Siwo de Kloet | Florida State University (original) (raw)

Papers by Siwo de Kloet

ABSTR^CT.--Single-copy DNA-DNA hybridization was used to establish phylogenetic relationships amo... more ABSTR^CT.--Single-copy DNA-DNA hybridization was used to establish phylogenetic relationships among 13 species of waterfowl (Anatidae) chosen from 10 tribes. On the basis of UPGMA clustering of ATto distances, we suggest that the tribes Anatini, Aythyini, Tadornini, Mergini, and Cairinini diverged more recently than the Anserini, Stictonettini, Oxyurini, Dendrocygnini, and Anseranatini. The Freckled Duck (Stictonetta naevosa, tribe Stictonettini) is only distantly related to the other Anatidae. Presumably the lineage diverged very early. The sheldgeese (tribe Tadornini) and the true geese (Anserini) are only remotely related. The Oxyurini, considered to be in the subfamily Anatinae, is remotely related to the other Anatidae. The Dendrocygnini form an isolated tribe with no close relationship to the swans and geese (subfamily Anserinae). We found that the screamers (Anhimidae) are distantly related to the Anatidae. RECENTLY, nucleic acid sequence analysis has been used to estimate re...

Genome, 1992

We have investigated the evolution of a 190 base pair tandemly repeated DNA sequence (RBMII) in 2... more We have investigated the evolution of a 190 base pair tandemly repeated DNA sequence (RBMII) in 27 different species of waterfowl. In this paper we show that the RBMII sequence is present in many species belonging to 7 of the 11 Anatid tribes. Inter- and intra-tribal differences in repeat presence indicate that, although the RBMII sequence has been maintained among widely divergent species, it is rapidly evolving. Restriction enzyme analyses suggest very different hierarchical repeat organizations among different species. DNA sequence comparisons of 32 cloned monomer units from five different species revealed what appears to be a nonrandom distribution of sequence divergence, as well as large differences (up to 25-fold) in intraspecific sequence variation between relatively closely related species.Key words: repeated DNA, Anatidae, sequence variation.

Gene, 1990

Two highly repeated nucleotide sequences (RBMI and RBMII) cloned from an EcoRI digest of DNA of t... more Two highly repeated nucleotide sequences (RBMI and RBMII) cloned from an EcoRI digest of DNA of the redbreasted merganser (Mergus senator) account for approx. 5 to 10 ~o of the DNA of M. senator and the closely related Mergus merganser. Complete DNA digestion of seven members ofthe Mergini with EcoRl produces distinct, relatively species-specific patterns of a few high-M r (> 1.5 kb) fragments of RBMl-like material. In such digests RBMII forms ladder-type patterns with monomers of approx. 200 bp. The sequence of a cloned 2.6-kb RBMI fragment from M. serrator contains several extended (up to 70 bp) and modified poly(dA) sequences, two open reading flames in opposite orientation to the longest poly(dA) sequence and two direct 10-bp repeats suggesting that RBMI is a rearranged retropseudogene-like element.

Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis, 1971

Heterogeneous nuclear RNA of higher organisms has been previously shown to be of very large molec... more Heterogeneous nuclear RNA of higher organisms has been previously shown to be of very large molecular weight (> 2 • lO 6) by sedimentation values. Sucrose gradient centrifugation of heterogeneous nuclear RNA thermally denatured in the presence of formaldehyde shows that this RNA consists of aggregates of smaller molecules with molecular weights ranging from about I • lO 5 to 1. 4 • io ~. Giant-size, rapidly labelled, heterogeneous nuclear RNA (heterogeneous nRNA) has been reported in the cells of higher organisms 1-11. This RNA is DNA-like in base composition and has sedimentation values ranging from IO S to greater than IOO S. These earlier reports have shown that heterogeneous nRNA consists of large polynucleotide chains and could not be disassociated into smaller RNA molecules. Under conditions where aggregates would be resolved (i.e. extraction with hot phenol and sodium dodecyl sulphate, EDTA treatment, thermal denaturation, low-ionic conditions, and 8 M urea) this heterogeneous nRNA maintained its sedimentation profile on sucrose gradients. Such high sedimentation values suggested that these giant polynucleotide RNA molecules have a molecular weight as high as 6 • lO 6 to I • lO 7, or more than four times as large as the 28-S ribosomal RNA species. Recently, we have shown that in yeast, a relatively primitive eukaryote, giant heterogeneous RNA, with very similar properties as those described for higher organisms, actually consists of aggregates of smaller molecules 12. This heterogeneous RNA in yeast is rapidly labelled and also accumulates in cells incubated with cycloheximide for longer periods. In either case, thermal denaturation of this RNA at 65 ° in the presence of formaldehyde causes its disaggregation or disassociation into smaller molecules. Other treatments (V. S. MAYO AI~D S. R. DE KLOET, unpublished data) such as thermal denaturation without formaldehyde and treatment with 95 ~o dimethyl sulphoxide at room temperature have similar effects but to a much lesser extent than the formaldehyde treatment. Also 6 M urea had almost no effect on the sedimentation pattern of the heterogeneous RNA in yeast. It therefore seemed that the more rigorous conditions of denaturation in the presence of formaldehyde might also be necessary to determine the molecular inte

Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis, 1976

Yeast messenger RNA was found to be methylated. A calculation of the specific methylation showed ... more Yeast messenger RNA was found to be methylated. A calculation of the specific methylation showed that the average yeast messenger RNA molecule contains only two methylated nucleosides which occur in one alkali stable oligonucleotide. Similar to other eukaryotic messengers, the 5' terminus of yeast messenger RNA is blocked by 7-methylguanosine, linked through a di-or triphosphate bridge to a ribosemethylated nucleoside. Contrary to the messengers of higher eucaryotic organisms, no additional base methylated constituents were found.

Biochemical and Biophysical Research Communications, 1970

Abstract In yeast, cycloheximide causes the accumulation of heterogeneous RNA, most of which is h... more Abstract In yeast, cycloheximide causes the accumulation of heterogeneous RNA, most of which is high molecular weight RNA sedimenting faster than the 26E ribosomal RNA component, which has a molecular weight of 1.3 × 106. Heating of this heterogeneous RNA in the presence of formaldehyde shows that this RNA is an aggregate of molecules tha t have molecular weights ranging from about 0.2 × 106 to 1.4 × 106.

Archives of Biochemistry and Biophysics, 1972

A study has been made of t,he effects of 5-fluorouracil on the synthesis and stability of ribosom... more A study has been made of t,he effects of 5-fluorouracil on the synthesis and stability of ribosomal RN-4 in yeast. The analog causes ribosomal precursor RNA to accumulate. Mature ribosomal RNA species synthesized in the presence of 5-fluorouracil are unstable and are degraded. Pulse chase experiments showed that the 26 S ribosomal RNA is more rapidly degraded than the 17 S component, explaining our observations that in long term experiments apparently less 26 S than 17 S ribosomal RNA is formed. Possible reasons for the instability of ribosomal RNA containing 5-fluorouracil are discussed.

Archives of Biochemistry and Biophysics, 1971

A study of yeast mitochondrial RNA showed that although this RNA sediments in sucrose density gra... more A study of yeast mitochondrial RNA showed that although this RNA sediments in sucrose density gradients considerably slower than cytoplasmic ribosomal RNA, both RNA species have very similar electrophoret,ic mobilit,ies on polyacrylamide gels. Denaturation in formaldehyde results in a relat,ively larger decrease in the rate of sedimentation of mitochondrial RNA than of cytoplasmic ribosomal RNA or Escherichia coli ribosomal RNA. This suggests that hydrogen bonding is relatively more important as a stabilizing factor of the secondary structure of mitochondrial ribosomal RNA than of the latter two RNA species. This result also demonstrates that profound differences exist between mitochondrial ribosomal RNA and bacterial ribosomal RNA. Cycloheximide, a powerful inhibitor of the formation of cytoplaamic ribosomal RNA, was also found to inhibit the formation of the mitochondrial225 and 155 RNA components. This shows that the formation of t,hese RNA species is controlled by cytoplasmic protein formation. Fractionation of yeast mitochondrial RNA by sucrose density gradient centrifugation followed by hybridization of the individual fractiorls with mitochondrial and nuclear DNA showed that a considerable degree of homology exists between mitochondrial DNA and a mitochondrial RNA fraction sedimenting at about 19s. This is most likely metabolically stable messenger RNA, and it cannot, be concluded from hybridization experiments between total mitochondrial RNA and mitochondrial DNA that mitochondrial ribosomal RNA is transcribed from mitochondrial DNA. Mitochondrial RNA homologous to nuclear DNA was found to sediment as materia.1 closely similar to the 225 component. The usefulness of sodium iodide gradiel1t.s for the fractionation of total yeast DNA into its mitochondrial and nuclear components is described.

Biochimica et Biophysica Acta (BBA) - Nucleic Acids and Protein Synthesis, 1968

A ffactionation by means of phenol treatment at different temperatures revealed that in yeast in ... more A ffactionation by means of phenol treatment at different temperatures revealed that in yeast in the presence of cycloheximide small amounts of ribosomal 28-S RNA are synthesized. Virtually no formation of ribosomal I8-S RNA occurs. In the presence of 5-fluorouracil both ribosomal RNA components are found to be made. A study of the methylation of RNA formed in the presence of cycloheximide and 5-fluorouracil confirmed these observations but suggested also that small amounts of ribosomal precursor RNA accumulate. A closer investigation of the fate of this precursor RNA synthesized in the presence of cycloheximide revealed that this RNA was utilized mainly for the formation of the ribosomal I8-S species, indicating a selective accumulation of a precursor RNA for this ribosomal RNA component by the antibiotic. The remainder of the RNA accumulating in the presence of the antibiotic is also converted into ribosomal RNA. 5-Fluorouracil was found to inhibit this latter conversion. The observations are discussed in view of current hypotheses with regard to the formation of ribosomal RNA.

Journal of Veterinary Diagnostic Investigation, 2011

Avian bornavirus (ABV) is the causative agent of proventricular dilatation disease (PDD), a highl... more Avian bornavirus (ABV) is the causative agent of proventricular dilatation disease (PDD), a highly devastating and contagious disease of psittacines (parrots and parakeets), which has resulted in the death of many captive birds. Accurate diagnosis of bornavirus infection is therefore important for the identification and isolation of infected birds. The current study showed that nonvascular contour (chest) feather calami provide a ready and minimally invasive source of RNA for the detection of ABV by reverse transcription polymerase chain reaction (RT-PCR). Storage of the feathers at room temperature for at least a month did not affect the results. Serological analysis by enzyme-linked immunosorbent assay (ELISA) showed that identification of anti-bornaviral nucleoprotein P40 antibodies can identify many birds with a past or present infection. The presence of anti-avian bornaviral P24 phosphoprotein and P16 matrix protein antibodies was quite variable, rendering these antibodies less...

Archives of Veterinary Science and Medicine, 2020

This study describes the occurrence of psittaciform bornavirus antigens and antibodies in tissues... more This study describes the occurrence of psittaciform bornavirus antigens and antibodies in tissues of birds persistently infected with psittaciform bornavirus. Analysis of serum of infected birds shows that antibodies against the P40 nucleoprotein occur most commonly, whereas antibodies to the glycoprotein are virtually completely absent. Classical Western blotting using rabbit antibodies showed that the P40 nucleoprotein is the only antigen which can be reliably detected in tissues as diverse as brain, liver, feather calami and material such as cloacal swabs. The sensitivity of the latter approach is about 1 µg. Using automated Western blotting (ProteinSimple, WES) improved this sensitivity to about 200 pg. Rabbit antibodies against the P24 phosphoprotein detect a cross-reacting protein of the same molecular size in a classical Western blot of tissue homogenates of uninfected birds. Rabbit antibodies against the P16 matrix protein do not detect the protein in a Western blot, classical or automated, possibly through shielding by other components in the tissue homogenates or prevention of the transfer of the protein from the gel to the PDVF membrane during the blotting, although such antibodies can be used as detection antibodies in a sandwich ELISA analysis where the capture antibodies are of avian origin. The latter approach allows the detection of the P24 phosphoprotein and the P16 matrix protein in feather calami and cloacal swabs at a sensitivity of approximately 200 pg.

Journal of Bacteriology

High-molecular-weight deoxyribonucleic acid (DNA) of Saccharomyces carls bergensis has been fract... more High-molecular-weight deoxyribonucleic acid (DNA) of Saccharomyces carls bergensis has been fractionated by sucrose density gradient centrifugation. The main DNA fraction has an average molecular weight of about 500 × 10 6 . A major fraction of the DNA molecules containing sequences homologous to ribosomal ribonucleic acid (RNA) sediments as material of this molecular weight. The remainder sediments as material of a molecular weight of about 250 × 10 6 . The latter fraction contains relatively more ribosomal RNA cistrons than the former. Studies on the buoyant density of high-molecular-weight DNA homologous to ribosomal RNA have led to the conclusion that the ribosomal RNA cistrons occur in groups attached to a relatively large amount of nonribosomal RNA and suggest that ribosomal RNA cistrons are distributed over a number of yeast chromosomes.

Avian Pathology, 2013

An enzyme-linked immunosorbent assay (ELISA) was developed to estimate levels of IgY antibody aga... more An enzyme-linked immunosorbent assay (ELISA) was developed to estimate levels of IgY antibody against the bacterium Erysipelothrix rhusiopathiae in serum samples collected from the critically endangered kakapo (Strigops habroptilus, Psittaciformes, Aves) before and after vaccination against this bacterium. Relative IgY antibody titres in pre-vaccination serum samples (n = 71 individual kakapo) were normally distributed with the exception of four outliers which displayed low IgY levels. Notably all four low IgY samples were collected from fledglings 3-6 months old. Pre-vaccination serum samples from nine nestlings <3 months old, seven of which were hatched in incubators and had no contact with either adult kakapo or their natural environment (e.g. soil), were found to have relatively high IgY levels, suggesting transfer of maternal IgY molecules to fledglings via the yolk. IgY levels in pre-vaccination serum samples from seven kakapo aged 25-30 months were also relatively high, suggesting that most kakapo naturally acquire anti-E.rhusiopathiae IgYs within their first 2 years. There was no evidence that vaccination increased the kakapo population's mean anti-E.rhusiopathiae IgY levels. However, there was a significant negative relationship between an individual bird's pre-vaccination IgY level and any subsequent increase following vaccination, suggesting that vaccination may only raise the IgY levels of birds with relatively low pre-vaccination IgY levels. A statistical model of the relationship between 'death from erysipelas' and sex, age and transfer from one to island sanctuary to another found that only transfer was significantly associated with death from erysipelas.

Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression, 1983

The ability of the four oligodeoxyribonucleotide primers oligo(dT)12-18, oligo(dA)12-18, oligo(dG... more The ability of the four oligodeoxyribonucleotide primers oligo(dT)12-18, oligo(dA)12-18, oligo(dG)12-18 and oligo(dC)12-18 to act as primers for avian myeloblastosis virus reverse transcriptase on denatured yeast double-stranded (ds) RNA templates was investigated. Oligo(dT) and oligo(dA) were found to prime the synthesis of 1.1 and 1.0 kb reverse transcripts, respectively, using denatured M dsRNA as a template. The oligo(dT)- and oligo(dA)-primed cDNAs of M dsRNA hybridized to the region of the M dsRNA that encoded the killer toxin and to each other. Addition of oligo(dT) to reverse transcription reactions of denatured L dsRNA produced a 4.3 kb cDNA. During the course of this investigation oligo(dC) was observed to be a highly efficient primer for reverse transcription of yeast 18 S ribosomal RNA. Oligo(dC) primed the synthesis of a 1.0 kb transcript of 18 S rRNA which hybridized to the large Eco RI fragment of the 18 S rRNA gene. Reverse transcription of double-stranded RNA and 25 S ribosomal RNA was found to occur to some extent in the absence of added oligonucleotide primer.

Genetica, 2003

Tinamous (Aves, Palaeognathae, Tinamiformes) are primitive birds, generally considered to be the ... more Tinamous (Aves, Palaeognathae, Tinamiformes) are primitive birds, generally considered to be the sister group to the ratites. Tinamous possess a W sex-chromosome, intermediate in heterochromatization between the largely euchromatic W chromosome of the ratites and the highly condensed W chromosome of the neognathous birds. Of the four genes which are known to have diverged copies on the neognathous avian W and Z chromosome (ATP5A1, CHD1, PKC and SPIN) only the spindlin gene has W- and Z-chromosomal forms in the tinamiformes. This paper describes experiments which show that the sequences of these forms are more similar to each other and to the homologous undifferentiated spindlin gene sequences in the ratite genome than to the W or Z forms of the spindlin gene in other, neognathous species. This suggests that cessation of recombination at the spindlin locus of the ancestral W and Z chromosomes of the paleognathous tinamiformes and the neognathous avian species were independent events.

The Auk, 1988

ABSTR^CT.-Single-copy DNA-DNA hybridization was used to establish phylogenetic relationships amon... more ABSTR^CT.-Single-copy DNA-DNA hybridization was used to establish phylogenetic relationships among 13 species of waterfowl (Anatidae) chosen from 10 tribes. On the basis of UPGMA clustering of ATto distances, we suggest that the tribes Anatini, Aythyini, Tadornini, Mergini, and Cairinini diverged more recently than the Anserini, Stictonettini, Oxyurini, Dendrocygnini, and Anseranatini. The Freckled Duck (Stictonetta naevosa, tribe Stictonettini) is only distantly related to the other Anatidae. Presumably the lineage diverged very early. The sheldgeese (tribe Tadornini) and the true geese (Anserini) are only remotely related. The Oxyurini, considered to be in the subfamily Anatinae, is remotely related to the other Anatidae. The Dendrocygnini form an isolated tribe with no close relationship to the swans and geese (subfamily Anserinae). We found that the screamers (Anhimidae) are distantly related to the Anatidae. A method to estimate missing cells in a data matrix of pairwise distances is presented.

Genome, 1994

The approximately 190-bp centromeric repeat monomers of the spur-winged lapwing (Vanellus spinosu... more The approximately 190-bp centromeric repeat monomers of the spur-winged lapwing (Vanellus spinosus, Charadriidae), the Chilean flamingo (Phoenicopterus chilensis, Phoenicopteridae), the sarus crane (Grus antigone, Gruidae), parrots (Psittacidae), waterfowl (Anatidae), and the merlin (Falco columbarius, Falconidae) contain elements that are interspecifically highly variable, as well as elements (trinucleotides and higher order oligonucleotides) that are highy conserved in sequence and relative location within the repeat. Such conservation suggests that the centromeric repeats of these avian species have evolved from a common ancestral sequence that may date from very early stages of avian radiation.Key words: satellite DNA, centromeric repeat, avian, sequence conservation.

Avian Diseases, 2012

Fertilized eggs were obtained from four pairs of sun conures (Aratinga solstitialis) infected wit... more Fertilized eggs were obtained from four pairs of sun conures (Aratinga solstitialis) infected with avian bornavirus (ABV) genotype 2, as determined by the sequence of the P24 gene. ABV RNA could be detected in early embryos of all four pairs. ABV RNA also was detected in brain, liver, and eyes of late-stage embryos of one of the pairs (Pair 4) and in blood of a 2-wk-old hatchling of this pair, demonstrating that vertical transmission can occur. ABV RNA could be detected in the liver but not in the brain or eyes of the late-stage embryos of another pair (Pair 3). Although it could be detected in the undeveloped eggs of the female parent and 8-day-old embryos, bornaviral RNA could not be found in the brain and liver of the late-stage embryos or in feathers and blood of young (5-9-wk-old) hatchlings of a third pair (Pair 2). At 11 wk, ABV RNA could be detected again in feathers and blood of these hatchlings and in the brain of one of the hatchlings of Pair 2 that suddenly died. ABV RNA could however be detected in throat swabs of the 5- and 9-wk-old hatchlings and their parents (Pair 2). Although the continued presence of ABV RNA in feathers and blood below the detection level of the reverse transcription-PCR used cannot be excluded, this result also may be attributable to feeding by the infected parents. Analysis by enzyme-linked immunosorbent assay showed that egg yolks and serum of late-stage embryos contain variable amounts of non-neutralizing anti-ABV-P40, -P10, -P24, and -P16 antibodies, the ratio of which reflected the antibody ratio in the serum of the female parent. Antibodies against the viral glycoprotein, which are considered neutralizing in mammals, and against ABV RNA polymerase were not detected. Whereas 5-wk-old hatchlings of the pair (Pair 2) that produced ABV RNA-free late-stage embryos were free of anti-ABV antibodies, such antibodies could be detected again in the serum of these hatchlings at 9 wk of age, before the age that bornaviral RNA could again be detected in feathers and blood. At 16 wk, these antibodies became abundant. The finding that late-stage embryos, presumably free of ABV RNA, can be obtained from eggs from infected parents suggests that hand- or foster-raising of such birds may be a method to obtain birnavirus-free offspring from some infected birds.

Avian Diseases, 2009

Recently a novel avian bornavirus has been described that has been suggested to be the possible e... more Recently a novel avian bornavirus has been described that has been suggested to be the possible etiological agent for proventricular dilatation disease or macaw wasting disease. This article describes two macaws that shed avian bornaviral RNA sequences and demonstrated anti-avian bornavirus antibodies as revealed by reverse transcriptase polymerase chain reaction (RT-PCR), enzyme-linked immunosorbent assay (ELISA), and Western blot, yet are free of outward clinical signs of the disease.

This study describes a further analysis of the detection of bornaviral antigens by sandwich ELISA... more This study describes a further analysis of the detection of bornaviral antigens by sandwich ELISA. The results show that using chicken anti-psittacine bornaviral P16 matrix protein antibody for capture and rabbit antibody to this protein for detection, recombinant matrix protein of mammalian as well as of distantly related snake bornavirus can be detected, suggesting that a single procedure can be used for the diagnosis of highly divergent bornavirus infections.