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Laura F Landweber

Publications and source records attributed to Laura F Landweber.

29 records · Page 2Linked to original sources
PubMed2004

Ligation activity of fragmented ribozymes in frozen solution: implications for the RNA world.

A vexing difficulty of the RNA world hypothesis is how RNA molecules of significant complexity could ever have evolved given their susceptibility to degradation. One way degradation might have been reduced is through low temperature. Here we report that truncated and fragmented derivatives of the hairpin ribozyme can catalyze ligation of a wide variety of RNA molecules to a given sequence in frozen solution despite having little or no activity under standard solution conditions. These results suggest that complex RNAs could have evolved in freezing environments on the early earth and perhaps elsewhere.

Base Sequence↗
PubMed2004

Genetic code.

Explore the source record for details and available documents.

Amino Acids↗
PubMed2004

Gene Unscrambler for detangling scrambled genes in ciliates.

UNLABELLED: Scrambled genes are surprisingly common in some species of ciliates. Until now there was no software available to analyze automatically these genes. We present here a program that can automatically align the macronuclear and micronuclear forms of a gene, outputting the location of the macronuclear destined segments and pointer sequences. AVAILABILITY: A web version of the program is available free of charge and can be accessed at http://oxytricha.princeton.edu/GeneUnscrambler.htm

Algorithms↗
PubMed2004

Sequence features of Oxytricha trifallax (class Spirotrichea) macronuclear telomeric and subtelomeric sequences.

We sequenced and analyzed the subtelomeric regions of 1356 macronuclear "nanochromosomes" of the spirotrichous ciliate Oxytricha trifallax. We show that the telomeres in this species have a length of 20 nt, with minor deviations; there is no correlation between telomere lengths at the two ends of the molecule. A search for open reading frames revealed that the 3' and 5' untranslated regions are short, with a median length of approximately 130 nt, and that surprisingly there are no detectable differences between sequences upstream and downstream of genes. Our results confirm a previously reported purine bias in the first approximately 80 nucleotides of the subtelomeric regions, but with this larger data set we curiously detected a 10 bp periodicity in the bias; we relate this finding to the possible regulatory and structural functions these regions must serve. Palindromic sequences in opposing subtelomeric regions, although present in most sequences, are not statistically significant.

Animals↗
PubMed2004

A micronuclear locus containing three protein-coding genes remains linked during macronuclear development in the spirotrichous ciliate Holosticha.

We have discovered a three-gene macronuclear chromosome in a spirotrichous ciliate of the genus Holosticha. From 5' to 3', this chromosome contains genes encoding a member of the small G-protein family, an NAD kinase domain-containing protein, and the large subunit of DNA polymerase alpha. These three genes are separated by 16 and 38 nucleotides, respectively, and are oriented in the same direction in both the macronuclear and the micronuclear genomes. Probes made to these genes all hybridize to a single, strong band of size 7.0 kbp on a Southern Blot of Holosticha sp. macronuclear DNA, corresponding to the size of the three-gene macronuclear chromosome. Mapping the 5' and 3' ends of each of these genes using RACE showed that the transcripts of these genes exist as discrete mRNAs that are capped and polyadenylated. No nucleotides appeared to be added at the 5' ends of these transcripts, indicating that these transcripts are not generated by alternative or trans-splicing, but rather that each gene is transcribed from its own distinct promoter. Analysis of these linked genes may help define the evolutionary pressures leading to the extensive chromosome fragmentation seen in spirotrichous ciliates.

Animals↗
PubMed2003

Molecular computing revisited: a Moore's Law?

Moore's Law states that the processing power of microchips doubles every one to two years. This observation might apply to the nascent field of molecular computing, in which biomolecules carry out logical operations. Incorporation of new technologies that improve sensitivity and throughput has increased the complexity of problems that can be addressed. It is an ultimate goal for molecular computers to use the full potential of massive parallelism.

Algorithms↗
PubMed2003

Polymorphism, recombination and alternative unscrambling in the DNA polymerase alpha gene of the ciliate Stylonychia lemnae (Alveolata; class Spirotrichea).

DNA polymerase alpha is the most highly scrambled gene known in stichotrichous ciliates. In its hereditary micronuclear form, it is broken into >40 pieces on two loci at least 3 kb apart. Scrambled genes must be reassembled through developmental DNA rearrangements to yield functioning macronuclear genes, but the mechanism and accuracy of this process are unknown. We describe the first analysis of DNA polymorphism in the macronuclear version of any scrambled gene. Six functional haplotypes obtained from five Eurasian strains of Stylonychia lemnae were highly polymorphic compared to Drosophila genes. Another incompletely unscrambled haplotype was interrupted by frameshift and nonsense mutations but contained more silent mutations than expected by allelic inactivation. In our sample, nucleotide diversity and recombination signals were unexpectedly high within a region encompassing the boundary of the two micronuclear loci. From this and other evidence we infer that both members of a long repeat at the ends of the loci provide alternative substrates for unscrambling in this region. Incongruent genealogies and recombination patterns were also consistent with separation of the two loci by a large genetic distance. Our results suggest that ciliate developmental DNA rearrangements may be more probabilistic and error prone than previously appreciated and constitute a potential source of macronuclear variation. From this perspective we introduce the nonsense-suppression hypothesis for the evolution of ciliate altered genetic codes. We also introduce methods and software to calculate the likelihood of hemizygosity in ciliate haplotype samples and to correct for multiple comparisons in sliding-window analyses of Tajima's D.

Animals↗
PubMed2002

Custom codons come in threes, fours, and fives.

In a laboratory coselection of reporter messages containing a single randomized essential two-, four-, five-, or six-base "codon" with suppressor tRNA(Ser) libraries whose members possessed randomized anticodon loops of varying sizes, only four- and five-base "codon-anticodon" interactions survived. These suppressor tRNAs accomplish +1 and -1 frameshift suppression, suggesting biological significance. They also display some properties common to serine tRNAs; such properties include a modest excess of Ser anticodons that might assist tRNA charging.

Codon↗
PubMed2002

Rewriting the information in DNA: RNA editing in kinetoplastids and myxomycetes.

RNA editing has a major impact on the genes and genomes that it modifies. Editing by insertion, deletion and base conversion exists in nuclear, mitochondrial and viral genomes throughout the eukaryotic lineage. Editing was first discovered in kinetoplastids, and recent work has resulted in the characterization of some components of the editing machinery. Two proteins with ligase activity have been identified in Trypanosoma brucei, and other proteins in the editosome complex are yielding to the probe of research. A second group of protists, myxomycetes, are unique in their use of four different types of editing within a single transcript. Phylogenetic analysis of editing in representative myxomycetes revealed a different history of the four types of editing in this lineage. Development of a soluble in vitro editing system has provided further support for the co-transcriptional nature of editing in Physarum polycephalum, and will certainly provide future opportunities for understanding this mysterious process.

Cytidine↗