α-Satellite DNA methylation in normal individuals and in ICF patients: heterogeneous methylation of constitutive heterochromatin in adult and fetal tissues

The methylation profile of ten α-satellites was investigated in normal individuals and in ICF (Immunodeficiency, Centromeric instability, Facial abnormalities) patients. Two out of three ICF patients showed modified methylation of these sequences, reproducing a placental profile. CENP-B boxes, the binding sites of centromeric protein B, were always skewed toward nonmethylation. Unexpected results were observed in normal individuals: in somatic adult tissues the methylation pattern of α-satellite DNA varied between chromosomes, and in fetal tissues these satellites were homogeneously undermethylated. Detailed methylation analysis of CENP-B boxes revealed that unmethylated α-satellite units coexist with thoroughly methylated regions. These observations showed that the two major components of constitutive heterochromatin are differently methylated in normal somatic and fetal tissues, since classical satellites are consistently methylated. The definite changes in the methylation profile of heterochromatin in somatic chromosomes and the asynchronous timing of methylation of classical and α-satellites during development may reflect specific roles of highly repeated sequences in genomic organization. Received: 29 October 1996 / Revised: 17 December 1996     

Microsatellite variation and population structure in the “Refractario” cacao of Ecuador

Utilization of germplasm for crop improvement is often hampered by absence of information regarding origin, genetic identity and genealogical relationships of germplasm groups or populations. Molecular marker technology offers an efficient tool to verify or reconstruct passport data. Using a high-throughput genotyping system with 15 microsatellite loci, we fingerprinted 482 accessions in 48 putative half-sib families of Refractario cacao (a group of germplasm collected from nine farms in Ecuador). Based on the multilocus profiles, a Bayesian method for individual assignment was applied to verify membership in each half-sib family. Multivariate statistical analysis showed that the Refractario genetic profile was different from other groups tested, except for the “Nacional” cacao from the coastal valley of Ecuador. Hierarchical partitioning of genetic variance in the Refractario cacao showed that 76% of the variation was contributed by intra-family difference, whereas the inter-family and inter-farm difference accounted for 15 and 9% of total variance, respectively. All three sources of variation were highly significant (P < 0.01). Cluster and Principal Coordinates Analyses revealed a population sub-structure in Refractario, which was also highly heterozygous, suggesting hybridization derived from Nacional cacao and multiple other parental varieties, which all shared a similar genetic background. The improved understanding of identities and structure in Refractario cacao will contribute to more efficient conservation and use of this germplasm group in cacao breeding.     

Interspecific “common” repetitive DNA sequences in salamanders of the genus Plethodon

Intermediate repetitive sequences of Plethodon cinereus which comprised about 30% of the genomic DNA were isolated and iodinated with ¹²⁵I. About 5% of the ¹²⁵I-repetitive fraction hybridized with a large excess of DNA from P. dunni at Cot 20. About half of the ¹²⁵I-DNA in the hybrids was resistant to extensive digestion with S-1 nuclease. The average molecular size of the S-1 nuclease-resistant fraction was about 100 nucleotide pairs. The melting temperature of the S-1 nuclease-resistant fraction was about 2° lower than that of the corresponding fraction made with P. cinereus DNA. These results are taken to indicate the presence in the genomes of P. cinereus and P. dunni of evolutionarily stable common repetitive sequences. The average frequency of repetition of the common repetitive sequences is about 6,000 × in both species. The common repetitive fraction is also present in the genomes of other species of Plethodon, although the general populations of intermediate repetitive sequences are markedly different from one species to another. The cinereus-dunni common repetitive sequences could not be detected in plethodontids belonging to different tribes, nor in more distantly related amphibians. The profiles of binding of the common repetitive sequences to CsCl or Cs₂SO₄-Ag⁺ density gradient fractions of P. dunni DNA suggested that these sequences consisted of heterogeneous components with respect to base compositions, and that they did not include large amounts of the genes for ribosomal RNA, 5S RNA, 4S RNA, or histone messenger RNA. — In situ hybridization of the ³H-labelled intermediate repetitive sequences of P. cinereus to male meiotic chromosomes of the same species gave autoradiographs after an exposure of seven days showing all 14 chromosomes labelled. The pattern of labelling appeared not to be random, but was impossible to analyse on account of the irregular shapes and different degrees of stretching of diplotene and prometaphase chromosomes. In situ hybridization of the same sequences to meiotic chromosomes from P. dunni gave autoradiographs after 60 d exposure in which all chromosomes were labelled. These heterologous in situ hybrids can only have involved the common repetitive sequences.     

Karyotype and cytogeography of the genus Heracleum （Apiaceae） in the Hengduan Mountains

In the present study, the karyotypes of 34 populations belonging to 11 species and one variety of Heracleum from the Hengduan Mountains in China were examined. Chromosome numbers and the karyotypes of three species （H. souliei, H. la＇ngdoni, and H. wenchuanense） are reported for the first time, as are the karyotypes of H. moellendorffii and H. henryi （tetraploid）. Populations of H. candicans, H. franchetii, and H. kingdoni in the Hengduan Mountains were found to consist of a mixture of diploid and tetraploid plants. Except for four species of Heracleum, namely H. candicans, H. franchetii, H. henryi, and H.kingdoni, which have both diploid and tetraploid karyotypes, all other species of Heracleum are were found to be diploid. All karyotypes were found to belong to the 2A type of Stebbins, with the exception ofH. candicans var. obtusifolium, which belongs to 2B, and H. hemsleyanum and H. franchetii （Mt. Dujuan, Daocheng, Sichuan, China）, which belong to 1A. There was only a slight difference in the karyotype asymmetry index, which suggests a close kinship for species of Heracleum and that the entire phylogenetic development of Heracleum is relatively primitive. Species that exhibited advanced morphological features were also more advanced in karyotype structure, with the order ofkaryotype evolution being 1A→2A→2B. This phenomenon indicates that the species distributed in the Hengduan Mountains have not diverged completely and that the Hengduan Mountains are a relatively young and active area for the evolution of Heracleum. Polyploidization in Heracleum may be an important evolutionary mechanisms for some species, generating diversity. The biological attributes, distribution range, and the geological history of the genus have all played a part in accelerating the evolution through polyploidization or aneuploidization. It is known that as the distribution latitude of Heracleum decreases from north to south, the chromosome number, ploidy level, and asymmetry structure appear to increase. In the Hengd     

Quantitative assessment of song-selectivity in the zebra finch “high vocal center”

1. Auditory responses in the zebra finch (Taenopygia guttata) song-system nucleus HVc were assessed at 54 recording sites by 3 different methods: discriminated action potentials; excitatory summed responses; and excitatory minus inhibitory summed responses. Four standard stimuli were presented at each site: the bird's own song; this song reversed; a conspecific song; and a noise burst. Responses were quantified by calculating a relative response index that partitioned the response, to provide a response profile, across the stimuli.
2. Regardless of analysis method, the strongest response was most often to the bird's own song (78–82%, depending on method). The predominant rank order of response strength across the remaining three stimuli was conspecific song > reversed song > noise.
3. The distribution of relative response magnitude was sensitive to analysis method. Discriminated spikes captured the heterogeneity of HVc neurons, whereas the excitatory summed responses reflected the overall trends more consistently. When inhibition was subtracted from excitation in the summed responses, the variance of the relative responses increased, but this method presented some problems for statistical analysis.
4. A small sample of neurons in other forebrain auditory areas was used for comparative analyses. At these recording sites, the bird's own song did not consistently elicit the best response and there were generally smaller differences in the relative responses to the four stimuli. The smaller degree of stimulus selectivity among these cells resulted in less sensitivity to differences in the assessment methods.

     

Niche expansion and the niche variation hypothesis: does the degree of individual variation increase in depauperate assemblages?

The niche expansion and niche variation hypotheses predict that release from interspecific competition will promote niche expansion in depauperate assemblages. Niche expansion can occur by different mechanisms, including an increase in within-individual, among-individual, or bimodal variation (sexual dimorphism). Here we explore whether populations with larger niche breadth have a higher degree of diet variation. We also test whether populations from depauperate lizard assemblages differ in dietary resource use with respect to variation within and/or among individuals and sexual dimorphism. We found support for the niche expansion and niche variation hypotheses. Populations in assemblages with low phylogenetic diversity had a higher degree of individual variation, suggesting a tendency for niche expansion. We also found evidence suggesting that the mechanism causing niche expansion is an increase in variation among individuals rather than an increase in within-individual variation or an increase in bimodal variation due to sexual dimorphism.     

Circadian variation in hepatic toxicity of the immunosuppressive agent “Mycophenolate Mofetil” in rats

Immunosuppressive drugs may have varying toxicity or efficacy depending on the administration time. This study investigates whether the liver toxicity of the mycophenolate mofetil (MMF) varies according to the circadian dosing-time in rats. 300 mg/kg of MMF was injected by intraperitonal route to different groups of animals at four different circadian stages (1, 7, 13, and 19 h after light onset, HALO). Biochemical variable (transaminase, alkaline phosphatase) and histopathological examinations on liver section were performed. The results obtained showed that MMF treatment induced hepato-toxicity depending on the circadian time. A severe toxicity in the liver was observed when the drug was injected at 7 HALO. The data obtained indicate that the maximum of hepato-toxicity is observed when MMF was injected in the middle of the light-rest span of rats which is physiologically analogous to the end of the activity of the diurnal phase in human patients.     

Why do the mounds of Mus spicilegus vary so much in size and composition?

Mound-building mice (Mus spicilegus) construct large and often enormous mounds, which may have several functions, including food storage, thermoregulation, and protection from predators. We examined variation in mound size and composition to help determine their adaptive significance. Like previous studies, we found much variation in mound size within and between geographic populations, and the main differences were between habitats: we found up to a 700-fold variation in mound size between corn fields and harvested grain fields. Mice mainly utilized three plants (Amaranthus spp., Chenopdium spp. and Setaria spp.) as building materials, and the availability of these may affect mound size. We found a positive correlation between the availability of plant material in the surrounding of the mound and mound size. Surprisingly, mound size was independent of the number of inhabitants within the mounds, which indicates that larger mounds are not constructed to shelter more individuals. Future studies need to examine how variation in mound size and composition affects overwinter survival, and also which individuals contribute to mound construction.     

Production and evolution pattern of “fruity smell” aggregation pheromones in genus Drosophila

Insects produce pheromones to serve a range of ecological functions throughout their lifetime. The chemical composition, production pattern, and interspecies specificity provide information for carrying out their function and biological significance. Several species of Drosophila produce a class of volatile esters considered as “fruity smells”; however, the production pattern and ecological functions of these “fruity smell” volatiles in genus Drosophila are poorly understood. Here, using the headspace solid-phase microextraction (SPME) method, we tested the production pattern of volatile pheromones in Drosophila immigrans and factors that possibly affected pheromone production, including mating, feeding conditions, age of adult flies, and geographical distribution. We also explored the evolution and production pattern of volatile pheromones in 14 species of genus Drosophila. Our result showed that male D. immigrans adult flies produce three male-specific volatile ester pheromones, which are also considered as “fruity smell” chemicals, in a relatively stable pattern. In addition, a series of “fruity smell” ester pheromones with similar structure and chemical properties were found to appear in the species of D. virilis and D. immigrans species group, but not in the species of D. melanogaster species group. The ester volatile pheromone production of male flies has a correspondence with the female's demand for host plants. Integrating the production and evolution pattern of these volatile chemicals, we inferred the interaction between insects and host plants reflected in the Drosophila “fruity smell” pheromones.     

Functional genetic variation in the Rev-Erbα pathway and lithium response in the treatment of bipolar disorder

Bipolar disorder (BD) is characterized by disruptions in circadian rhythms such as sleep and daily activity that often normalize after lithium treatment in responsive patients. As lithium is known to interact with the circadian clock, we hypothesized that variation in circadian 'clock genes' would be associated with lithium response in BD. We determined genotype for 16 variants in seven circadian clock genes and conducted a candidate gene association study of these in 282 Caucasian patients with BD who were previously treated with lithium. We found that a variant in the promoter of NR1D1 encoding Rev-Erbα (rs2071427) and a second variant in CRY1 (rs8192440) were nominally associated with good treatment response. Previous studies have shown that lithium regulates Rev-Erbα protein stability by inhibiting glycogen synthase kinase 3β (GSK3β). We found that GSK3β genotype was also suggestive of a lithium response association, but not statistically significant. However, when GSK3β and NR1D1 genotypes were considered together, they predicted lithium response robustly and additively in proportion to the number of response-associated alleles. Using lymphoblastoid cell lines from patients with BD, we found that both the NR1D1 and GSK3β variants are associated with functional differences in gene expression. Our findings support a role for Rev-Erbα in the therapeutic mechanism of lithium and suggest that the interaction between Rev-Erbα and GSK3β may warrant further study.     

Removal of “Podon” polyphemoides from the genus podon

Summary It is argued that Podon polyphemoides does not belong in the genus Podon, since the only similarity with the other species in this genus is the body outline, a characteristic of minor importance in generic distinction in the Polyphemoidea. The new name Pleopis polyphemoides is proposed.

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Resumen Se argumenta que Podon polyphemoides no debe colocarse más en el genero Podon, ya que solamente tiene similitud con las otras especies de este género en la configuración del cuerpo, una caracteristica de menor importancia en la distinción del Orden Polyphemoidea. Se propone el nombre nuevo Pleopis polyphemoides.

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Based on part of a dissertation, titled The Cladocera of the North Atlantic and the North Sea: Biological and Ecological Studies, and submitted in partial fulfillment of the requirements for the Ph.D. degree at McGill University, Montreal, Canada.     

Quantitative mapping of cocaine-induced ΔFosB expression in the striatum of male and female rats

ΔFosB plays a critical role in drug-induced long-term changes in the brain. In the current study, we evaluated locomotor activity in male and female rats treated with saline or cocaine for 2 weeks and quantitatively mapped ΔFosB expression in the dorsal striatum and nucleus accumbens of each animal by using an anti-FosB antibody that recognizes ΔFosB isoforms preferentially. Behavioral analysis showed that while there was little difference between males and females that sensitized to cocaine, nonsensitizing rats showed a large sex difference. Nonsensitizing males showed low behavioral activation in response to cocaine on the first day of treatment, and their activity remained low. In contrast, nonsensitizing females showed high activation on the first day of treatment and their activity remained high. Western blot and immunohistochemical analyses indicated that basal levels of ΔFosB were higher in the nucleus accumbens than the dorsal striatum, but that the effect of cocaine on ΔFosB was greater in the dorsal striatum. Immunostaining showed that the effect of cocaine in both the dorsal striatum and nucleus accumbens was primarily to increase the intensity of ΔFosB immunoreactivity in individual neurons, rather than to increase the number of cells that express ΔFosB. Detailed mapping of ΔFosB-labeled nuclei showed that basal ΔFosB levels were highest in the medial portion of the dorsal striatum and dorsomedial accumbens, particularly adjacent to the lateral ventricle, whereas the cocaine-induced increase in ΔFosB was most pronounced in the lateral dorsal striatum, where basal ΔFosB expression was lowest. Sex differences in ΔFosB expression were small and independent of cocaine treatment. We discuss implications of the sex difference in locomotor activation and regionally-specific ΔFosB induction by cocaine.     

Copy number variation of transposable elements in Triticum–Aegilops genus suggests evolutionary and revolutionary dynamics following allopolyploidization

Key message

Here, we report on copy number variation of transposable elements and on the genome-specific proliferation in wheat. In addition, we report on revolutionary and evolutionary dynamics of transposons.

Abstract

Wheat is a valuable model for understanding the involvement of transposable elements (TEs) in speciation as wheat species (Triticum–Aegilops group) have diverged from a common ancestor, have undergone two events of speciation through allopolyploidy, and contain a very high fraction of TEs. However, an unbiased genome-wide examination of TE variation among these species has not been conducted. Our research utilized quantitative real time PCR to assess the relative copy numbers of 16 TE families in various Triticum and Aegilops species. We found (1) high variation and genome-specificity of TEs in wheat species, suggesting they were active throughout the evolution of wheat, (2) neither Ae. searsii nor Ae. speltoides by themselves can be the only contributors of the B genome to wheat, and (3) nonadditive changes in TE quantities in polyploid wheat. This study indicates the apparent involvement of large TEs in creating genetic variation in revolutionary and evolutionary scales following allopolyploidization events, presumably assisting in the diploidization of homeologous chromosomes.     

Molecular characterization of “inverted” pericentromeric heterochromatin of chromosome 3

Summary Inversion of the pericentromeric region of human chromosome 3 [inv (3) (p11q11.2)] is a rare event. Initially, this inversion was identified with staining for Q-bands by fluorescence using quinacrine (QFQ) and later characterized with staining for C-bands by CBG technique. The molecular methods of fluorescence in situ hybridization (FISH) and AluI/Giemsa and TaqI/Giemsa techniques were utilized. The findings suggest that the variable band q11.2 on chromosome 3 contains alphoid DNA sequences, which appear to be similar to those identified by conventional methods in the centromeric region (band p11).     

Effect of treatment of cow’s urine “Gomutra” and antioxidants in alleviating the lindane-induced oxidative stress in kidney of Swiss mice (Mus musculus)

The study aimed to evaluate the effect of cow urine and combination of antioxidants against lindane induced oxidative stress in Swiss mice. Male healthy mice, 8–10 weeks old, weighing 30 ± 5 g were randomly selected and divided into eight groups, namely, control (C); lindane (L); antioxidant (A), antioxidant+lindane (A+L), cow urine (U), cow urine+lindane (U+L), cow urine+antioxidants (U+A) and cow urine+antioxidants+lindane (U+A+L). Group C animals were administered only the vehicle (olive oil); doses selected for other treatments were: lindane: 40 mg/kg b.w.; antioxidants: 125 mg/kg b.w. (vitamin C: 50 mg/kg b.w., vitamin E: 50 mg/kg b.w., α-lipoic acid: 25 mg/kg b.w.) and cow urine: 0.25 ml/kg b.w. In group A+L and U+L antioxidants and cow urine were administered 1 h prior to lindane administration and in group U+A and U+A+L cow urine was administered 10 min before antioxidants. All treatments were administered orally continuously for 60 days. Lindane treated group showed increased lipid peroxidation, whereas glutathione, glutathione peroxidase, superoxide dismutase, catalase, protein and endogenous levels of vitamin C and E were significantly decreased compared to control. Administration of cow urine and antioxidants alleviated the levels of these biochemical parameters.     

On the systematic position of the Early Cretaceous fern genus “Athyrium”

The oldest fossils assigned to Athyrium (mostly based on the sorus morphology) comprise fronds and spores from the Lower Cretaceous of Northeast Asia. However, most molecular dating suggests that extant Athyrium diverged from its sister genus during the Eocene or later, implying that the Cretaceous fossils probably belong to another polypodiaceous taxon. By examining the sorus morphology of extant genera related to the family Athyriaceae, we found that the primary diagnostic feature for assigning the Cretaceous fossils to Athyrium, i.e., the sorus shape, is common to the entire extant family, or plesiomorphic for the genus. As the fronds are more commonly preserved than the reproductive parts, we compared the fossil frond morphology with those of living taxa of the family that is divided into two types. The Cretaceous fossil we examined here bears the frond’s costal groove characters on adaxial side, which is more closely related to that of the Deparia-clade instead of the clade including Athyrium and other genera of the family. The observation is further confirmed by the cladistic analysis using morphological characters. The systematic position of the Early Cretaceous “Athyrium” was resolved as a stem member of the total Athyriaceae using a tip-dating approach with the Fossilized Birth-Death model in a Bayesian framework. Our study suggests that Early Cretaceous fossils previously assigned to Athyrium require taxonomic revision.