Luminescence detection of tightly bound stacking aggregates of adenine and adenosine in aqueous solutions--the candidates for the role of the first genetic templates.
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Adenine↗
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Rh(0) or D, -D- and the blocking patterns. A genetic (template) explanation.
By the use of the gene template it will be shown that D appears at two different sites on the Rh locus, and that the locus cannot simply be DCE - or a similar one. Further, -D- does not appear to be a super Rh(0) as described by Wiener. Finally, a simple explanation is offered for the action of incomplete (blocking) and agglutinating antibodies.
Antigen-Antibody Reactions↗
Molecular evolution: first enzymes, gases as substrates and genetic templates.
A fundamental problem in biology is the self-assembly of the first cells capable of growth and division under anoxic conditions on the Earth. Evolution proceeded by self-assembling and self-replicating cells that reproduced their own genetic information and also changed their genetic code over time. Was it also possible that some of the first proteins were catalytic and used gases as substrates and also acted as genetic templates? This paper explores the possibility that primitive protein enzymes used gases as their substrates, and reverse translation may have been a feature in the self-assembly of the first cell(s).
Cells↗
The transcription of chromatin templates.
Genetic and biochemical approaches have recently been used to demonstrate the pivotal role of chromatin structure in gene regulation at two levels of organization. The three-dimensional folding of DNA mediated by chromatin structural proteins over several hundred base pairs has been shown to be critical for the local control of both transcriptional activation and repression. Nuclear domains also exist in which the further long-range organization of chromatin over 5-50 kb exerts a global control on the transcription process.
Animals↗
Interaction of herpes simplex virus type 1 DNA polymerase and the UL42 accessory protein with a model primer template.
Genetic and biochemical studies have shown that the products of the herpes simplex virus type 1 (HSV-1) DNA polymerase (UL30) and UL42 genes are both required for viral DNA replication. A number of studies have previously suggested that these two proteins specifically interact, and more recent studies have confirmed that the viral DNA polymerase from HSV-1-infected cells consists of a heterodimer of the UL30 (Pol; the catalytic subunit) and UL42 polypeptides. A comparison of the catalytic properties of the Pol-UL42 complex with those of the isolated subunits of the enzyme purified from recombinant baculovirus-infected insect cells indicated that the Pol-UL42 complex is more highly processive than Pol alone on singly primed M13 single-stranded substrates. The results of these studies are consistent with the idea that the UL42 polypeptide is an accessory subunit of the HSV-1 DNA polymerase that acts to increase the processivity of polymerization. Preliminary experiments suggested that the increase in processivity was accompanied by an increase in the affinity of the polymerase for the ends of linear duplex DNA. We have further characterized the effect of the UL42 polypeptide on a defined hairpin primer template substrate. Gel shift and filter binding studies show that the affinity of the Pol catalytic subunit for the 3' terminus of the primer template increases 10-fold in the presence of UL42. DNase I footprinting experiments indicate that the Pol catalytic subunit binds to the primer template at a position that protects 14 bp of the 3' duplex region and an adjacent 18 bases of the single-stranded template. The presence of the UL42 polypeptide results in the additional protection of a contiguous 5 to 14 bp in the duplex region but does not affect the 5' position of the Pol subunit. Free UL42 protects the entire duplex region of the substrate but does not bind to the single-stranded region. Taken together, these results suggest that the increase in processivity in the presence of UL42 is related to the double-stranded DNA-binding activity of free UL42 and that the role of UL42 in the DNA polymerase complex is to act as a clamp, decreasing the probability that the polymerase will dissociate from the template after each cycle of catalysis.
Animals↗
DNA template amplification genetic studies on archival human preimplantation biopsied microtubed cell samples.
Biopsied cell samples can remain in storage following an initial, unequivocally successful preimplantation genetic diagnosis (PGD). The fidelity of the DNA template for polymerase chain reaction (PCR) amplification of microtubed human preimplantation embryonic cells stored at -70 degrees C for extended periods of time (6 months to 4 years) has been assessed. PCR protocols and specific nested primer sets for the beta-globin, ZP3 and CA repeat motif successfully used for previous human embryo PGD research were employed for these studies. The results show that the DNA template of microtubed biopsied blastomere and mural trophectoderm cell samples stored for periods of up to 4 years may be successfully amplified by PCR. Specific gene sequences were able to be analysed at the 1-2 or 3-5 biopsied cell level with a 71-100% success rate. Analysis of DNA fragments amplified from the CA dinucleotide repeat locus showed that in 8/9 samples both alleles were amplified at the cellular level. No DNA contamination was detected in the stored microtubed samples, or in the experimental controls.
Actins↗
Chromatin as a eukaryotic template of genetic information.
In eukaryotes, chromatin is essential for heredity. Chromatin architecture is sometimes "epistatic" over the DNA and imparts a different heritable state to the same DNA sequence or the same functional state to unrelated DNA sequences. This has been documented recently in a wide variety of studies focused on regulation of the yeast mating type, the function of Polycomb and trithorax group proteins, the specification of eukaryotic centromeres and neocentromeres, and genomic imprinting.
Animals↗
Allele drop-out can occur in alleles differing by a single nucleotide and is not alleviated by preamplification or minor template increments.
The ability to analyze the genetic material of single cells by the PCR opens up new prospects for diagnostics. Because only two copies of the genetic template are available for amplification, a problem that frequently arises when examining heterozygous loci in single cells is allele drop-out (ADO). ADO results from the preferential amplification of one of a pair of heterozygous alleles, in which the other allele is totally under-represented. In examining single cells from carriers heterozygous for beta-thalassemia mutations, we have found ADO to occur in alleles differing by a single nucleotide, where either the normal or the mutant genotype was absent. We have found that ADO is not overcome by either increasing the amount of DNA template to 20 pg or by primer extension preamplification (PEP), but rather that the best diagnostic accuracy is obtained by examining multiple single cells and basing a diagnosis on the combined results of such an examination.
Alleles↗
Stereotypy in neocortical microcircuits.
A central debate regarding neocortical function concerns the degree to which the underlying microcircuitry is stereotypically organized. Stereotypy reflects invariance in structure and function, as a result of common genetic templates and environmental conditions, whereas uniqueness can be caused by genetic variations, differences in environmental conditions as well as random processes. Stereotypy is an appealing concept because it provides strong support for determinism in the formation of neuronal microcircuits and in the relationship between their specific structure and function.
Animals↗
A mitochondrial model for premature ageing of somatically cloned mammals.
Cloned sheep have recently been discovered to have an unexpectedly advanced biological age. We propose that the explanation is a simple consequence of inheritance of acquired, free radical-induced cellular damage with somatic mitochondria that contribute to the mitochondrial population of cloned cells but not to zygotes produced by fertilization in normal sexual reproduction. Each increment of ageing in cloning experiments is therefore predicted to be maternally inherited. The hypothesis suggests practical ways of decreasing the effect. The hypothesis is itself a prediction of the recent proposal that mitochondria of the female germ line function primarily as genetic templates.
Aging↗
Evolutionary genetics. Europeans trace ancestry to Paleolithic people.
Y chromosome data show that living Europeans have deep roots in the region--and researchers say genetic markers may be linked to cultures known from archaeological remains. In a report on page 1155, an international team reports that a wealth of data from the Y chromosome show that more than 80% of European men have inherited their Y chromosomes--which are transmitted only from father to son--from Paleolithic ancestors who lived 25,000 to 40,000 years ago. Thus, the genetic template for European men was set as early as 40,000 years ago, then modified--but not recast--by the Neolithic farmers who arrived in the region about 10,000 years ago.
Anthropology, Physical↗
Cyclin D1 gene contains a cryptic promoter that is functional in human cancer cells.
A novel cyclin D1 (CCND1)-TROP2 fusion oncogene has been isolated from human cancer cells. Unexpectedly, the chimeric cDNA was found to express TROP2 in the absence of exogenous promoters. Mutagenesis of the TROP2 and CCND1 sequences and in vitro transcription/translation show that a cryptic promoter is present in the 3' coding region of CCND1. The CCND1 cryptic promoter is functional in luciferase assays, where it augments the basal expression levels by eightfold and efficiently cooperates with an SV-40 enhancer. The transcription start sites of the cryptic promoter map at bases 797 and 935 of CCND1, as determined by RNase protection assays. The cryptic promoter possesses canonical binding sites for ubiquitous transcription factors and W/S, X1, and CAAT/Y boxes that are characteristic of major histocompatibility complex class II gene promoters. Remarkably, the cryptic CCND1 promoter is active in human cancer cells and generates a truncated transcript that contains CCND1 instability sequences. Thus, this novel CCND1 transcription unit may play a role in the regulation of the expression of cyclin D1 and in tumor cell growth.
3T3 Cells↗
A selection for mutants of the RNA polymerase III transcription apparatus: PCF1 stimulates transcription of tRNA and 5S RNA genes.
A genetic approach has been developed to study transcription by RNA polymerase III. A pair of Schizosaccharomyces pombe nonsense suppressor tRNA genes were arranged in tandem such that expression of the downstream (supS1) tRNA suppressor was dependent upon transcription initiated by the internal promoter of the upstream (sup9-e) gene. Dominant mutant strains of Saccharomyces cerevisiae were isolated that suppress in trans the effect of an A block promoter mutation (A19) in the sup9-e gene and restore supS1 suppressor activity. Fifteen mutant strains, eight of which were independently isolated, all have elevated steady-state levels of sup9-e A19 RNA consistent with an increase in gene transcription. Extracts of a strain carrying the dominant mutant gene, PCF1, show a general 6-fold stimulation in transcription of mutant (A19) and wild-type tRNA genes and increase 5S gene transcription 4-fold compared with extracts from a wild-type strain. A transcription factor exclusion assay was used to show that the PCF1 mutation affects two distinct stages in transcription: one prior to and one after stable complex formation; and that these effects are mediated by a component of the stable complex. Further evidence of an effect during complex assembly was obtained in a time-course experiment that showed a shortened lag phase in the PCF1 extract. The results indicate that PCF1 is either a component of the stable complex or a positive regulator of its activity.
Base Sequence↗
Studies in the replication of viral RNA.
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Acrylic Resins↗
An in vitro transcription system for the study of thyroid-specific transcription.
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Animals↗
Dynamics of bacteriophage T4 DNA polymerase function: identification of amino acid residues that affect switching between polymerase and 3' --> 5' exonuclease activities.
Many DNA polymerases are multifunctional with the ability to replicate DNA as well as to proofread misincorporated nucleotides. Since polymerase and 3'--> 5' exonuclease activities appear to reside in spatially distinct active centers, there must be some mechanism for coordinating replication with proofreading and for transferring DNA between the two active centers. We have designed a genetic selection scheme to isolate bacteriophage T4 mutant DNA polymerases that are defective in "switching" between polymerase and exonuclease activities. Amino acid residues that affected active-site-switching were identified in four regions of the T4 DNA polymerase: two regions in the proposed exonuclease domain. Representative mutant DNA polymerases from each region were purified for biochemical studies. We propose that amino acid substitutions identified by mutational analysis affect critical contacts between T4 DNA polymerase and DNA that are required for transfer of DNA between the polymerase and exonuclease active centers.
Amino Acids↗
New insights into the mechanisms of RNA recombination.
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Animals↗
A model for macromolecular selection in complementary instructing systems.
In this paper we consider a model for the selection and evolution of biological macromolecules when their reproduction is based on complementary instruction. The model is an extension of one of Eigen's models for selection and takes in account explicitly the formation of both single stranded and double stranded molecular complexes. We construct exact solutions to the rate equations for the case of constant rate parameters and error distributions. Criteria for selection are discussed.
Biological Evolution↗