Friedreich's ataxia (GAA)n•(TTC)n repeats strongly stimulate mitotic crossovers in Saccharomyces cerevisae

Expansions of trinucleotide GAA•TTC tracts are associated with the human disease Friedreich''s ataxia, and long GAA•TTC tracts elevate genome instability in yeast. We show that tracts of (GAA)₂₃₀•(TTC)₂₃₀ stimulate mitotic crossovers in yeast about 10,000-fold relative to a “normal” DNA sequence; (GAA)_n•(TTC)_n tracts, however, do not significantly elevate meiotic recombination. Most of the mitotic crossovers are associated with a region of non-reciprocal transfer of information (gene conversion). The major class of recombination events stimulated by (GAA)_n•(TTC)_n tracts is a tract-associated double-strand break (DSB) that occurs in unreplicated chromosomes, likely in G1 of the cell cycle. These findings indicate that (GAA)_n•(TTC)_n tracts can be a potent source of loss of heterozygosity in yeast.     

Abundance and degree of dispersion of genomic d(GA) n ·d(TC) n sequences

Summary The abundance of d(GA) _n ·d(TC) _n tracts was determined in genomes of rodents and primates. Dot blot hybridization assays revealed that such tracts constitute 0.40%, 0.30%, and 0.40%, respectively, of the rat, hamster, and mouse genomes, but only 0.07% and 0.05% of the human and monkey genomes. A plaque hybridization assay of rat and human genomic libraries showed that 37% and 16%, respectively, of the recombinant phages in these libraries contain d(GA) _n ·d(TC) _n tracts. A survey of sequences stored in the GenBank data bank showed that a significant fraction of the stored rodent genes (about 2.0%) contain long d(GA) _n ·d(TC) _n tracts (n> 30) with <10% mismatching. The primate genes contain only shorter tracts (n<15) with <10% mismatching. In addition, the rodent and the primate genes contain tracts with larger degrees of mismatching. The chicken, which represents an entirely different branch of the evolutionary tree, was found to be as low in d(GA) _n ·d(TC) _n tracts as the primates. It is suggested that a common ancestor of the rodents has acquired the ability to amplify d(GA) _n ·d(TC) _n tracts.     

Computational investigation of the geometric structures of [(CN)5PtTl(CN)n]n− (n=0, 1, 2 or 3)

[(CN)₅PtTl(CN)_n]ⁿ⁻ (n=0–3, complexes I–IV) have been studied computationally using quasi-relativistic gradient-corrected density functional theory. Good agreement is obtained with previous EXAFS and Raman data for complexes II–IV, but calculations significantly overestimate the PtTl bond length and underestimate ν(PtTl) for complex I. The addition of co-ordinating water molecules to the thallium atom in complexes I–III has little effect on complexes II and III, but significantly shortens the PtTl bond in complex I, bringing it into excellent agreement with experiment. The bond length shortening is traced to intramolecular hydrogen bonding. The total molecular bonding energies of hydrated I and I′ (in which the axial ligands on the thallium and platinum atoms are interchanged) are found to be very similar to one another, suggesting that complex I might exist as a mixture of isomers in solution.     

A Structural Transition in d(AT) n ·d(AT) n Inserts within Superhelical DNA

Abstract

We have constructed plasmids carrying d(AT)_n·d(AT)_n inserts of different lengths. Two- dimensional gel electrophoresis patterns show that an increase in the negative superhelicity of these DNAs brings about a structural transition within the inserts, resulting in a reduction of the superhelical stress. However, this reduction corresponds to the expected values neither for cruciform nor for the Z form. Those DNA topoisomers in which the structural transition had occurred proved to be specifically recognizable by single-strand-specific endonuclease SI, with the cleavage site situated at the centre of the insert. These data, as well as kinetic studies, suggest that the cloned d(AT)_n·d(AT) _n sequences adopt a cruciform rather than the Z-form structure. We discuss plausible reasons of the discrepancy between the observed superhelical stress release and that expected for the transition of the insert to the cruciform state.     

Altered replication in human cells promotes DMPK (CTG)(n) · (CAG)(n) repeat instability

Myotonic dystrophy type 1 (DM1) is associated with expansion of (CTG)(n) · (CAG)(n) trinucleotide repeats (TNRs) in the 3' untranslated region (UTR) of the DMPK gene. Replication origins are cis-acting elements that potentiate TNR instability; therefore, we mapped replication initiation sites and prereplication complex protein binding within the ~10-kb DMPK/SIX5 locus in non-DM1 and DM1 cells. Two origins, IS(DMPK) and IS(SIX5), flanked the (CTG)(n) · (CAG)(n) TNRs in control cells and in DM1 cells. Orc2 and Mcm4 bound near each of the replication initiation sites, but a dramatic change in (CTG)(n) · (CAG)(n) replication polarity was not correlated with TNR expansion. To test whether (CTG)(n) · (CAG)(n) TNRs are cis-acting elements of instability in human cells, model cell lines were created by integration of cassettes containing the c-myc replication origin and (CTG)(n) · (CAG)(n) TNRs in HeLa cells. Replication forks were slowed by (CTG)(n) · (CAG)(n) TNRs in a length-dependent manner independent of replication polarity, implying that expanded (CTG)(n) · (CAG)(n) TNRs lead to replication stress. Consistent with this prediction, TNR instability increased in the HeLa model cells and DM1 cells upon small interfering RNA (siRNA) knockdown of the fork stabilization protein Claspin, Timeless, or Tipin. These results suggest that aberrant DNA replication and TNR instability are linked in DM1 cells.     

Polymorphic microsatellites in nēnē, the endangered Hawaiian goose (Branta sandvicensis)

The nēnē (Branta sandvicensis) is an endangered Hawaiian goose endemic to the Hawaiian Islands. The nēnē nearly went extinct in the mid-19.00s and the majority of the approximately 1300 individuals currently in Hawai'i are descendants from less than 30 birds. The low adult breeding success and juvenile survival is likely due, in part, to inbreeding depression in wild individuals. Thirty-eight microsatellite primer sets developed in nēnē, Canada goose, and waterfowl species provided 8 polymorphic loci. Four of these polymorphic loci exhibited only two alleles, which is likely a reflection of the high inbreeding in this species.     

四川梅花鹿(CAG)n微卫星文库构建

应用Dynal磁珠-生物素标记的微卫星探针与四川梅花鹿基因组酶切片段杂交,捕获200～750 bp含有微卫星序列的DNA片段,连接pMD18-T载体,再转化到感受态细胞JM109中以构建文库.通过PCR方法从(CAG)n文库中筛选阳性克隆,从576个转化子中获得了234个阳性克隆,对其全部进行序列测定,其中73个含有微卫星序列.除获得的目的微卫星序列(CAG)n外,还观察到(AG)n、(AT)n的重复序列.本研究表明,经过优化的磁珠富集法能够稳定、高效地获得四川梅花鹿微卫星标记.     

Microsolvation and hydration enthalpies of CaC2O4(H2O) n (n = 0-16) and C2O4 2-(H2O) n (n = 0-14): an ab initio study

We studied hydrated calcium oxalate and its ions at the restricted Hartree–Fock RHF/6-31G* level of theory. Performing a configurational search seems to improve the fit of the HF/6-31G* level to experimental data. The first solvation shell of calcium oxalate contains 13 water molecules, while the first solvation shell of oxalate ion is formed by 14 water molecules. The first solvation shell of Ca(II) is formed by six water molecules, while the second shell contains five. At 298.15 K, we estimate the asymptotic limits (infinite dilution) of the total standard enthalpies of hydration for Ca(II), oxalate ion and calcium oxalate as ?480.78, –302.78 and –312.73 kcal mol^?1, resp. The dissociation of hydrated calcium oxalate is an endothermic process with an asymptotic limit of +470.84 kcal mol^?1.

Selective isolation of highly polymorphic (dC−dA)n · (dG−dT)n microsatellites by stringent hybridization

We defined a hybridization condition for isolation of clones carrying long (dC−dA)_n · (dG−dT)_n microsatellites from a genomic plasmid library. By using (dC−dA)₂₀ oligonucleotide as a probe and hybridizing under stringent conditions, more than two-thirds of the obtained plasmid carried the repeats that were longer than (dC−dA)₁₄ and higly polymorphic.     

Ab initio investigations on planar (MgO)n clusters (n = 1–5) and their hydrogen adsorption behaviour

Ab initio calculations (B3LYP and PBE-D3) of the structures, stabilities, vibrational, electronic and hydrogen adsorption behaviour of (MgO)_n clusters are performed using 6-311+ + G(d,p) basis set. The planar (MgO)_n clusters are found to be global minima for n ≤ 3 and local minima for n = 4 and 5. In addition, we have also analysed global minimum structures of (MgO)₄ and (MgO)₅. The binding energies suggest that their stabilities increase successively. Vibrational frequencies and IR intensities further support the enhanced stability with an increase in the size of (MgO)_n clusters. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) surfaces are used to explain and discuss the electronic properties. Finally, we have demonstrated hydrogen storage capacity of (MgO)_n clusters, considering hydrogen adsorption on planar as well as global minimum (MgO)₄ and (MgO)₅ clusters. We have noticed that four and five H₂ molecules can be easily adsorbed by (MgO)₄ and (MgO)₅ clusters having adsorption energy of 0.13–0.14 eV with mass ratio of 4.76%. Thus, the present study is expected to motivate further the applications of small clusters for efficient hydrogen energy storage.     

Eolimna martinii n. gen., n. sp. (Bacillariophyceae) aus dem Unter-Oligozän von Sieblos/Rhön im Vergleich mit ähnlichen rezenten Taxa

The laminated sediments of the Lower Oligocene ‘Sieblos-Schichten’ (dysodile and kieselgur-sediments) contain many individuals of a naviculoid diatom species. Formerly this group of diatoms would have been classified without doubt as Navicula (section ‘Minusculae’). After splitting this extremely heterogeneous genus in Navicula sensu stricto and some other homogeneous genera, the pattern of structures of this fossil species does not correspond to any established genus. For that reason this form will be described as the generotype of a new genus Eolimna. Furthermore it became evident that some Recent species (assigned to Navicula) show the same pattern of structures as the new genus Eolimna (generotype: E. martinii) which represents one of the first naviculoid diatoms of limnic origin. The essential criteria of this genus are: comparatively small cells with narrow girdle; simple alveolated rib system; areolae with a hymen in approximately medium position between relatively large sized foramina outside and inside of the valve; a single row of more or less irregular arranged areolae in close position to each other, on one or several of the copulae. The differences to supposed related genera are discussed.     

Mercury contamination in Lake Xolotlán (Managua)

Total mercury was measured in different compartments of Lake Xolotlán's (Managua) ecosystemviz., sediments, water, fish and men. Sediments from 18 localities at 5 depths inside the sediment (5, 10, 15, 20 and 25 cm) contained an average concentration of 0.62 g Hg.g^–1±0.46 at the surface, with extreme values of 0.16 and 1.8 g.g^–1. The highest concentration was observed at 25 cm depth in front of the chlor-alkaly factory (ELPESA). This maximum is associated with the period of highest production of this factory. The highest mercury concentrations in water were also measured close to the discharge of ELPESA,viz. 787 g.Hg^–1 in January and 506 g.g^–1 in April. The mean mercury concentrations measured in the muscles of the most consumed fish were 0.63 g.g^–1±0.22 (extreme values 0.22 and 1.45) inCichlasoma managuense, and 0.07 g.g^–1±0.14 (extreme values 0.004 and 0.63) inC. citrinellum. The concentration in the liver was 0.79 g.g^–1±1.29 inC. managuense and 0.62 g.g^–1±0.44 inC. citrinellum. Human hairs (n=98) of fishermen and their families contained 5.03 g.g^–1±6.2 (extreme values 0.02 and 38.22). The mean concentration measured in men was 6.22 g.g^–1±6.34 (n=58), and in women 3.39 g.g^–1±5.7 (n=40). The average mercury concentration of hairs of workers of ELPESA was 91.24 g.g^–1±156.9 (extreme values 0.46 and 724.53; n=32). We conclude that total mercury levels in the various ecosystem compartments are very high and mercury contamination in the lake may be considered as dangerous for human health.