Karyotypes of tragopogon (Compositae: Lactuceae)

Karyotypes of 24 diploid (2n=12)Tragopogon species are similar with one long pair of chromosomes (A), two medium-length pairs (B and C), and three short pairs (D, E, and F). These species may be divided into three karyotypic groups: 1) seven species with a satellite on A and on D; 2) 14 species with a satellite on A only; and 3) three species with a satellite on D only. Most species within karyotype groups may be separated from each other either by distinctive features of certain chromosomes or by statistical differences in length of chromosome arms or long arm: short arm ratios of chromosome A. Three tetraploid (2n=24) species had two long pairs (A,A′), four medium-length pairs (B,B′;C,C′), and six short pairs (D,D′;E,E′;F,F′). Suggestions are made as to the putative diploid parents of these presumed allotetraploids.     

LRRC3B gene is frequently epigenetically inactivated in several epithelial malignancies and inhibits cell growth and replication

Chromosome 3 specific NotI microarrays containing 180 NotI linking clones associated with 188 genes were hybridized to NotI representation probes prepared using matched tumor/normal samples from major epithelial cancers: breast (47 pairs), lung (40 pairs) cervical (43 pairs), kidney (34 pairs of clear cell renal cell carcinoma), colon (24 pairs), ovarian (25 pairs) and prostate (18 pairs). In all tested primary tumors (compared to normal controls) methylation and/or deletions was found. For the first time we showed that the gene LRRC3B was frequently methylated and/or deleted in breast carcinoma - 32% of samples, cervical - 35%, lung - 40%, renal - 35%, ovarian - 28%, colon - 33% and prostate cancer - 44%. To check these results bisulfite sequencing using cloned PCR products with representative two breast, one cervical, two renal, two ovarian and two colon cancer samples was performed. In all cases methylation was confirmed. Expression analysis using RT-qPCR showed that LRRC3B is strongly down-regulated at the latest stages of RCC and ovarian cancers. In addition we showed that LRRC3B exhibit strong cell growth inhibiting activity (more than 95%) in colony formation experiments in vitro in KRC/Y renal cell carcinoma line. All these data suggest that LRRC3B gene could be involved in the process of carcinogenesis as a tumor suppressor gene.     

Chromosome studies on capsicum (Solanaceae) I. Karyotype analysis in C. Chacoënse

The somatic chromosomes and karyotypes of two Argentine populations of Capsicum chacoënse A. T. Hunz. have been studied, both of which have 2n=24. The karyotypes are symmetrical, being composed of 11 m paris + one st pair; two pairs of chromosomes are satellied: pairs 1 and 12 in one population and pairs 11 and 12 in the other one. A heteromorphic pair of satellited chromosomes in one individual suggests a spontaneous reciprocal translocation. Results are compared with previous reports for the species and genus. Data show an intraspecific karyotype variation.     

Genome analysis of ground squirrels of the genus Citellus (Rodentia,Sciuridae) II. DNA sequence organization

The organization of the DNA sequences in five specics of Citellus (C. pygmaeus, C. fulvus, C. major, C. parryi and C. undulatus) was determined from the reassociation kineties of DNA fragments of various lengths and the size distribution of SI-nuclease-resistant duplexes of repetitive DNA. Only 15% of the genome of all the species studied consists of short unique and repeated sequences interspersed with a period less than 2 3 kb, whereas the major part of the genome is occupied by much more extensive sequences of two types, moderately long (3–15 kb) and very long (much more than 15 kb). On the basis of the number of moderately long single-copy sequences the species under study are divided into two groups, coinciding with their division into short-tailed and long-tailed ground squirrels: the short-tailed (C. pygmaeus, C. major and C. fulvus) possess far more such sequences (17–24%) than do the long-tailed ones (C. parryi and C. undulatus) (1–7%). The same division is observed in the amount of very long single-copy sequences. The repeated DNA sequences of Citellus vary widely in size, i.e. from 70 up to some thousands of nucleotide pairs, sequences of more than 1200 nucleotide pairs being most common. In addition, part of the repetitions contain between 70 and 150 base pairs. About one-third of C. parryi repeats (10% of the genome) are characterized by such very short sequences whereas their amont is much less in the other Citellus species (1–4% of the genome).     

Autosomal genes of autosomal/X-linked duplicated gene pairs and germ-line proliferation in Caenorhabditis elegans

We report molecular genetic studies of three genes involved in early germ-line proliferation in Caenorhabditis elegans that lend unexpected insight into a germ-line/soma functional separation of autosomal/X-linked duplicated gene pairs. In a genetic screen for germ-line proliferation-defective mutants, we identified mutations in rpl-11.1 (L11 protein of the large ribosomal subunit), pab-1 [a poly(A)-binding protein], and glp-3/eft-3 (an elongation factor 1-α homolog). All three are members of autosome/X gene pairs. Consistent with a germ-line-restricted function of rpl-11.1 and pab-1, mutations in these genes extend life span and cause gigantism. We further examined the RNAi phenotypes of the three sets of rpl genes (rpl-11, rpl-24, and rpl-25) and found that for the two rpl genes with autosomal/X-linked pairs (rpl-11 and rpl-25), zygotic germ-line function is carried by the autosomal copy. Available RNAi results for highly conserved autosomal/X-linked gene pairs suggest that other duplicated genes may follow a similar trend. The three rpl and the pab-1/2 duplications predate the divergence between C. elegans and C. briggsae, while the eft-3/4 duplication appears to have occurred in the lineage to C. elegans after it diverged from C. briggsae. The duplicated C. briggsae orthologs of the three C. elegans autosomal/X-linked gene pairs also display functional differences between paralogs. We present hypotheses for evolutionary mechanisms that may underlie germ-line/soma subfunctionalization of duplicated genes, taking into account the role of X chromosome silencing in the germ line and analogous mammalian phenomena.     

Two new species of mazocraeid monogeneans from Clupanodon punctatus (Temminck & Schlegel) (Clupeiformes: Clupeidae) found in Daya Bay, South China Sea, with the proposal of Chelimazocraes n. g.

Chelimazocraes liaoi n. g., n. sp. and Chelimazocraes ascidiformis n. sp. (Monogenea: Mazocraeidae) are described from the gills of Clupanodon punctatus (Temminck & Schlegel) in Daya Bay (South China Sea). The new genus is characterised by the following features: (i) the haptor is distinctly separated from the body proper, and the arrangement of the clamps is bilaterally symmetrical but longitudinally heteromorphic; (ii) the anterior three pairs of clamps are of the mazocraeid-type, whereas the fourth pair is of a non-mazocraeid type with three sclerites; (iii) all three pairs of clamps are similar in shape but their size gradually becomes smaller from the anterior to the posterior; (iv) the inner spines of the copulatory organ have a similar shape; and (v) the testes are numerous and arranged longitudinally posterior to the ovary. The two new species are easily distinguished from other members of the Mazocraeidae by the unique structure of the fourth pair of clamps; however, there are some noticeable differences between the two species. The major differences are as follows: (i) the body of C. liaoi n. sp. is significantly larger than that of C. ascidiformis n. sp.; (ii) the anterior three pairs of clamps consist of different sclerites in the two species; and (iii) the copulatory organ has one pair of outer spines and 15–16 pieces of inner spines in C. liaoi n. sp. (vs two pairs of outer spines and 22–26 pieces of inner spines in C. ascidiformis n. sp.).     

Genetic analysis and molecular mapping of a novel recessive gene xa34(t) for resistance against Xanthomonas oryzae pv. oryzae

A new bacterial blight recessive resistance gene xa34(t) was identified from the descendant of somatic hybridization between an aus rice cultivar (cv.) BG1222 and susceptible cv. IR24 against Chinese race V (isolate 5226). The isolate was used to test the resistance or susceptibility of F₁ progenies and reciprocal crosses of the parents. The results showed that F₁ progenies appeared susceptibility there were 128R (resistant):378S (susceptible) and 119R:375S plants in F₂ populations derived from two crosses of BG1222/IR24 and IR24/BG1222, respectively, which both calculates into a 1R:3S ratio. 320 pairs of stochastically selected SSR primers were used for genes?? initial mapping. The screened results showed that two SSR markers, RM493 and RM446, found on rice chromosome 1 linked to xa34(t). Linkage analysis showed that these two markers were on both sides of xa34(t) with the genetic distances 4.29 and 3.05?cM, respectively. The other 50 SSR markers in this region were used for genes?? fine mapping. The further results indicated that xa34(t) was mapped to a 1.42?cM genetic region between RM10927 and RM10591. In order to further narrow down the genomic region of xa34(t), 43 of insertion/deletion (Indel) markers (BGID1-43) were designed according to the sequences comparison between japonica and indica rice. Parents?? polymorphic detection and linkage assay showed that the Indel marker BGID25 came closer to the target gene with a 0.4?cM genetic distance. A contig map corresponding to the locus was constructed based on the reference sequences aligned by the xa34(t) linked markers. Consequently, the locus of xa34(t) was defined to a 204?kb interval flanked by markers RM10929 and BGID25.     

Development and characterization of 29 microsatellite markers for Ligumia nasuta (Bivalvia: Unionidae) using an Illumina sequencing approach

Ligumia nasuta (Say, 1817; Eastern Pondmussel) is an imperiled freshwater mussel (Unionidae) in eastern North America. Population declines in the Laurentian Great Lakes resulting from the introduction of dreissenid mussels and habitat destruction in the 20th Century have greatly reduced and limited its distribution. To properly inform restoration and management efforts for L. nasuta, fine-scale genetic analyses must be performed on the remnant populations. This study used Illumina paired-end shotgun sequencing to identify potential microsatellite loci for L. nasuta, utilizing two samples to develop the Illumina paired-end shotgun library. Forty-eight primer pairs were tested on the remaining 24 samples. Twenty-nine of the 48 microsatellite primer sets screened were successfully amplified using 24 L. nasuta samples collected from the Great Lakes watershed. The estimated fragment size ranged from 167 to 445 base-pairs (bp) and the number of alleles per locus varied between 5 and 16 (mean = 9.7). Only five of the loci deviated significantly from Hardy–Weinberg expectations after Bonferroni corrections. The development of these new microsatellite loci will greatly facilitate future genetic studies on L. nasuta.     

Karyotype Analysis of Gossypium arboreum × G. bickii by Genome in situ Hybridization

By using genome in situ hybridization (GISH) on root somatic chromosomes of allotetraploid derived from the cross Gossypium arboreum × G. bickii with genomic DNA (gDNA) of G. bickii as a probe, two sets of chromosomes, consisting of 26 chromosomes each, were easily distinguished from each other by their distinctive hybridization signals. GISH analysis directly proved that the hybrid GarboreumxG. bickii is an allotetraploid amphiploid. The karyotype formula of the species was 2n = 4x = 52 = 46m (4sat) + 6sm (4sat). We identified four pairs of satellites with two pairs in each sub-genome. FISH analysis using 45S rDNA as a probe showed that the cross G. arboreumxG. bickii contained 14 NORs. At least five pairs of chromosomes in the G sub-genome showed double hybridization (red and blue) in their long arms, which indicates that chromatin introgression from the A sub-genome had occurred.     

Physical localization of rRNA genes by fluorescence in situ hybridization (FISH) and analysis of spacer length variants of 45S rRNA (slvs) genes in some species of genus Sesbania

The somatic chromosome numbers 2n = 12 in S. macrantha, S. coerulescens and 2n = 24 in S. simplicuscula were determined, additionally the contradictory chromosome numbers of S. bispinosa (2n = 12, 13, 14, 24) and S. pachycarpa (2n 12, 14) were determined as 2n = 24 and 2n = 14, respectively. The number of 5S rDNA sites in chromosome pair 1 was highly conserved in all the diploid and tetraploid species studied irrespective of their geographic distribution, suggesting that all diploid and tetraploid species/cytotypes of Sesbania analyzed in the present study are in close proximity. Cytogenetic mapping of the 45S multi-gene family was also carried out using fluorescence in situ hybridization. 45S rDNA was consistently located on short or long arms of two sub-metacentric chromosome pairs except on one chromosome pair in S. macrantha and on three chromosome pairs in S. bispinosa and S. cannabina. Out of these nine species, we observed the homogenization of intergenic spacer in six species and find only one spacer length variant (slv) located on one to three chromosome loci. However, three of the species were observed to have two slvs located on two different chromosomes. The species were grouped as per their evolutionary relationship on the basis of the results of the present study.     

A new species of Amphictene (Annelida,Pectinariidae) from the Gulf of Mexico,with a redescription of Amphictene guatemalensis (Nilsson, 1928)

The genus Amphictene is reported for the first time from Mexico. Previous records for America are restricted to Brazil (Amphictene catharinensis) (Grube, 1870), and Guatemala (Amphictene guatemalensis) (Nilsson, 1928). In this paper we describe a new species, Amphictene helenae sp. n., characterized by the presence of three pairs of tentacular cirri, while other species have only two pairs. The new species is closely similar to Amphictene catharinensis, and can be distinguished by the presence of a circular group of glandular papillae inserted between the lines of glandular cirri present from the second segment. Amphictene guatemalensis is redescribed based on type material; it differs from the new species in the presence of two pairs of tentacular cirri on segments 1 and 2, six pairs of glandular cirri on the third segment, and four glandular lobes fused in pairs on the fourth segment.     

Karyotypes of two Antarctic fishes,Notothenia gibberifrons andNotothenia coriiceps neglecta

The chromosomes of two species of Antarctic fishes,Notothenia (Gobionotothen) gibberifrons andNotothenia (Notothenia) coriiceps neglecta, were prepared by the air-drying method at the Polish Antarctic Station “Henryk Arctowski” during the austral summer 1984–1985. ForN. (G.) gibberifrons the diploid number is2n = 46 consisting of 2 metacentric (m) pairs, 1 submetacentric (sm) pair and 20 telocentric (t) or subtelocentric (st) pairs. ForN. (N.) coriiceps neglecta the diploid number is 2n = 22 consisting of 9 m pairs, 1 sm pair and 1st pair. Some aspects of karyological evolution of these fishes are discussed.     

The Host Genotype and Environment Affect Strain Types of Bifidobacterium longum subsp. longum Inhabiting the Intestinal Tracts of Twins

To investigate the influences of host genotype and environment on Bifidobacterium longum subsp. longum inhabiting human intestines at the strain level, six pairs of twins, divided into two groups (children and adults), were recruited. Each group consisted of two monozygotic (MZ) twin pairs and one dizygotic (DZ) twin pair. Child twins had been living together from birth, while adult twins had been living separately for 5 to 10 years. A total of 345 B. longum subsp. longum isolates obtained from 60 fecal samples from these twins were analyzed by multilocus sequence typing (MLST), and 35 sequence types (STs) were finally acquired. Comparison of strains within and between the twin pairs showed that no strains with identical STs were observed between unrelated individuals or within adult DZ twin pairs. Eight STs were found to be monophyletic, existing within MZ twins and child DZ twins. The similarity of strain types within child cotwins was significantly higher than that within adult cotwins, which indicated that environment was one of the important determinants in B. longum subsp. longum strain types inhabiting human intestines. However, although these differences between MZ and DZ twins were observed, it is still difficult to reach an exact conclusion about the impact of host genotype. This is mainly because of the limited number of subjects tested in the present study and the lack of strain types tracing in the same twin pairs from birth until adulthood.     

Chromosomal localization of 45S and 5S rDNA in 14 species and the implications for genome evolution of genus Epimedium

Studying the genome structure of Epimedium has been hindered by the large genomes and uniform karyotypes. Consequently our understanding of the genome organization and evolutionary changes of Epimedium is extremely limited. In the present study, the 45S and 5S rDNA loci of 14 Epimedium species were physically mapped by double-probe FISH for the first time. Results showed the following: (1) Chromosomes I and II of all 14 species examined, except for E. shuichengense, hosted one pair of 45S rDNA sites, respectively. Most of the 45S rDNA sites gave clear signals and were positioned in the distal regions of the short arms. (2) All species studied of section Diphyllon were found to have one pair of 5S rDNA sites localized in the interstitial regions of the long arm of chromosome IV, and the two species of section Epimedium, E. alpinum and E. pubigerum, had two pairs of 5S rDNA sites localized in the interstitial regions of the long arm of chromosomes IV and V, respectively. (3) In section Diphyllon, all species of small flower taxa, except E. shuichengense, had three pairs of 45S rDNA sites, clearly more than species of big flower taxa, except E. davidii, with two pairs of 45S rDNA sites. Based on the 45S and 5S rDNA distribution patterns and other chromosomal morphological characteristics, six pairs of chromosomes can be unambiguously identified in all 14 Epimedium species. The stable differentiation in 45S and 5S rDNA FISH patterns between the two sections suggests that chromosomal rearrangements and transpositional events played a role in the splitting of the two sections, and section Diphyllon may be more primitive than section Epimedium. In the same way, big flower taxa may be more primitive than small flower taxa in section Diphyllon.     

Musculature of the male genitalia of Xylophagus cinctus (De Geer) and relationships within the superfamily Xylophagoidea (Diptera, Brachycera)

There is no general agreement on relationships within Xylophagoidea (Diptera, Brachycera). The musculature of the male genitalia of Xylophagus cinctus (De Geer) (Xylophagidae, the most primitive family of Brachycera) is described and compared with that of some other Xylophagoidea: Exeretonevridae (Exeretonevra angustifrons Hardy), Coenomyiidae (Anacanthaspis biafasciata Röder), and Rhagionidae (Rhagio montanus Becker, Chrysopilus dives Loew, and Ch. helvolus Meigen) discussed earlier (Ovtshinnikova, 1989, 1998; Palmer et al., 2000). In spite of the differences in the structure of the genital sclerites, Xylophagidae possess all the muscles found in Coenomyiidae and Rhagionidae. The musculature of the male genitalia of Xylophagus cinctus includes two muscle pairs of the aedeagus sheath (M1 and M2); three muscle pairs of the ejaculatory complex (M30, M31, and M32); one muscle pair of the gonocoxites (M33); two muscle pairs of the gonostyli (M27 and M28); one muscle pair of the proctiger (M21), one muscle pair of the cerci (M29); two pairs of the tergosternal muscles (M5 ¹ and M5 ²); and two pairs of the pregenital muscles (M18 and M19). Muscles of the family Exeretonevridae are mostly the same, except for the muscles of the cerci M29, proctiger M29, and pregenital muscles M18 and M19, that are subdivided into two parts. This fact and also a different degree of the development of muscles M32 and M5 ² clearly distinguish Exeretonevridae from closely related families. The attachment places of the muscles of the aedeagus sheath M2 and of the gonostyli M28, as well as the split character of the tergosternal muscle pair M5 ¹ makes it possible to distinguish two sister groups, Xylophagidae plus Exeretonevridae, versus Coenomyiidae plus Rhagionidae. It should be noted that the muscles of the male genitalia of Xylophagidae, Exeretonevridae, Coenomyiidae, and Rhagionidae possess similar plesiomorphic characters, and these families should be united into the superfamily Xylophagoidea. This superfamily is the most primitive superfamily of Brachycera Orthorrhapha and possesses the most stable set and arrangement of male genital muscles within the entire suborder. An improved dendrogram of the phylogenetic relationships between the known groups of Xylophagoidea is proposed on the basis of the structure of male genital muscles.     

Analysis of the myogenic lineage in chick embryos: I. Studies on the terminal cell division

An antibody prepared against the MM isozyme of creatine phosphokinase (M-CK) stained multinucleated myotubes and post-mitotic mononucleated myoblasts in mass cultures of myogenic cells taken from the breast muscles of 11-day chick embryos. No cycling cells bound the antibody. Single cells isolated either directly from the embryo or from mass cultures were seeded at clonal density and allowed to undergo one division. The resulting pairs of cells were stained with the antibody and were scored as (a) both members of the pair M-CK⁺; (b) both M-CK^?; or (c) mixed (one M-CK⁺ and one M-CK^?). No mixed pairs were observed. Conditioned medium did not induce all myogenic pairs to differentiate and growth medium did not keep myogenic pairs in the cell cycle. About 10% of clonal pairs established from 10 h cultures were M-CK⁺, while about 27% of pairs established from 30 h mass cultures were M-CK⁺. These results indicate that (1) the myogenic lineage ends in a symmetrical division whose products are two post-mitotic M-CK⁺ cells; (2) the expression of the muscle phenotype is not determined exclusively by the environment; (3) the terminal cells are the product of an intrinsic program or cell lineage in which only the last cells can synthesize muscle-specific proteins.     

Four base recognition by triplex-forming oligonucleotides at physiological pH

We have achieved recognition of all 4 bp by triple helix formation at physiological pH, using triplex-forming oligonucleotides that contain four different synthetic nucleotides. BAU [2′-aminoethoxy-5-(3-aminoprop-1-ynyl)uridine] recognizes AT base pairs with high affinity, ^MeP (3-methyl-2 aminopyridine) binds to GC at higher pHs than cytosine, while ^APP (6-(3-aminopropyl)-7-methyl-3H-pyrrolo[2,3-d]pyrimidin-2(7H)-one) and S [N-(4-(3-acetamidophenyl)thiazol-2-yl-acetamide)] bind to CG and TA base pairs, respectively. Fluorescence melting and DNase I footprinting demonstrate successful triplex formation at a 19mer oligopurine sequence that contains two CG and two TA interruptions. The complexes are pH dependent, but are still stable at pH 7.0. BAU, ^MeP and ^APP retain considerable selectivity, and single base pair changes opposite these residues cause a large reduction in affinity. In contrast, S is less selective and tolerates CG pairs as well as TA.