Triple Helix Binding of Oligodeoxyribonucleotides Containing 8-Oxo-2′-deoxyadenosine

Abstract

Formation of a triple helix between an oligodeoxyribonucleotide containing 8-oxo-2′-deoxyadenosine and a DNA duplex target was studied as a function of pH. Above pH 7.4, the triple helix with the 8-oxo-2′-deoxyadenosine was more stable than the complex with an analogous oligodeoxyribonucleotide containing deoxycytidine instead of 8-oxo-2′-deoxyadenosine.     

Thermal sensitivity of heart rate and insensitivity of blood pressure in the Antarctic nototheniid fish <Emphasis Type="Italic">Pagothenia borchgrevinki</Emphasis>

The Antarctic notothenioids are among the most stenothermal of fishes, well adapted to their stable, cold and icy environment. The current study set out to investigate the thermal sensitivity/insensitivity of heart rate and ventral aortic blood pressure of the Antarctic nototheniid fish Pagothenia borchgrevinki over a range of temperatures. The heart rate increased rapidly from –1 to 6°C (Q₁₀=2.0–3.3), but was relatively insensitive to temperature above the ~6°C lethal limit of the species (Q₁₀=1.2). The increase in heart rate from –1 to 6°C was the result of a 45% increase in excitatory adrenergic tone, masking a 37% increase in inhibitory cholinergic tone. Ventral aortic pressure was regulated well above the lethal limit, up to at least 10°C. With the return of the fish to environmental temperatures, the heart rate rapidly decreased back to control levels, while ventral aortic pressure increased and remained elevated for over an hour following a 6°C exposure.     

Identification of differentially methylated markers among cytogenetic risk groups of acute myeloid leukemia

Aberrant DNA methylation is known to occur in cancer, including hematological malignancies such as acute myeloid leukemia (AML). However, less is known about whether specific methylation profiles characterize specific subcategories of AML. We examined this issue by using comprehensive high-throughput array-based relative methylation analysis (CHARM) to compare methylation profiles among patients in different AML cytogenetic risk groups. We found distinct profiles in each group, with the high-risk group showing overall increased methylation compared with low- and mid-risk groups. The differentially methylated regions (DMRs) distinguishing cytogenetic risk groups of AML were enriched in the CpG island shores. Specific risk-group associated DMRs were located near genes previously known to play a role in AML or other malignancies, such as MN1, UHRF1, HOXB3, and HOXB4, as well as TRIM71, the function of which in cancer is not well characterized. These findings were verified by quantitative bisulfite pyrosequencing and by comparison with results available at the TCGA cancer genome browser. To explore the potential biological significance of the observed methylation changes, we correlated our findings with gene expression data available through the TCGA database. The results showed that decreased methylation at HOXB3 and HOXB4 was associated with increased gene expression of both HOXB genes specific to the mid-risk AML, while increased DNA methylation at DCC distinctive to the high-risk AML was associated with increased gene expression. Our results suggest that the differential impact of cytogenetic changes on AML prognosis may, in part, be mediated by changes in methylation.     

Opportunities for Nonnative Ecological Replacements in Ecosystem Restoration

Translocations can take a variety of forms, and there is considerable debate as to what defines an acceptable translocation. This is particularly so if a proposal suggests moving a species beyond its natural range, which might be necessary for conservation purposes if habitat within the natural range is extensively modified. An extension of this approach is to use closely related ecological analogs to replace extinct species. This approach is controversial, and opportunities to do so will be rare, particularly for vertebrate species, but the use of ecological analogs is not without precedent, and ultimately will provide for more complete ecological restoration. We discuss the current use of ecological analogs to replace extinct species and conclude with a rare opportunity to replace the extinct New Zealand quail Coturnix novaezelandiae with the extant Australian brown quail Coturnix ypsilophora.     

Effects of Rewarding and Unrewarding Experiences on the Response to Host-induced Plant Odors of the Generalist Parasitoid <Emphasis Type="BoldItalic">Cotesia marginiventris</Emphasis> (Hymenoptera: Braconidae)

Associative learning is known to modify foraging behavior in numerous parasitic wasps. This is in agreement with optimal foraging theory, which predicts that the wasps will adapt their responses to specific cues in accordance with the rewards they receive while perceiving these cues. Indeed, the generalist parasitoid Cotesia marginiventris shows increased attraction to a specific plant odor after perceiving this odor during contact with hosts. This positive associative learning is common among many parasitoids, but little is known about the effects of unrewarding host searching events on the attractiveness of odors. To study this, preferences of female C. marginiventris for herbivore-induced odors of three plant species were tested in a six-arm olfactometer after the wasps perceived one of these odors either i) without contacting any caterpillars, ii) while contacting the host caterpillar Spodoptera littoralis, or iii) while contacting the non-host caterpillar Pieris rapae. The results confirm the effects of positive associative learning, but showed no changes in innate responses to the host-induced odors after “negative” experiences. Hence, a positive association is made during an encounter with hosts, but unsuccessful host-foraging experiences do not necessarily lead to avoidance learning in this generalist parasitoid.     

Structure of the cyanobacterial Magnesium Chelatase H subunit determined by single particle reconstruction and small-angle X-ray scattering

The biosynthesis of chlorophyll, an essential cofactor for photosynthesis, requires the ATP-dependent insertion of Mg²⁺ into protoporphyrin IX catalyzed by the multisubunit enzyme magnesium chelatase. This enzyme complex consists of the I subunit, an ATPase that forms a complex with the D subunit, and an H subunit that binds both the protoporphyrin substrate and the magnesium protoporphyrin product. In this study we used electron microscopy and small-angle x-ray scattering to investigate the structure of the magnesium chelatase H subunit, ChlH, from the thermophilic cyanobacterium Thermosynechococcus elongatus. Single particle reconstruction of negatively stained apo-ChlH and Chl-porphyrin proteins was used to reconstitute three-dimensional structures to a resolution of ∼30 Å. ChlH is a large, 148-kDa protein of 1326 residues, forming a cage-like assembly comprising the majority of the structure, attached to a globular N-terminal domain of ∼16 kDa by a narrow linker region. This N-terminal domain is adjacent to a 5 nm-diameter opening in the structure that allows access to a cavity. Small-angle x-ray scattering analysis of ChlH, performed on soluble, catalytically active ChlH, verifies the presence of two domains and their relative sizes. Our results provide a basis for the multiple regulatory and catalytic functions of ChlH of oxygenic photosynthetic organisms and for a chaperoning function that sequesters the enzyme-bound magnesium protoporphyrin product prior to its delivery to the next enzyme in the chlorophyll biosynthetic pathway, magnesium protoporphyrin methyltransferase.     

Distribution of insertion element IS1 in natural isolates of Escherichia coli

Total DNAs from twelve natural isolates of Escherichia coli from animals and humans were examined by hybridization with a probe for IS1. Considerable variation in copy number was found. In the case of two strains isolated from the same individual, one strain contained no copies of IS1 and the other, much greater than 30. Evidence was also obtained for the existence of IS1-like elements (iso-IS1s) of greater than 15% sequence divergence relative to the IS1 from antibiotic resistance plasmid R100.     

The peptide motif of the single dominantly expressed class I molecule of the chicken MHC can explain the response to a molecular defined vaccine of infectious bursal disease virus (IBDV)

In contrast to typical mammals, the chicken MHC (the BF-BL region of the B locus) has strong genetic associations with resistance and susceptibility to infectious pathogens as well as responses to vaccines. We have shown that the chicken MHC encodes a single dominantly expressed class I molecule whose peptide-binding motifs can determine resistance to viral pathogens, such as Rous sarcoma virus and Marek’s disease virus. In this report, we examine the response to a molecular defined vaccine, fp-IBD1, which consists of a fowlpox virus vector carrying the VP2 gene of infectious bursal disease virus (IBDV) fused with β-galactosidase. We vaccinated parental lines and two backcross families with fp-IBD1, challenged with the virulent IBDV strain F52/70, and measured damage to the bursa. We found that the MHC haplotype B15 from line 15I confers no protection, whereas B2 from line 6₁ and B12 from line C determine protection, although another locus from line 6₁ was also important. Using our peptide motifs, we found that many more peptides from VP2 were predicted to bind to the dominantly expressed class I molecule BF2*1201 than BF2*1501. Moreover, most of the peptides predicted to bind BF2*1201 did in fact bind, while none bound BF2*1501. Using peptide vaccination, we identified one B12 peptide that conferred protection to challenge, as assessed by bursal damage and viremia. Thus, we show the strong genetic association of the chicken MHC to a T cell vaccine can be explained by peptide presentation by the single dominantly expressed class I molecule.     

NEUROTRANSMITTER UPTAKE INTO SLICES OF RAT CEREBRAL CORTEX IN VITRO: EFFECT OF SLICE SIZE

Abstract— The uptake of [¹⁴C]GABA, [¹⁴C]taurine, [³H] β -alanine and [¹⁴C]dopamine was compared in slices of rat cerebral cortex of three different sizes (0.1 × 0.1 × 2 mm, 0.2 × 0.2 × 2 mm and 0.4 × 0.4 × 2 mm prepared with a mechanical tissue chopper). [¹⁴C]Taurine and [³H] β -alanine uptake increased whereas [¹⁴C]GABA uptake decreased with increasing slice size. [¹⁴C]Dopamine uptake was optimal in 0.2 × 0.2 × 2 mm slices. Increasing slice size was shown to decrease inhibition of [³H] β -alanine and [¹⁴C]GABA uptake by l -2,4-diaminobutyric acid. Lactate dehydrogenase activity increased with increasing slice size indicating decreased tissue damage or increased cellular integrity. The possibility that varying slice size can be used to distinguish between neuronal and glial uptake is discussed. It is suggested that taurine uptake in the cerebral cortex is predominantly glial.