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R J Herrera

Publications and source records attributed to R J Herrera.

10 recordsLinked to original sources
PubMed1992

Genome canalization: the coevolution of transposable and interspersed repetitive elements with single copy DNA.

Transposable and interspersed repetitive elements (TIREs) are ubiquitous features of both prokaryotic and eukaryotic genomes. However, controversy has arisen as to whether these sequences represent useless 'selfish' DNA elements, with no cellular function, as opposed to useful genetic units. In this review, we selected two insect species, the Dipteran Drosophila and the Lepidopteran Bombyx mori (the silkmoth), in an attempt to resolve this debate. These two species were selected on the basis of the special interest that our laboratory has had over the years in Bombyx with its well known molecular and developmental biology, and the wealth of genetic data that exist for Drosophila. In addition, these two species represent contrasting repetitive element types and patterns of distribution. On one hand, Bombyx exhibits the short interspersion pattern in which Alu-like TIREs predominate while Drosophila possesses the long interspersion pattern in which retroviral-like TIREs are prevalent. In Bombyx, the main TIRE family is Bm-1 while the Drosophila group contains predominantly copia-like elements, non-LTR retroposons, bacterial-type retroposons and fold-back transposable elements sequences. Our analysis of the information revealed highly non-random patterns of both TIRE biology and evolution, more indicative of these sequences acting as genomic symbionts under cellular regulation rather than useless or selfish junk DNA. In addition, we extended our analysis of potential TIRE functionality to what is known from other eukaryotic systems. From this study, it became apparent that these DNA elements may have originated as innocuous or selfish sequences and then adopted functions. The mechanism for this conversion from non-functionality to specific roles is a process of coevolution between the repetitive element and other cellular DNA often times in close physical proximity. The resulting interdependence between repetitive elements and other cellular sequences restrict the number of evolutionarily successful mutational changes for a given function or cistron. This mutual limitation is what we call genome canalization. Well documented examples are discussed to support this hypothesis and a mechanistic model is presented for how such genomic canalization can occur. Also proposed are empirical studies which would support or invalidate aspects of this hypothesis.

Animals↗
PubMed1991

Amplification dynamics of human-specific (HS) Alu family members.

We have investigated the distribution of several recently inserted Alu family members within representatives of diverse human groups. Human population studies using 65 unrelated human DNA samples, as well as a familial study to test inheritance, showed that individual Alu family members could be divided into three groups. The first group consisted of relatively older Alu family members which were monomorphic (homozygous) throughout the population tested (HS C3N1 and C4N6). The second group (HS C4N2, C4N5 and C4N8), apparently inserted into other repetitive regions of the genome, resulting in inconclusive results in the PCR test used. However, it is clear that these particular Alu insertions were present in a majority if not all of the loci tested. The third group was comprised of three dimorphic Alu family members (HS C2N4, C4N4 and TPA 25). Only a single Alu family member (TPA 25) displayed a high degree of dimorphism within the human population. This latter example also showed different allele frequencies in different human groups. The isolation and characterization of additional highly dimorphic Alu family members should provide a useful tool for human population genetics.

Alleles↗
PubMed1991

Enrichment of biologically active U1 small nuclear RNAs by ion-exchange high-performance liquid chromatography.

The use of ion-exchange high-performance liquid chromatography in conjunction with preparative electrophoresis to facilitate the purification of biologically active snRNAs is described. Separation of total nuclear RNA from a Bombyx mori cell line was done with a Bio-Rad MA7 plasmid column in a HRLC 500 system. Individual fractions were subjected to electrophoresis through 14% polyacrylamide gels for identification. High levels of U1 RNA were confirmed by Northern analysis with a human U1 probe. Biological activity of RNAs from the column was demonstrated by their ability to incorporate 32P-AMP at the 3' end. Ion-exchange chromatography provides a rapid, automated method for purifying large amounts of RNAs that can then be utilized in further studies.

Adenosine Monophosphate↗
PubMed1991

Evidence for a relationship between the Bombyx mori middle repetitive Bm1 sequence family and U1 snRNA.

Several genomic library equivalents of Bombyx mori were constructed in the EMBL-4 lambda derivative. The genomic bank was screened with purified Bombyx mori U1 RNA and twenty positive clones for the U1 gene were isolated. Three U1-related sequences were subcloned and sequenced. Two of the sequences are U1 pseudogenes while a third sequence represents a member of the Bm 1 family of repetitive elements of B.mori with significant sequence similarity to U1 small nuclear RNA. The U1-related Bm1 element exhibits 82% sequence similarity with the Bm1 consensus sequence and, under less stringent computer comparison parameters, 60% similarity with a composite B.mori/Drosophila melanogaster U1 gene. The Bm1 family consensus sequence exhibits 53% sequence similarity with the composite U1 gene. The two pseudogenes possess highly conserved sequences with the B.mori U1 gene only for the first 101 nucleotides. These findings are indicative of at least two different categories of U1-related sequences in B.mori, one with a possible evolutionary relationship to the Bm1 family of repetitive elements and the other representing characteristic processed pseudogenes with retroposon mode of dispersion and target selection for the TTTA hotspot. In addition, the U1-related Bm1 element may demonstrate for the first time that a family of retroposons is ultimately derived from a U snRNA.

Animals↗
PubMed1986

A highly reiterated family of transcribed oligo(A)-terminated, interspersed DNA elements in the genome of Bombyx mori.

A library of low Cot DNA (Cot is the molar concentration of DNA times the incubation time in seconds) from Bombyx mori was used to isolate five independent clones of highly reiterated sequences from the genome of this organism. Sequence analysis revealed that all five clones belong to a single family of repetitive DNA elements, which we have named Bm1, and whose reiteration frequency is approximately 2.3 X 10(4) copies per haploid genome. Probing of a Bombyx genomic library (in lambda phage) with a Bm1 clone reveals that this repetitive sequence is dispersed throughout the genome. The pattern of interspersion was confirmed by Southern blot mapping of a large (270 X 10(3) base-pairs) domain of the chorion locus of Bombyx, where at least 13 independent regions were found to hybridize to Bm1. Four additional Bm1 elements have been sequenced from a 4.8 X 10(3) base-pair genomic fragment containing an early chorion gene. Two of these four elements are bounded by short (4 to 12 base-pairs) direct repeats. The nine Bm1 elements which have been sequenced are greater than 88% homologous to each other, and tend to fall in at least two size classes (253 base-pairs and 450 base-pairs). Seven of the nine Bm1 elements have a short 6 to 10 base-pair oligo(A) sequence at the 3' end. A sequence of about 29 base-pairs at the 3' end, including the oligo(A), shows 86% homology to the equivalent 3'-terminal domain of human Alu family repetitive elements. A 129 base-pair domain at the 5' end of Bm1 shows 66% homology to a Drosophila valine transfer RNA gene; thus the 5' end of Bm1 may contain the split internal RNA polymerase III promoter that is characteristic of most transcribed tRNA-like retroposons. Dot-blot analysis of Bombyx RNA shows that Bm1 DNA is indeed transcribed, and that the transcripts are well-represented in the total RNA of an ovarian-derived permanent cell line and posterior silk glands early in the fifth instar, but are less abundant in the RNA of pupae or silk glands late in the fifth instar.

Animals↗
PubMed1986

Spontaneous and induced sister-chromatid exchanges in cultured mosquito cells.

Four mosquito cell lines derived from species of the genus Aedes were examined for spontaneous and induced sister-chromatid exchanges by the BrdU-labelling method. The five agents tested for SCE induction were: ethyl methanesulphonate (EMS), methyl methanesulphonate (MMS), ethyl nitrosourea (ENU), methyl nitrosourea (MNU), and 5-bromo-2-deoxyuridine (5-BrdU). It was found that there is significant interspecific and even intraspecific variation in the spontaneous frequency of SCEs. All five agents were effective inducers of SCEs and the induction was dose-dependent within the range of chemical concentrations used. This study shows that the mosquito cell lines may provide a simple and reliable in vitro assay system for testing the genotoxic effects of various agents, particularly on insects.

Aedes↗
PubMed1985

Replication pattern of double minutes derived from an insect cell line.

The DNA replication pattern of double minutes derived from an established cell line of Aedes albopictus is described. Although the vast majority of double minutes replicate semiconservatively once during the S phase, some double minutes appear to exhibit different pattern(s). Two theories are suggested as possible explanations of our findings.

Aedes↗
PubMed1985

Isolation and partial characterization of U1-U6 small RNAs from Bombyx mori.

We have used a variety of techniques to characterize the U-series small nuclear RNAs from the posterior silk gland of Bombyx mori. Six molecular species have been identified which correspond to the vertebrate U1-U6 RNAs by the following criteria: (a) presence of the RNAs in ribonucleoprotein particles which can be immunoprecipitated by lupus Sm antisera; (b) presence of a 2,2,7-trimethylguanosine cap, as assayed by immunoprecipitation with anti-2,2,7-trimethylguanosine IgG; (c) size, as assayed by acrylamide/urea gel electrophoresis using HeLa cell U-RNA markers; and (d) primary nucleotide sequence, as determined by chemical/enzymatic cleavage of end-labeled molecules. The high conservation of primary sequence (66-81% homology based on partial sequences) relative to the corresponding vertebrate U-RNAs has permitted unambiguous identification of each molecule. With the exception of two subspecies of U3 RNA, the U-snRNAs of Bombyx exhibit a striking conservation of secondary structure relative to the proposed structures of the U-RNAs of vertebrates. This conservation is best exemplified by several compensatory base alterations that result in the maintenance of hairpin structures. These are particularly evident in U1 and U5 RNAs. Bombyx U3 is interesting in that two subspecies (of a total of four that were sequenced) diverge considerably in sequence (and presumably in structure) relative to the U3 RNA of vertebrates. The most abundant U-RNAs in the posterior silk gland appear to be U1 and U2, while U3-U6 are present in relatively small amounts.

Animals↗