-type-specific enhancer function.

Alu elements are one of the most successful families of transposons in the human genome. A portion of Alu elements is transcribed by RNA Pol III, whereas the remaining ones are part of Pol II transcripts. Because Alu elements are highly repetitive, it has been difficult to identify the Pol III-transcribed elements and quantify their expression levels. In this study, we generated high-resolution, long-genomic-span RAMPAGE data in 155 biosamples all with matching RNA-seq data and built an atlas of 17,249 Pol III-transcribed Alu elements. We further performed an integrative analysis on the ChIP-seq data of 10 histone marks and hundreds of transcription factors, whole-genome bisulfite sequencing data, ChIA-PET data, and functional data in several biosamples, and our results revealed that although the human-specific Alu elements are transcriptionally repressed, the older, expressed Alu elements may be exapted by the human host to function as cell-type-specific enhancers for their nearby protein-coding genes.

Alu Elements↗

PubMed1999

Systematic toxicological analysis of drugs and poisons in biosamples by hyphenated chromatographic and spectroscopic techniques.

The introduction of hyphenated chromatographic-spectroscopic techniques represented a substantial step-forward for Systematic Toxicological Analysis (STA), increasing the amount and quality of information obtainable from the analysis of a biological sample, and enhancing the possibilities of identifying unknown drugs and poisons. STA methods based either on GC-MS or on HPLC-UV published in the last decade are reviewed in this paper. The different analytical phases, i.e. sample preparation (pretreatment, extraction, derivatisation), chromatographic separation and detection/identification are examined in detail in order to emphasise the complementarity of the two approaches. In addition, the first STA method based on HPLC-MS is illustrated and some applications of TLC-UV to drug screening are also described. Finally, an overview of semi- and fully-automated STA methods is given.

Chromatography↗

PubMed2026

An encyclopedia of human enhancer-gene regulatory interactions.

Identifying transcriptional enhancers and their target genes is essential for understanding gene regulation and the effect of human genetic variation on disease1-6. Here we create and evaluate a resource of more than 92 million enhancer-gene regulatory interactions across 1,458 biosamples covering 369 cell types and tissues, by integrating predictive models, chromatin states, three-dimensional contacts and large-scale genetic perturbations generated by the ENCODE Consortium7. We first create a systematic benchmarking pipeline to compare predictive models, assembling a dataset of 10,356 element-gene pairs measured in CRISPR perturbation experiments, more than 30,000 fine-mapped expression quantitative trait loci and 569 fine-mapped genome-wide association study (GWAS) variants linked to a probable causal gene. Using this framework, we develop ENCODE-rE2G, a predictive model achieving state-of-the-art performance across several prediction tasks, demonstrating that iterative perturbations and supervised machine learning can build increasingly accurate predictive models of enhancer regulation. Using ENCODE-rE2G, we build an encyclopedia of enhancer-gene regulatory interactions in the human genome, revealing global properties of enhancer networks, identifying differences in regulatory complexity across genes and improving analyses linking noncoding variants to target genes and cell types for common complex diseases. By interpreting the model, we find that beyond enhancer activity and three-dimensional enhancer-promoter contacts, additional features that guide enhancer-promoter communication include promoter class and enhancer-enhancer synergy. These genome-wide maps of enhancer-gene regulatory interactions, benchmarking software, predictive models and insights about enhancer function provide a valuable resource for future studies of gene regulation and human genetics.

Humans↗

PubMed1995

Viral, host and environmental risk factors for hepatocellular carcinoma: a prospective study in Haimen City, China.

To identify specific environmental, viral, and genetic risk factors for hepatocellular carcinoma (HCC) and the interaction of such factors, we are conducting a prospective study in a high-incidence area of China. Questionnaires were completed and biosamples collected by 60,984 men ages 30-64 years, at study entry. Within 2.5 years, 183 deaths from HCC had occurred. Each HCC case was matched with 5 controls and compared for items on the questionnaire. In addition to chronic hepatitis B virus (HBV) infection, the significant risk factors were: occupation (peasant), corn consumption (in the 1970s), family history of HCC, and history of an episode of acute hepatitis as an adult. HBV, consumption of aflatoxins, a genetic factor, and possibly a second hepatitis virus infection contribute to the risk of HCC.

Adult↗

PubMed2001

Comprehensive drug screening by integrated use of gas chromatography/mass spectrometry and Remedi HS.

The authors evaluated an integrated approach for the screening of drugs in biosamples consisting of gas chromatography/mass spectrometry analysis of serum or whole blood (SB/GC-MS) and of high-performance liquid chromatographic and ultraviolet (HPLC-UV) analysis of urine with the REMEDi HS Biorad system (U/REM) (Bio-rad; Segrate, MI, Italy). Urine and blood samples from 26 suspected intoxicated patients and from 22 suspected lethal poisoning cases were examined. Eighty-one of the 99 parent drugs/main metabolites detected were identified by SB/GC-MS and 54 with U/REM. Thirty-six drugs/metabolites were identified with both methods, 45 by SB/GC-MS alone, and 18 by U/REM alone. Absence of the mass spectrometry (MS) spectra in the reference library and high polarity of the analytes were the main reasons for failed identification by SB/GC-MS. Unsuccessful identifications with U/REM were basically caused by the absence of the UV spectra in the reference library or by low chromatographic and spectroscopic selectivity as in the case of barbiturates and benzodiazepines (BZD), which represented 11% and 51%, respectively, of the 45 SB/GC-MS unique identifications. Urine samples of 14 BZD-positive cases were also submitted to enzymatic hydrolysis and analyzed with the REMEDi UBz assay, and results were compared with those obtained by SB/GC-MS: 14 of the 22 identified BZD were detected with both methods, three by U/REM only, and five by SB/GC-MS only. In conclusion, the integrated use of SB/GC-MS and U/REM approaches greatly enhances the amount and quality of analytical information obtainable by applying either method alone.

Chromatography, High Pressure Liquid↗

PubMed2025

Logan: Planetary-Scale Genome Assembly Surveys Life's Diversity.

The breadth of life's diversity is unfathomable, but public nucleic acid sequencing data offers a window into the dispersion and evolution of genetic diversity across Earth. However the rapid growth and accumulation of sequence data have outpaced efficient analysis capabilities. The largest collection of freely available sequencing data is the Sequence Read Archive (SRA), comprising 27.3 million datasets or 5 × 1016 basepairs. To realize the potential of the SRA, we constructed Logan, a massive sequence assembly transforming short reads into long contigs and compressing the data over 100-fold, enabling highly efficient petabase-scale analysis. We created Logan-Search, a k-mer index of Logan for free planetary-scale sequence search, returning matches in minutes. We used Logan contigs to identify >200 million plastic-degrading enzyme homologs, and validate novel enzymes with catalytic activities exceeding current reference standards. Further, we vastly expand the known diversity of proteins (30-fold over UniRef50), plasmids (22-fold over PLSDB), P4 satellites (4.5-fold), and the recently described Obelisk RNA elements (3.7-fold). Logan also enables ecological and biomedical data mining, such as global tracking of antimicrobial resistance genes and the characterization of viral reactivation across millions of human BioSamples. By transforming the SRA, Logan democratizes access to the world's public genetic data and opens frontiers in biotechnology, molecular ecology, and global health.

Journal Article↗

PubMed1999

Stereochemical determination of selegiline metabolites in postmortem biological specimens.

In this study, findings related to an aircraft accident are reported. Biological specimens collected at autopsy from the pilot of the fatal accident and two types of tablets found at the accident scene were submitted for toxicological evaluation. It was determined that the pilot was dead at the crash site and the cause of death was multiple traumatic injuries. The tablets were identified as selegiline and levodopa, commonly prescribed for the treatment of Parkinson's disease. Selegiline, a stereospecific compound, is biotransformed into (-)-N-desmethylselegiline, (-)-methamphetamine, and (-)-amphetamine. The latter two levorotatory metabolites cannot be easily distinguished by routine analysis from their dextrorotatory isomers, which are controlled substances. It was, therefore, prudent to differentiate these isomers to determine if they resulted from the ingestion of a controlled substance, (+)-methamphetamine. Initial immunoassay drug screenings revealed the presence of amphetamine class drugs (867 ng/mL) in urine, amphetamine/methamphetamine (261 ng/mL) in urine, and methamphetamine (46 ng/mL) in blood. The gas chromatography-mass spectrometry (GC/MS) results revealed the presence of methamphetamine in the concentrations of 76 ng/mL of blood and 685 ng/mL of urine. The concentration of amphetamine was 52 ng/mL in blood and 320 ng/mL in urine. To determine the stereospecificity of these amines, the isolated amines from the biosamples were derivatized by a stereospecific agent, (S)-(-)-N-(trifluoroacetyl)-prolyl chloride, and characterized by a GC/MS method to be levorotatory. The 2.14 ratio of (-)-methamphetamine to (-)-amphetamine concentrations in the urine was consistent with a selegiline study in the recent literature. The stereospecific analysis, in conjunction with the history of the pilot being on Parkinson's medications, suggests that the source of these amines was selegiline. This conclusion substantiates the importance of the identification of enantiomers in evaluating and interpreting related analytical results for accident investigations.

Accidents, Aviation↗