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At least 19 recordsLinked to original sources
PubMed2026

Paralog-aware assembly and filtering strategies reveal minimal nucleotide variation on the macro germline-restricted chromosome of the zebra finch.

The germline-restricted chromosome (GRC) of passerines is a remarkable tissue-specific chromosome that accumulated paralogs of genes from the regular "A chromosomes" over millions of years, often amplified into dozens of gene copies. In addition to its repetitive content, typically uniparental inheritance, and lack of recombination, the GRC resembles non-recombining sex chromosomes and some B chromosomes, for all of which assembly and single-nucleotide polymorphisms (SNPs) calling are difficult. Here, we first show that much of the Australian zebra finch macro-GRC can be assembled using accurate long reads. We then describe a paralog-aware Snakemake pipeline, ParaVar, to map short reads from the GRC to retrieve GRC regions suitable for haplotype-based analysis. ParaVar reliably calls hundreds of SNPs across the GRC, thereby providing an estimate of nucleotide diversity on the highly repetitive zebra finch macro-GRC. Our results show significantly lower nucleotide diversity (20- to 50-fold lower) on the GRC compared to the mitogenome and autosomes, and a strong phylogenetic discordance between the GRC and the mitochondrial genome. Beyond the contribution of background selection, our results suggest that a single GRC haplotype recently spread through the populations while jumping across matrilines via occasional paternal inheritance. We anticipate that our paralog-aware pipeline will be useful for SNP calling and population genetics analyses of repetitive GRCs, sex chromosomes, and B chromosomes.

Animals↗
PubMed1978

Response of the pyrimidine pathway of Escherichia coli K 12 to exogenous adenine and uracil.

The effect of exogenous adenine or uracil upon the de novo pathway for synthesis of pyrimidine nucleotides in Escherichia coli K12 was investigated. Parameters studied were levels of the enzymes carbamoyl phosphate synthase (EC 2.7.2.9), aspartate carbamoyltransferase (EC 2.1.3.2) and orotate phosphoribosyltransferase (EC 2.4.2.10) and the intermediates carbamoyl phosphate, aspartate and orotate, together with the contributions of exogenous uracil and aspartate to intracellular pyrimidine nucleotide. Taken with earlier data [Bagnara, A.S. & Finch, L. R. (1974) Eur. J. Biochem- 41, 421--430] on contents of UTP, CTP and 5-phosphoribosyl 1-diphosphate in cultures of this strain after the addition of adenine or uracil, the results obtained provide new insights into the regulatory mechanisms operating on the pathway in vivo. These insights enable evaluation of the contributions of such factors as limitation for a substrate, feed-back allosteric control by end products and enzyme repression/depression mechanisms. The evidence presented indicates that depressed levels of orotate phosphoribosyltransferase in E. coli K12 result in the wasteful ultilization of asparatate for excess synthesis of pyrimidine nucleotide precursors during balanced growth of the strain in minimal medium. Exogenous adenine increases the excessive accumulation of these precursors by lowering the intracellular content of 5-phosphoribosyl 1-diphosphate (Bagnara and Finch, 1974). This causes a decrease in the conversion of orotate to orotidine 5'-monophosphate, thus lowering the utilization or orotate and its precursors for synthesis of pyrimidine nucleotides. Further, since the contents of these nucleotide end products are thereby decreased (Bagnara nad Finch, 1974), theri feed-back on the early steps in the pathway is diminished and the production of the precursors is increased. It is postulated that growth of E. coli K12 under these conditions is limited by a compound that is metabolically related to precursors to aspartate.

Adenine↗
PubMed2025

Sex-Chromosome-Dependent Ageing in Female Heterogametic Methylomes.

Recent research in humans and both model and non-model animals has shown that DNA methylation (DNAm), an epigenetic modification, is one of the mechanisms underlying the ageing process. DNAm-based indices predict mortality and provide valuable insights into biological ageing mechanisms. Although sex-dependent differences in lifespan are ubiquitous and sex chromosomes are thought to play an important role in sex-specific ageing, they have been largely ignored in epigenetic ageing studies. We characterised the genome-wide distribution of age-related CpG (Cytosine-phosphate-Guanine) sites from longitudinal samples in two avian species (zebra finch and jackdaw), including for the first time the avian sex chromosomes (Z and the female-specific, haploid W). In both species, we find a small fraction of the CpG sites to show age-related changes in DNAm with the majority of them being located on the haploid, female-specific W chromosome, where DNAm levels predominantly decrease with age. Age-related CpG sites were over-represented on the zebra finch but under-represented on the jackdaw Z chromosome. Our results highlight distinct age-related changes in sex chromosome DNAm compared to the rest of the genome in two avian species, suggesting this previously understudied feature of sex chromosomes may be instrumental in sex-dependent ageing. Moreover, studying the DNAm of sex chromosomes might be particularly useful in ageing research, facilitating the identification of shared (sex-dependent) age-related pathways and processes between phylogenetically diverse organisms.

Animals↗
PubMed1978

Histone packing in the nucleosome core particle of chromatin.

The chromatin core particle DNA conformation deduced in broad outline by Finch et al. [Finch, J. T., Lutter, L. C., Rhodes, D., Brown, R. S., Rushton, B., Levitt, M. & Klug, A. (1977) Nature 269, 29-36] can be described in detail using other available experimental results. Histone binding sites compatible with the pattern of pancreatic DNase I digestion (Simpson, R. T. & Whitlock, J. P., Jr. (1976) Cell 9, 347-353; Noll, M. (1977) J. Mol. Biol. 116, 49-71; Lutter, L. C. (1977) J. Mol. Biol. 117, 53-69] lend to core particle DNA pseudosymmetry characteristic of molecular point group D(3). DNA symmetry and pseudosymmetry, in turn, imply equivalence and quasi-equivalence properties of the histone packing arrangement that support the following deductions: (i) One and only one alpha(2)beta(2) histone tetramer, presumably (H3)(2)(H4)(2), can serve as a stable subassembly within the histone octamer. (ii) There is a unique, strand-specific way to assign DNA binding domains to the arginine-rich histones (H3 and H4). (iii) Histones H3 and H4 alone should suffice to impose a supercoiled structure on DNA, as is observed experimentally, because only the tetramer can mimic a screw dislocation and thereby complement the screw symmetry of the DNA supercoil. (iv) The two slightly lysine-rich histones H2A and H2B are probably responsible, each in a different way, for dividing the eukaryotic chromatin fiber into discrete subunits. (v) The proposed arrangement of four distinct proteins appears to be a minimum formal requirement for making nucleosomes; that is, for introducing regularly spaced supercoiled DNA folds without also allowing formation of an indefinitely long (and genetically inert) DNA superhelix.

Binding Sites↗
PubMed1979

Analyses of changes in verbal behavior following a cognitive-behavioral treatment for impulsivity.

Analyses were conducted to examine further the results of a cognitive-behavioral treatment for impulsivity in emotionally disturbed children (Kendall & Finch, 1978). The verbal behaviors of treated impulsive children, impulsive controls, and reflective children, recorded during MFF performance at pretreatment, posttreatment, and follow-up, were examined. The results indicated nonsignificant effects for several specific codes; however, the impulsive children that had received treatment evidenced a significant increase in total on-task verbal behavior at posttreatment. Discussion includes a consideration of these findings in regard to the efficacy of the cognitive-behavioral treatment and the need for research on the assessment of cognitive variables in children.

Behavior Therapy↗
PubMed2025

Birds of a feather flock together: social context exacerbates the effects of light pollution on circadian disruption.

Artificial light at night (ALAN), a growing pervasive pollutant, disrupts physiological and behavioural rhythms across organisms. Social interactions play a significant role in shaping individual and group biological rhythms, but they are often overlooked in the context of environmental stressors, such as ALAN. We explore how dim ALAN affects zebra finches (Taeniopygia guttata) in social and isolated environments, examining behavioural, physiological and molecular rhythms. We found that social birds under ALAN had an earlier activity onset and greater disruption in hypothalamic and liver circadian gene expression than control or isolated counterparts under ALAN. Additionally, we found that activity onset correlated negatively with hypothalamic bmal1 and cry1 expression in birds exposed to ALAN. Within ALAN-exposed birds, there was a larger disassociation between central and peripheral clock gene expression for social birds than in isolated birds. However, rhythmic melatonin concentrations did not differ among treatment groups. We show that social interactions may exacerbate the effects of ALAN, which highlights the impact of social interactions on circadian regulation at a molecular level and a critical need to consider social contexts in biological studies.

Animals↗
PubMed1978

Hypothalamic-pituitary-ovarian interactions during reproductive senescence in the rat.

The neuroendocrine status of Long-Evans female rats was evaluated at several key stages of reproductive senescence. Young (4-8 mo), middle-aged (10-14 mo) and old (24-30 mo) animals were studied according to reproductive state. The reproductive states studied were (1) regularly cycling, (2) constant estrus and (3) pseudopregnant, as determined by vaginal smear cytology. Neuroendocrine parameters at the levels of the hypothalamus, pituitary and steroid-producing organs were compared between each group. DA3, E and NE concentrations in the median eminence of the hypothalamus were determined by a highly sensitive radioenzymatic assay. LRF content in the median eminence was measured by radioimmunoassay. Circulating levels of LH, FSH, PRL and six steroids were determined. Changes in hormone and neurotransmitter concentrations were deomonstrated in association with the various stages of reproductive senescence and with age advancement. These changes involved the hypothalamic, pitiutary and steroid systems. NE content in the median eminence, FSH in serum and circulating androstenedione were all significantly increased in middle-aged, cyclic rats prior to the onset of senescent anovulation. DA concentration in 24 mo. old constant estrous rats (30.7 +/- 7.7 pg/microgram, N = 6) and in 30 mo. old pseudopregnant rats (27.5 +/- 7.1 pg/microgram, N = 6) was significantly reduced compared to young (6 mo. old), cyclic controls on proestrous (55.0 +/- 4.7 pg/microgram, N = 12). This DA reduction was associated with a 3-fold increase in circulating prolactin. The results are discussed in terms of a regulatory cascade model of female reproductive senescence (Finch, 1976).

Aging↗
PubMed1977

Electron microscopy of fibers and discs of hemoglobin S having sixfold symmetry.

Aggregated forms of deoxyhemoglobin S were examined with a field emission transmission electron microscope. Images of isolated helical fibers were obtained from sickled cell lysates stained directly on the electron microscope grid. Optical and digital analyses of the electron micrographs showed that the fibers are similar to those characterized by J. T. Finch, M. F. Perutz, J. F. Bertles, and J. Döbler [(1973) Proc. Natl. Acad. Sci. USA 70, 718-722] in that they consist of stacked discs each composed of six hemoglobin molecules. The fibers exhibit an outer diameter of 160-170 A and an inner diameter of about 60 A with an axial spacing of 58 A per disc. The fiber can be described as a helix consisting of 56 discs per helical turn. We observed discs of six hemoglobin molecules, which may be stable substructural components of the fibers. They were observed in preparations of hemoglobin fibers and exhibited 6-fold symmetry by power spectrum analysis. A reconstructed image of a disc digitally filtered for 6-fold symmetry has a maximum external diameter of approximately 170 A and a central hole of 60 A diameter and is similar to the axial projection of a single disc from a low-resolution, three-dimensional reconstructed model of a fiber.

Computers↗
PubMed1979

Involvement of histone H1 in the organization of the nucleosome and of the salt-dependent superstructures of chromatin.

We describe the results of a systematic study, using electron microscopy, of the effects of ionic strength on the morphology of chromatin and of H1-depleted chromatin. With increasing ionic strength, chromatin folds up progressively from a filament of nucleosomes at approximately 1 mM monovalent salt through some intermediate higher-order helical structures (Thoma, F., and T. Koller, 1977, Cell 12:101-107) with a fairly constant pitch but increasing numbers of nucleosomes per turn, until finally at 60 mM (or else in approximately 0.3 mM Mg++) a thick fiber of 250 A diameter is formed, corresponding to a structurally well-organized but not perfectly regular superhelix or solenoid of pitch approximately 110 A as described by Finch and Klug (1976, Proc. Natl. Acad. Sci. U.S.A. 73:1897-1901). The numbers of nucleosomes per turn of the helical structures agree well with those which can be calculated from the light-scattering data of Campbell et al. (1978, Nucleic Acids Res. 5:1571-1580). H1-depleted chromatin also condenses with increasing ionic strength but not so densely as chromatin and not into a definite structure with a well-defined fiber direction. At very low ionic strengths, nucleosomes are present in chromatin but not in H1-depleted chromatin which has the form of an unravelled filament. At somewhat higher ionic strengths (greater than 5 mM triethanolamine chloride), nucleosomes are visible in both types of specimen but the fine details are different. In chromatin containing H1, the DNA enters and leaves the nucleosome on the same side but in chromatin depleted of H1 the entrance and exit points are much more random and more or less on opposite sides of the nucleosome. We conclude that H1 stabilizes the nucleosome and is located in the region of the exit and entry points of the DNA. This result is correlated with biochemical and x-ray crystallographic results on the internal structure of the nucleosome core to give a picture of a nucleosome in which H1 is bound to the unique region on a complete two-turn, 166 base pair particle (Fig. 15). In the formation of higher-order structures, these regions on neighboring nucleosomes come closer together so that an H1 polymer may be formed in the center of the superhelical structures.

Chromatin↗
PubMed1979

A model of imprinting evolved from neurophysiological concepts.

The imprinting process is described by a model evolved from physiological data. For the case of sexual imprinting in zebra finches a second sensitive phase, occurring at sexual maturity, is considered. The first sensitive phase is not restricted exclusively to the imprinting of sexual objects. Properties of the model allow for the explanation of apparent reversibility of imprinting. The same physiological mechanisms involved in the organization of simple neuronal connections are assumed to operate in the highly complex networks associated with imprinting phenomena.

Animals↗
PubMed2024

Repeated evolution on oceanic islands: comparative genomics reveals species-specific processes in birds.

Understanding the interplay between genetic drift, natural selection, gene flow, and demographic history in driving phenotypic and genomic differentiation of insular populations can help us gain insight into the speciation process. Comparing patterns across different insular taxa subjected to similar selective pressures upon colonizing oceanic islands provides the opportunity to study repeated evolution and identify shared patterns in their genomic landscapes of differentiation. We selected four species of passerine birds (Common Chaffinch Fringilla coelebs/canariensis, Red-billed Chough Pyrrhocorax pyrrhocorax, House Finch  Haemorhous mexicanus and Dark-eyed/island Junco Junco hyemalis/insularis) that have both mainland and insular populations. Changes in body size between island and mainland populations were consistent with the island rule. For each species, we sequenced whole genomes from mainland and insular individuals to infer their demographic history, characterize their genomic differentiation, and identify the factors shaping them. We estimated the relative (Fst) and absolute (dxy) differentiation, nucleotide diversity (π), Tajima's D, gene density and recombination rate. We also searched for selective sweeps and chromosomal inversions along the genome. All species shared a marked reduction in effective population size (Ne) upon island colonization. We found diverse patterns of differentiated genomic regions relative to the genome average in all four species, suggesting the role of selection in island-mainland differentiation, yet the lack of congruence in the location of these regions indicates that each species evolved differently in insular environments. Our results suggest that the genomic mechanisms involved in the divergence upon island colonization-such as chromosomal inversions, and historical factors like recurrent selection-differ in each species, despite the highly conserved structure of avian genomes and the similar selective factors involved. These differences are likely influenced by factors such as genetic drift, the polygenic nature of fitness traits and the action of case-specific selective pressures.

Animals↗
PubMed1977

The neuro-endocrine complex in the gastro-entero-pancreatic endocrine system.

The pancreatic islet is one of the well-studied endocrine tissues in regard to innervation. This neuro-insular complex has been known since the 1920's. The direct contact of the nervous element to the gastro-enteric endocrine cells has recently been reported in the proventricular mucosa of the finch. Here, the majority of the endocrine cells lie in the lamina propria and form a neuro-endocrine complex with unmyelinated nerve fibers. A similar neuro-endocrine complex was also reported in the rat stomach and in the duodenum of the human fetus. The occurrence of the neuro-endocrine complexes in the gastro-entero-pancreatic endocrine system might provide supportive data to the neuro-ectodermal theory on the origin of the endocrine cells proposed by Professors A. G. E. PEARSE and T. FUJITA.

Animals↗
PubMedDate not supplied

Experimental Newcastle disease virus infections in three species of wild birds.

Three species of wild birds--the red-winged blackbird (Agelaius phoeniceus), an African weaver finch (Quelea quelea), and the sandhill crane (Grus canadensis)--were exposed to Newcastle disease virus (NDV) to determine susceptibility and host response. The NDV used were a vaccine strain (LaSota) and a viscerotropic velogenic strain (New York Parrot). Host response was monitored by virus isolation, signs of disease, and serologic response. Both the red-winged blackbirds and the quelea shed little virus and developed low antibody titers. A low mortality in the blackbirds did not appear to be due to ND alone. Vaccinated cranes were well protected against velogenic challenge, whereas unvaccinated cranes shed the velogenic virus from the cloaca for weeks. The ramifications of the low antibody titers produced in birds of two species are discussed, as well as the potential involvement of each species in transmission of the virus.

Animal Population Groups↗