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At least 19 recordsLinked to original sources
PubMed2025

Cloning and validating systems for high throughput molecular recording.

Molecular recording technologies record and store information about cellular history. Lineage tracing is one form of molecular recording and produces information describing cellular trajectories during mammalian development, differentiation and maintenance of adult stem cell niches, and tumor evolution. Our molecular recorder technology utilizes CRISPR-Cas9 barcode editing to generate mutations in genomically integrated, engineered DNA cassettes, which are read out by single-cell RNA sequencing and used to produce high-resolution lineage trees. Here, we describe optimized cloning and validation procedures to construct the molecular recorder lineage tracing system. We include information on considerations of technology design, cloning procedures, the generation of lineage tracing cell lines, and time course experiments to assess their performance.

Cloning, Molecular↗
PubMed2025

MitoScribe single-cell molecular recorder logs graded signaling dynamics into mitochondrial DNA.

Genetically encoded DNA recorders convert transient biological events into stable genomic mutations, offering a means to reconstruct past cellular states. However, current approaches to log historical events by modifying genomic DNA have limited capacity to record the magnitude of biological signals within individual cells. Here, we introduce MitoScribe, a mitochondrial DNA (mtDNA)-based recording platform that uses mtDNA base editors (DdCBEs) to write graded biological signals into mtDNA as neutral, single-nucleotide substitutions at a defined site. Taking advantage of the hundreds to thousands of mitochondrial genome copies per cell, we demonstrate MitoScribe enables reproducible, highly sensitive, non-destructive, durable, and high-throughput measurements of molecular signals, including hypoxia, NF-κB activity, BMP and Wnt signaling. We show multiple modes of operation, including multiplexed recordings of two independent signals, and coincidence detection of temporally overlapping signals. Coupling MitoScribe with single-cell RNA sequencing and mitochondrial transcript enrichment, we further reconstruct signaling dynamics at the single-cell transcriptome level. Applying this approach during the directed differentiation of human induced pluripotent stem cells (iPSCs) toward mesoderm, we show that early heterogeneity in response to a differentiation cue predicts the later cell state. Together, MitoScribe provides a scalable platform for high-resolution molecular recording in complex cellular contexts.

Journal Article↗
PubMed1991

Identification of three human pseudogenes for subunit VIb of cytochrome c oxidase: a molecular record of gene evolution.

Three pseudogenes for the nuclear-encoded subunit VIb of cytochrome c oxidase (COX) were isolated by screening a human genomic library with cloned human cDNA coding for COX subunit VIb. The nucleotide sequences of the pseudogenes, designated psi COX6b-1, psi COX6b-2 and psi COX6b-3, were determined. Pseudogene psi COX6b-1 bears all the hallmarks of a processed pseudogene and diverged from the parental gene after the divergence of man and cow. Alu repetitive elements were integrated into the structural sequences of the other two pseudogenes. Comparison with the human and bovine cDNA sequences encoding COX subunit VIb suggests that psi COX6b-2 and psi COX6b-3 were formed earlier in evolution than psi COX6b-1. Genomic Southern analysis indicated that a few more pseudogenes for COX subunit VIb are likely to be present in the human genome. Identical nt differences with respect to the human cDNA sequence in the pseudogenes provide some clues on the evolution of the ancestral gene coding for COX subunit VIb.

Amino Acid Sequence↗
PubMed1993

A 6,000-year sedimentary molecular record of chemocline excursions in the Black Sea.

The Black Sea is the world's largest anoxic basin; it is also a contemporary analogue of the environment in which carbonaceous shales and petroleum source beds formed. Recently, Repeta et al. reported that anoxygenic photosynthesis may be an important component of carbon cycling in the present Black Sea, owing to a shoaling of the chemocline and consequent penetration of the photic zone by anaerobic waters in the past few decades. It has been suggested that this was due to an anthropogenic decrease in freshwater input to the Black Sea, although natural causes were not ruled out. Here we report the distributions of sequestered photosynthetic pigments in eight core samples of sediments from the Black Sea ranging in age from zero to 6,200 years before the present. Our results show that photosynthetic green sulphur bacteria (Chlorobiaceae [correction of Clorobiaceae]) have been active in the Black Sea for substantial periods of time in the past. This finding indicates that the penetration of the photic zone by anaerobic waters is not a recent phenomenon, and suggests that natural causes for shoaling of the chemocline are more likely than anthropogenic ones.

Bacteria↗
PubMed2005

Origin of the Eumetazoa: testing ecological predictions of molecular clocks against the Proterozoic fossil record.

Molecular clocks have the potential to shed light on the timing of early metazoan divergences, but differing algorithms and calibration points yield conspicuously discordant results. We argue here that competing molecular clock hypotheses should be testable in the fossil record, on the principle that fundamentally new grades of animal organization will have ecosystem-wide impacts. Using a set of seven nuclear-encoded protein sequences, we demonstrate the paraphyly of Porifera and calculate sponge/eumetazoan and cnidarian/bilaterian divergence times by using both distance [minimum evolution (ME)] and maximum likelihood (ML) molecular clocks; ME brackets the appearance of Eumetazoa between 634 and 604 Ma, whereas ML suggests it was between 867 and 748 Ma. Significantly, the ME, but not the ML, estimate is coincident with a major regime change in the Proterozoic acritarch record, including: (i) disappearance of low-diversity, evolutionarily static, pre-Ediacaran acanthomorphs; (ii) radiation of the high-diversity, short-lived Doushantuo-Pertatataka microbiota; and (iii) an order-of-magnitude increase in evolutionary turnover rate. We interpret this turnover as a consequence of the novel ecological challenges accompanying the evolution of the eumetazoan nervous system and gut. Thus, the more readily preserved microfossil record provides positive evidence for the absence of pre-Ediacaran eumetazoans and strongly supports the veracity, and therefore more general application, of the ME molecular clock.

Animals↗
PubMed2002

New views on fungal evolution based on DNA markers and the fossil record.

Molecular markers have facilitated a better understanding of the evolution of fungi. Molecular phylogenetics determined the closest relatives of fungi and defined natural groups within the true fungi. The impact of molecular markers on the population biology of fungi has been enormous, helping to define cryptic species and elucidating fungal breeding biology. The interaction between molecular phylogenetics and the fungal fossil record is discussed.

Fossils↗
PubMed2005

Four well-constrained calibration points from the vertebrate fossil record for molecular clock estimates.

Recent controversy about the use of the vertebrate fossil record for external calibration of molecular clocks centers on two issues, the number of dates used for calibration and the reliability of the fossil calibration date. Viewing matters from a palaeontological perspective, we propose three qualitative, phylogenetic criteria that can be used within a comparative framework for the selection of well-constrained calibration dates from the vertebrate fossil record. On the basis of these criteria, we identify three highly suitable new fossil calibration dates for molecular clock estimates: the lungfish-tetrapod split (between 419 and 408 Ma), the bird-crocodile split (between 251 and 243 Ma), and the alligator-caiman split (between 71 and 66 Ma). Together with our previously suggested bird-lizard split (between 252 and 257 Ma), these four fossil dates span a range of very different ages. They are, in our opinion, more suitable for molecular clock calibration than the traditionally used mammal-bird split, which is less well constrained. We plea for closer interactions between paleontologists and molecular biologists in studying the timescale of vertebrate evolution.

Animals↗
PubMed1995

The effects of heavy meteorite bombardment on the early evolution--the emergence of the three domains of life.

A characteristic of many molecular phylogenies is that the three domains of life (Bacteria, Archaea, Eucarya) are clearly separated from each other. The analyses of ancient duplicated genes suggest that the last common ancestor of all presently known life forms already had been a sophisticated cellular prokaryote. These findings are in conflict with theories that have been proposed to explain the absence of deep branching lineages. In this paper we propose an alternative scenario, namely, a large meteorite impact that wiped out almost all life forms present on the early Earth. Following this nearly complete frustation of life on Earth, two surviving extreme thermophilic species gave rise to the now existing major groups of living organisms, the Bacteria and Archaea. [The latter also contributed the major portion to the nucleo-cytoplasmic component of the Eucarya]. An exact calibration of the molecular record with regard to time is not yet possible. The emergence of Eucarya in fossil and molecular records suggests that the proposed late impact should have occurred before 2100 million years before present (BP). If the 3500 million year old microfossils [Schopf, J. W. 1993: Science 260: 640-646] are interpreted as representatives of present day existing groups of bacteria (i.e., as cyanobacteria), then the impact is dated to around 3700 million years BP. The analysis of molecular sequences suggests that the separation between the Eucarya and the two prokaryotic domains is less deep then the separation between Bacteria and Archaea. The fundamental cell biological differences between Archaea and Eucarya were obtained over a comparatively short evolutionary distance (as measured in number of substitution events in biological macromolecules). Our interpretation of the molecular record suggests that life emerged early in Earth's history even before the time of the heavy bombardment was over. Early life forms already had colonized extreme habitats which allowed at least two prokaryotic species to survive a late nearly ocean boiling impact. The distribution of ecotypes on the rooted universal tree of life should not be interpreted as evidence that life originated in extremely hot environments.

Amino Acid Sequence↗
PubMed2006

Quantitative treatment of coarsely binned low-resolution recordings in molecular absorption spectroscopy.

Optical multichannel detectors like photodiode arrays or CCD cameras combined with grating spectrometers are commonly used as detection systems in quantitative absorption spectroscopy. As a trade-off to broad spectral coverage, banded spectral features are sometimes recorded with insufficient spectral resolution and/or insufficiently fine detector binning. This renders the true physical spectrum of recorded intensities changed by instrumental and spectrum specific artefacts thus impeding comparability between results from different set-ups. In this work, it is demonstrated that in the case of a "well-behaved"--i.e. free of ro-vibronic structure--absorption band like the iodine monoxide IO(4<--0) transition, these effects can easily change the apparent peak absorption by up to 50%. Also deviations from the strict linearity (Beer-Lambert's law) between absorber concentration and apparent, i.e. pixelwise optical density occur. This can be critical in studies of chemical kinetics. It is shown that the observed non-linearity can cause errors of up to 50% in the determination of a second order rate coefficient for the IO self reaction. To overcome the problem, a consistent and rigorous integral approach for the treatment of intensity recordings is developed. Linearity between optical density and absorber concentration thereby is re-established. The method is validated using artificial test data as well as experimental data of the IO(4<--0) absorption transition, obtained in the context of I2/O3 photochemistry studies. The agreement is accurate to within +/-2% (test data) and +/-3% (experimental data) supporting the validity of the approach. Possible consequences for other spectroscopic work are indicated.

Iodine Compounds↗
PubMed2003

Molecular fossil record of elevated methane levels in late Pleistocene coastal waters.

Accumulating evidence suggests that methane has been released episodically from hydrates trapped in sea floor sediments during many intervals of rapid climate warming. Here we show that sediments from the Santa Barbara Basin deposited during warm intervals in the last glacial period contain molecular fossils that are diagnostic of aerobic and anaerobic methanotrophs. Sediment intervals with high abundances of these compounds indicate episodes of vigorous methanotrophic activity in methane-laden water masses. Signals for anaerobic methanotrophy in 44,100-year-old sediment are evidence for particularly intense methane emissions and suggest that the basin's methane cycle can profoundly affect oxygen budgets in the water column.

Aerobiosis↗
PubMed2001

Baseline mass resolution of peptide isobars: a record for molecular mass resolution.

Baseline resolution of two peptides, RVMRGMR and RSHRGHR, of neutral monoisotopic mass, approximately 904 Da, has been achieved by microelectrospray ionization Fourier transform ion cyclotron resonance mass spectrometry at a mass resolving power of approximately 3 300 000. The elemental compositions of these molecules differ by N40 vs. S2H8 (0.000 45 Da), which is less than one electron's mass (0.000 55 Da)! This result establishes a new record for the smallest resolved mass difference between any two molecules. This achievement is made possible by a combination of high magnetic field (9.4 T), large-diameter (4-in.) Penning trap, and low ion density. The implications for proteomics based on accurate mass measurements are discussed briefly.

Amino Acid Sequence↗
PubMed1994

Phylogeny from function: evidence from the molecular fossil record that tRNA originated in replication, not translation.

We propose a phylogeny for the evolution of tRNA that is based on the ubiquity and conservation of tRNA-like structures in the replication of contemporary genomes. This phylogeny is unique in suggesting that the function of tRNA in replication dates back to the very beginnings of life on earth, before the advent of templated protein synthesis. The origin we propose for tRNA has distinct implications for the order in which other components of the modern translational apparatus evolved. We further suggest that the "top half" of modern tRNA-a coaxial stack of the acceptor stem on the T psi C arm--is the ancient structural and functional domain and that the "bottom half" of tRNA--a coaxial stack of the dihydrouracil arm on the anticodon arm--arose later to provide additional specificity.

Animals↗
PubMed2026

Multichannel genomic recording of biological information with ENGRAM.

Molecular recording is an emerging paradigm for measuring biology over time. Enhancer-mediated genomic recording of activity in multiplex (ENGRAM) is a recently described synthetic biology circuit architecture that converts the transient activity of cis-regulatory elements (CREs) into stable genomic records that can be retrospectively recovered via DNA sequencing. Here we provide a step-by-step protocol for conducting ENGRAM experiments and analyzing the resulting data. We also describe key design considerations for ENGRAM recorders, summarize the strengths and limitations of ENGRAM, and highlight applications, including multiplex signal recording and high-throughput CRE screening. In contrast to other systems for DNA-based recording in mammalian systems, ENGRAM relies on prime editing-mediated insertions to record the activity of a given CRE, such that it is inherently multiplexable-for example, four-base-pair insertions can represent the activities of up to 256 distinct CREs. A further contrast lies with ENGRAM's compatibility with DNA Typewriter, which facilitates the capture of signal order. For users with basic skills in molecular biology, mammalian cell culture and DNA sequencing analysis, ENGRAM experiments can typically be completed within 5-6 weeks.

Genomics↗
PubMed2005

Immunolocalization and characterization of cornification proteins in snake epidermis.

Little is known about specific proteins involved in keratinization of the epidermis of snakes, which is composed of alternating beta- and alpha-keratin layers. Using immunological techniques (immunocytochemistry and immunoblotting), the present study reports the presence in snake epidermis of proteins with epitopes that cross-react with certain mammalian cornification proteins (loricrin, filaggrin, sciellin, transglutaminase) and chick beta-keratin. alpha-keratins were found in all epidermal layers except in the hard beta- and alpha-layers. beta-keratins were exclusively present in the oberhautchen and beta-layer. After extraction and electrophoresis, alpha-keratins of 40-67 kDa in molecular weights were found. Loricrin-like proteins recorded molecular weights of 33, 50, and 58 kDa; sciellin, 55 and 62 kDa; filaggrin-like, 52 and 65 kDa; and transglutaminase, 45, 50, and 56 kDa. These results suggest that alpha-layers of snake epidermis utilize proteins with common epitopes to those present during cornification of mammalian epidermis. The beta-keratin antibody on extracts from whole snake epidermis showed a strong cross-reactive band at 13-16 kDa. No cross-reactivity was seen using an antibody against feather beta-keratin, indicating absence of a common epitope between snake and feather keratins.

Animals↗
PubMed1998

Allele-specific population structure of Drosophila melanogaster alcohol dehydrogenase at the molecular level.

The history of the Drosophila melanogaster alcohol dehydrogenase (ADH) Fast/Slow polymorphism was studied by recording molecular variation and inversion polymorphism in 233 chromosomes from European and African populations. Silent molecular variation in the Slow allele was very different between standard chromosomes and chromosomes bearing the In(2L)t inversion. Within populations, inverted Slow haplotypes were more variable than standard Slow haplotypes. Between populations, geographical structure was almost nonexistent for inverted Slow haplotypes and highly significant for standard Slow. All Fast haplotypes occurred on standard chromosomes. They showed little variation within and between populations. They were highly significantly closer to standard Slow haplotypes from Europe. These results suggest that the current range of Fast and In(2L)t Slow haplotypes is recent and that an older genetic differentiation between populations was followed by allele-specific gene flow.

Alcohol Dehydrogenase↗
PubMed2003

Molecular weight characteristics of humic substances from different environments as determined by size exclusion chromatography and their statistical evaluation.

Recorded molecular weights (MWs) for humic substances (HS) range from a few hundred to millions of daltons. For purposes of defining HS as a specific class of chemical compounds, it is of particular importance to ascertain if this broad range of MWs can be attributed to actual variability in molecular properties or is simply an artifact of the analytical techniques used to characterize HS. The main objectives of this study were (1)to establish if a preferential range of MWs exists for HS and (2) to determine any consistent MW properties of HS. To reach the goal, we have undertaken an approach to measure under standardized conditions the MW characteristics of a large set of HS from different natural environments. Seventy-seven humic materials were isolated from freshwater, soil, peat, and coal, such that each possessed a different fractional composition: humic acid (HA), fulvic acid (FA), and a nonfractionated mixture of HA and FA (HF). Size exclusion chromatography (SEC) was used as the analytical technique to determine molecular weight characteristics. The MW distributions were characterized by number (Mn) and weight (Mw) average MW, and by polydispersity. The complete range of Mw values varied within 4.7-30.4 kDa. The maximum Mw values were observed for peat HF and soil HA, whereas the smallest weights were measured for river water HF. Maximum values of polydispersity (3.5-4.4) were seen for peat HF and soil HA, while much lower values (1.6-3.1) were found for all preparations isolated with XAD-resins. Statistical evaluation showed consistent Mw and Mn variations with the HS source, while polydispersity was mostly a function of the isolation procedure used. A conclusion was made that HS have a preferential range of MW values that could characterize them as a specific class of chemical compounds.

Chromatography, Gel↗
PubMed2003

Identification and characterization of over 100 mitochondrial ribosomal protein pseudogenes in the human genome.

The human (nuclear) genome encodes at least 79 mitochondrial ribosomal proteins (MRPs), which are imported into the mitochondria. Using a comprehensive approach, we find 41 of these give rise to 120 pseudogenes in the genome. The majority of the MRP pseudogenes are of processed origin and can be aligned to match the entire coding region of the functional MRP mRNAs. One processed pseudogene was found to have originated from an alternatively spliced mRNA transcript. We also found two duplicated pseudogenes that are transcribed in the cell as confirmed by screening the human EST database. We observed a significant correlation between the number of processed pseudogenes and the gene CDS length (R = -0.40; p < 0.001), i.e., the relatively shorter genes tend to have more processed pseudogenes. There is also a weaker correlation between the number of processed pseudogenes and the gene CDS GC content. Our study provides a catalogue of human MRP pseudogenes, which will be useful in the study of functional MRP genes. It also provides a molecular record of the evolution of these genes. More details are available at http://pseudogene.org/.

Animals↗