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At least 19 recordsLinked to original sources
PubMed2026

DNAvi: integration, statistics, and visualization of cell-free DNA fragment traces.

SUMMARY: DNAvi is a Python-based tool for rapid grouped analysis and visualization of cell-free DNA fragment size profiles directly from electrophoresis data, overcoming the need for sequencing in basic fragmentomic screenings. It enables normalization, statistical comparison, and publication-ready plotting of multiple samples, supporting quality control and exploratory fragmentomics in clinical and research workflows. AVAILABILITY AND IMPLEMENTATION: DNAvi is implemented in Python and freely available on GitHub at https://github.com/anjahess/DNAvi under a GNU General Public License v3.0, along with source code, documentation, and examples. An archived version is available under https://doi.org/10.5281/zenodo.18401705.

Software↗
PubMed2026

A rare and atypical case of long-distance indirect DNA transfer: Contamination from an investigator never present at the scene.

To maximize the usefulness of DNA obtained from biological samples in forensic genetics, it is crucial to avoid DNA contamination throughout all procedures, from sample collection at crime scenes to STR profile generation in DNA laboratories. This study reports a rare and atypical case of DNA contamination in a forensic setting. During the analysis of biological evidence from a cold case preserved for 18 years, the STR profile obtained from the surface of a plastic bag matched that of an investigator, identified through the DNA elimination database. Case reconstruction confirmed that the investigator-who was located 80 km from the DNA laboratory and had never entered the crime scene or the sample storage room-was not a suspect and that the obtained STR profile originated from contamination. The most plausible explanation for the contamination was indirect transfer: investigator's DNA had adhered to a colleague's clothing and was subsequently dislodged and deposited onto the surface of the plastic bag as the colleague approached the sample pretreatment area. This study integrates trace DNA profiling of challenged samples with rapid contamination investigation and proposes prevention and control measures. This case underscores that, although DNA is widely regarded as the "gold standard" in forensic genetics, its interpretation must be considered within the context of the entire case. Conclusions should not be drawn based solely on a single DNA result.

Humans↗
PubMed2026

The prevalence and persistence of DNA in vehicles from incidental drivers and other occupants, and their associates, including after reuse by regular drivers.

It is common knowledge that when driving a vehicle, people leave traces of DNA behind. However, in the context of vehicle crimes, it is helpful for the police and investigative personnel to know the vehicle locations in which a perpetrator most likely left DNA during the incident. By specifying the most informative locations to sample for incidental driver DNA, time and resources can be saved in criminal investigations. This study extends previous knowledge by focusing on the prevalence and persistence of incidental driver DNA in vehicles. Furthermore, the current study investigates the prevalence of DNA on vehicle locations from the regular driver and the close associates of the regular driver and incidental driver. The same experiment was conducted by two laboratories, allowing for inter-laboratory comparisons. The results confirm that DNA from the last driver of the vehicle is most likely recovered from high contact areas for operation of the vehicle like the steering wheel and gear shift. Most sampled sites within the vehicle contain DNA from the regular driver of that vehicle. DNA from an incidental driver is most likely to persist, even after resumed use of the vehicle by the regular driver, on locations with a higher retention capacity for biological materials like the car seats and seat belts. Overall, this paper highlights the patterns of DNA transfer, persistence and recovery that occur depending on an individual's relationship to a vehicle. This information can be used by crime scene investigators for targeting the most relevant sampling locations given different scenarios of vehicle use.

Humans↗
PubMedDate not supplied

[DNA synthesis on the heterogeneous nuclear RNA template catalysed by DNA polymerase of avian myeloblastosis virus].

Template activity of nuclear pre-mRNA has been investigated in DNA-polymerase reaction. Active synthesis of DNA was demonstrated on pre-mRNA as a template in the absence of primer. A part of synthetic activity may be attributed to the traces of DNA present in the pre-mRNA preparation. Addition of oligo(dT)10 to the template stimulated the synthesis of DNA product due to transcription of heteropolymeric regions near the poly(A). The rate of DNA synthesis was different depending on the fraction of template used: the RNA extracted by hot phenol at 85 degrees showed higher template activity without adding of primer than the 65 degrees C fraction. On the contrary 65 degrees C pre-mRNA which is known to contain greater quantity of molecules with poly(A) at the 3'-end is more strongly stimulated by addition of oligo(dT). The nuclear RNA corresponding to the precursors of rRNAs extracted at 40 degrees C were not transcribed by the reverse transcriptase. The size of the DNA-product (about 7-8S in alkaline sucrose gradient) did not depend on the size of the template neither on the presence of oligo(dT)10 primer. The inhibition of the second DNA strand synthesis with actinomycin D had also no influence on the size of DNA-product.

Avian Leukosis Virus↗
PubMed1975

Purification of S1 muclease from Takadiastase by affinity chromatography on single-stranded DNA-acrylamide columns.

When S1 nuclease from Takadiastase was partially purified according to previously reported methods, it showed a 10 to 15 fold increase in specificactivity. Although such preparations were highly active on single-stranded DNA, they had traces of activity on native DNA and were contaminated by T1-RNase. The S1 enzyme was further purified by a single step of affinity chromatography on single-stranded DNA-acrylamide column to a final purification of 275-fold. This preparation was free of T1-RNase and had an absolute specificity for single-stranded DNA.

Acrylamides↗
PubMed1977

Reversibly contractile nuclear matrix. Its isolation, structure, and composition.

From Tetrahymena macronuclei we have isolated a reversibly contractile nucleo-skeleton, i.e., an "expanded" nuclear matrix which reversibly contracts when the total concentration of the bivalent cations, Ca and Mg (3:2), is decreased to 5 mM or increased to 125 mM. During contraction the average diameter of the expanded matrix becomes reduced by about 24%; this corresponds to a volume contraction of about 55%. The reversible contraction of the nuclear matrix does not depend on ATP and cannot be inhibited by salygran. The expanded matrix is obtained by removing carefully from the macronuclei 89.7% of the phospholipid, 99.6% of the DNA, 98.5% of the RNA, and 74.8% of the protein by treatment with Triton X-100 and digestion with DNase and RNase followed by an extraction with 2 M NaCl. Electron microscopy reveals, within the expanded matrix, residual equivalents to the structures characteristic for macronuclei: (a) a residual nuclear envelope with nuclear pore complexes; (b) residual nucleoli at the periphery; (c) a fibrillar internal network. The expanded matrix is essentially composed of proteins (96.2%) and traces of DNA (0.8%), RNA (0.5%), phospholipid (1.6%), and carbohydrates (0.9%). The last, which have been determined by gas chromatography, contain glucose, mannose, and an unidentified sugar in the ratio 1:5.4:5.7. The ratio of acidic to basic amino acids of the expanded matrix is 1.55. Sodium dodecyl sulfate (SDS) gel electrophoresis reveals a predominant protein with a mol wt of 18,000 which is apparently involved in the reversible contractile process. The mechanism of this reversible contraction of the expanded matrix remains to be elucidated, but it differs both from actin-myosin contraction systems and from the contractile spasmoneme system in vorticellids.

Calcium↗
PubMed2026

Epigenetic Regulation of the BDNF Gene by Molybdenum in 9 to 11-Year-Old Children: A Targeted Gene DNA Methylation Study.

While essential trace minerals are known to influence DNA methylation (DNAm), molybdenum's (Mo) role in epigenetic regulation remains largely unexplored. This study examined associations between Mo status and DNAm of the brain-derived neurotrophic factor (BDNF) gene, a critical regulator of neurogenesis, in children aged 9-11 years, focusing on 107 CpG sites across BDNF and its antisense transcript (BDNF-AS).BDNF and BDNF-AS methylation was analyzed in blood samples from 72 children randomly selected from a cohort of 292 participants. Dietary Mo intake was estimated from food records, and creatinine-adjusted urinary Mo levels were quantified. Higher urinary molybdenum was significantly associated with decreased methylation at five BDNF 5'UTR sites (p<.05) and increased methylation of BDNF-AS (p = &#xa0;.0001), consistent with enhanced BDNF transcriptional activity. African American children exhibited lower urinary Mo excretion than European American children, suggesting greater retention, and showed cortisol-associated increases in BDNF methylation not observed in European American children.These findings demonstrate associations between molybdenum status and DNA methylation patterns at the BDNF locus in children. While functional validation through BDNF protein measurement is needed, results suggest molybdenum may influence neurotrophin gene regulation through epigenetic mechanisms, highlighting the importance of trace mineral nutrition during neurodevelopment.

Humans↗
PubMed1976

Relationships between intracisternal type A and extracellular oncornavirus-like particles produced in murine MOPC-460 myeloma cells.

Oncornavirus-like particles of the "A" (both intracisternal and intracytoplasmic) and "B" or "C" (extracellular) types are produced by murine MOPC-460 myeloma cells. This communication describes a comparative study on tracisternal A and extracellular particles. Both types of particles contain an RNA-dependent DNA polymerase activity, traces of 35S and 70 S RNA in addition to larger amounts of degraded RNA, and proteins of approximately 76,000 and 45, 000 daltons. The 76,000-dalton proteins from intracisternal A and extracellular particles have the same cyanogen bromide peptides. Hybridization kinetic analysis indicates that the RNAs in the two particles are identical or very closely related and share partial homology with Moloney leukemia virus RNA. In contrast, the particles appear to have little or no relationship to murine mammary tumor virus as judged by several different criteria. Electron microscope studies indicate that the extracellular particles arise from the budding of core components through the plasma membrane. These results suggest that the intracisternal A and extracellular oncornavirus-like particles produced by MOPC-460 cells are closely related.

Animals↗
PubMed1979

Repair promoted by plasmid pKM101 is different from SOS repair.

In E. coli K12 bacteria carrying plasmid pKM101, prophage lambda was induced at UV doses higher than in plasmid-less parental bacteria. UV-induced reactivation per se was less effective. Bacteria with pKM101 showed no alteration in their division cycle. Plasmid pKM101 coded for a constitutive error-prone repair different from the inducible error-prone repair called SOS repair. Plasmid pKM101 protected E. coli bacteria from UV damage but slightly sensitized them to X-ray lesions. Protection against UV damage was effective in mutant bacteria deficient in DNA excision-repair provided that the recA, lexA and uvrE genes were functional. Survival of phages lambda and S13 after UV irradiation was enhanced in bacteria carrying plasmid pKM101; phage lambda mutagenesis was also increased. Plasmid pKM101 repaired potentially lethal DNA lesions, although wild-type DNA sequences may not necessarily be restored; hence the mutations observed are the traces of the original DNA lesions.

DNA Repair↗
PubMed1979

Estrogen withdrawal in chick oviduct. Evidence for continued expression of active unique genes using an "expressed" DNA probe.

We have analyzed the effect of estrogen on the kinds of unique DNA sequences which are transcriptionally expressed in chick oviduct with an "expressed" DNA probe. Steady-state nRNA in estrogen-stimulated chick oviduct represents about 25% of the complexity of total chick unique DNA. To purify this expressed DNA fraction, chick unique DNA was isolated, nick-translated, and hybridized to chemically mercurated oviduct nRNA (Hg-nRNA); the resulting hybrids were bound to sulfhydryl-Sepharose, and DNA was selectively recovered by thermal elution in formamide buffer. To compare the sequence homology between nRNAs isolated from oviduct before or up to 6 days after estrogen withdrawal, trace amounts of expressed DNA derived from estrogen-stimulated oviduct were hybridized in RNA-excess reactions. All nRNAs hybridized with equal efficiency. Furthermore, hybridization of expressed DNA to nRNA mixtures showed that nRNA from nonwithdrawn and withdrawn oviduct contained a similar set of unique sequences. The data indicate that, at most, only a small percentage (0--5%) of transcriptionally active unique DNA sequences are shut down when estrogen is removed from the circulation.

Animals↗
PubMed1977

Expression of the chloroplast ribosomal RNA genes of Euglena gracilis during chloroplast development.

The cellular content and transcription program of the chloroplast ribosomal RNA genes of Euglena gracilis Z have been determined during the light-induced development of chloroplasts by hybridization of total cell DNA or RNA to purified 3H-labeled chloroplast ribosomal DNA ([3H]ctrDNA). Pancreatic DNase activated, partially purified chloroplast rDNA was enzymatically labeled in vitro by E. coli DNA polymerase I with [3H]TTP as a substrate. The [3H] DNA was denatured and hybridized with a vast excess of purified chloroplast 16 and 23S rRNA. The rRNA-[3H]ct rCNA hybrid was isolated by chromatography on hydroxylapatite. The [3H]ct rDNA was purified and characterized by the kinetics of its renaturation with chloroplast DNA and rRNA, and by the thermal stability of [3H]DNA-DNA and [3H]DNA-RNA hybrids. [3H]ct rDNA was hybridized in trace amounts to cellular RNA or DNA isolated from Euglena cells 0,4,8,12,24,48, and 72 h after the onset of chloroplast development. From a comparison of the kinetics of hybridization with hybridization of standards of known kinetic complexity quantitative estimates of the cellular rRNA and rDNA gene content were made. Chloroplast rRNA increases from 2 to 26% of the cellular RNA during development, while the percentage of cellular DNA represented by ct rDNA increases two- to threefold. Correcting for the change in cellular RNA and DNA content during development, the number of copies of the rRNA gene increases less than twofold, while the number of copies of rRNA per cell increases sixfold. The results are consistent with either a transcriptional activation of the ribosomal genes or an increased rRNA stability during developmental.

Animals↗
PubMed2025

Paired Single-Cell Transcriptome and DNA Barcode Detection in Zebrafish Using ScarTrace.

ScarTrace is a CRISPR/Cas9-based genetic lineage tracing method that allows for uniquely barcoding the DNA of single cells at a target GFP sequence during developing zebrafish embryos. Single cells from barcoded adult zebrafish can be isolated from various tissues (e.g., marrow, brain, eyes, fins), and their transcriptome and barcode sequences are captured by single-cell cDNA amplification and genomic DNA nested PCR, respectively. Computationally, cell type and barcode identification permit clone tracing and lineage tree reconstruction of tissues to unravel fate decisions during embryogenesis.

Animals↗
PubMed1977

DNA-dependent RNA polymerases from Artemia salina. IV. appearance of nuclear RNA polymerase activity during pre-emergence development of encysted embryos.

Dessicated and encysted gastrulae of the brine shrimp Artemia salina remain metabolically dormant until they are rehydrated. At this time development resumes, culminating in the hatching of free swimming nauplius larvae. The resumption of embryogenesis provides a convenient system for studying biochemical events which accompany development of a eukaryotic organism, and in particular Artemia has proven useful for studies of the transcriptional regulation of gene expression. Encysted gastrulae of Artemia yielded only trace amounts of DNA-dependent RNA polymerase activity when crude nuclear pellets were subjected to sonication at high ionic strength. Furthermore, when crude nuclear pellets from encysted gastrulae and developing nauplius larvae were mixed prior to sonication, subsequent solubilization of proteins from the mixture did not yield RNA polymerase activity; sonication of the pellet from nauplii alone resulted in the solubilization of large quantities of RNA polymerases I and II as we have previously found [1]. RNA polymerases I and II were detectable in sonicates of crude nuclear pellets after 1-h incubation of Artemia cysts in sea water. This presents the possibility that dormant gastrulae of the brine shrimp contain RNA polymerase which is inactive, and that the rapid appearance of nuclear enzymatic activity which accompanies the resumption of development may not require de novo synthesis of the polymerase.

Animals↗
PubMed1978

[Reaction of cells in the anterior lobe of the rat pituitary after acute cooling].

The anterior hypophysis (AH) of rat exposed to total cooling at --10 degrees C for 6 min was studied histologically and autoradiographically. 3, 6, 12, 18, and 24 hours after the exposure the diurnal cycle of modifications of the functional state of the AH secretory cells, the number of mitoses and of the labeled DNA-synthesizing cells was traced. In 12 hours a considerable activation of the thyrotrops and a doubling of mitoses occurred; there was no change of the labeled cells index for twenty four hours. The data obtained showed that stress reaction to cold was characterized by the intensification of the thyrotropic function and an acceleration of mitotic process in the AH cells.

Animals↗
PubMed1975

Specific detection and semiquantitation of micro-organisms in tissue by nucleic acidhybridization. I. Characterization of the method and application to model systems.

On the basis of circumstantial evidence, a number of human diseases have been postulated to result from the presence of occult infection. To investigate this problem amethod of specifically detecting and semiquantitaing trace quantities of bacterial DNA in infected tissue has been devised. It is based on RNA-DNA hybridization using radiolabeled RNAcomplementary to the DNA of the organism being sought. The characteristics of the reaction are shown to conform to those expected for RNA-DNA hybridization and the sensitivity of the method is shown to correspond to approximately one organism per 50 mammalian cells. Specificity at this level of sensitivity is sufficient to clearly distinguish between infections with Listeria monocytogenes and Erysipelothrix insidiosa. This approach may have general applicability forthe study of diseases putatively caused by chronic infection not readily demonstrable bythe usual cultural or immunologic techniques. It may also be useful for helping distinguish contaminants from pathogens when isolates are obtained from diseases tissue. Unique to this approach is the value of negative information in excluding the presenceof an organism within its limits of sensitivity.

Animals↗
PubMed1977

[Oncogeny of herpes simplex viruses and lupidon].

The part of the herpes simplex virus type 2 in the development of the cervex carcinoma of women is still an open question. After the serological findings that patients with cervix carcinoma have a higher rate of antibodies against type 2 than healthy women, which were initially published with great expectation, the molecular-virological examinations which were meanwhile carried out by several work groups to find traces of the herpes simplex virus type 2 in the carcinoma cells were negative, except some few but not confirmed cases. Hitherto but the results of transformation of embryonic hamster cells by UV-inactivated virus were the strongest indication for the herpes simplex virus possibly having oncogenic power, although one of the most important demonstrations, i.e. that of the virus DNA, is still lacking even for these transformed cells, which induce fibrosarcoma if injected to newborn hamsters. Possibly the transformation of the normal hamster cell into a tumor cell requires but such a small quantity of the herpes simplex virus DNA that it cannot be traced with the present methods. In connection with the question of the herpes simplex virus being oncogenic also LUPIDON which contains heat-inactivated herpes simplex virus, was examined. For this purpose extended transformation experiments in vitro and animal experiments with new-born hamsters were carried out. All these experiments had a negative result. There is thus no indication for LUPIDON having oncogenic properties.

Animals↗
PubMed1977

Isolation and characterization of plasma membranes and intact nuclei from lymphoid cells.

A method has been developed for the rapid large scale isolation of plasma membranes and intact nuclei from RAJI lymphoid cells utilizing hypotonic lysis of cells after intracellular loading with glycerol followed by combined flotation-sedimentation within a discontinuous sucrose gradient. Nuclei may be isolated in about 1 h and plasma membranes in about 6 h from 1 to 20 g of cells. Intact nuclei, obtained in 90 to 95% yield based on lysed cells, was isolated by differential centrifugation and contained 16% DNA and about 30% of total cell sialic acid. A crude plasma membrane fraction was isolated by centrifugation onto a cushion of 38% sucrose (d 1.1683) and subsequently resolved into two subfractions. The less dense vesicles had an average d 1.127 and showed a 7-fold increase in specific activity for thymidine phosphodiesterase while the more dense (d 1.151) had a 20-fold concentration of enzyme activity. Activity of enzymes indicative of contamination with lysosomes, microsomes, mitochondria, and cytoplasm was negligible in these plasma membrane fractions. The less dense vesicles had a cholesterol:phospholipid ratio of 0.97 which was higher than that of the more dense vesicles (0.69). Otherwise, the analytical values for the two types of membrane vesicles were similar as both fractions contained like percentages of protein (approximately 30%), lipid (approximately 30%), and carbohydrate (approximately 15%) with trace amounts of RNA and DNA. Twenty-five per cent of the total cell sialic acid was in the plasma membrane fractions.

Burkitt Lymphoma↗