Thermodynamic and structural factors in the removal of bulky DNA adducts by the nucleotide excision repair machinery

The function of the human nucleotide excision repair (NER) apparatus is to remove bulky adducts from damaged DNA. In an effort to gain insights into the molecular mechanisms involved in the recognition and excision of bulky lesions, we investigated a series of site specifically modified oligonucleotides containing single, well-defined polycyclic aromatic hydrocarbon (PAH) diol epoxide-adenine adducts. Covalent adducts derived from the bay region PAH, benzo[a]pyrene, are removed by human NER enzymes in vitro. In contrast, the stereochemically analogous N(6)-dA adducts derived from the topologically different fjord region PAH, benzo[c]phenanthrene, are resistant to repair. The evasion of DNA repair may play a role in the observed higher tumorigenicity of the fjord region PAH diol epoxides. We are elucidating the structural and thermodynamic features of these adducts that may underlie their marked distinction in biologic function, employing high-resolution nuclear magnetic resonance studies, measurements of thermal stabilities of the PAH diol epoxide-modified oligonucleotide duplexes, and molecular dynamics simulations with free energy calculations. Our combined findings suggest that differences in the thermodynamic properties and thermal stabilities are associated with differences in distortions to the DNA induced by the lesions. These structural effects correlate with the differential NER susceptibilities and stem from the intrinsically distinct shapes of the fjord and bay region PAH diol epoxide-N(6)-adenine adducts.     

Plantlet regeneration from subculturable nodular callus of Pinus radiata

An efficient planlet regeneration system via nodular callus formation is described for Pinus radiata. Subculturable nodular callus was induced at its highest frequency (93%) on embryonic explants excised from seeds at an early stage of germination (radicle length 2–5 mm). The optimal medium for nodular callus tissue proliferation was LP basal medium that was modified by reducing the concentration of potassium nitrate to 500 mg l^–1 and supplemented with 22.2 M 6-benzyladenine (BAP) and 2.85 M indole-3-butyric acid (IBA). Bud differentiation from the nodules was achieved by reducing BAP and sucrose concentrations in the culture medium. The maximum frequency of adventitious bud formation occurred on LP basal medium containing 2% sucrose and 0.44 M BAP on which about 61% of the transferred nodules formed buds. During the next 6 weeks of culture on the same cytokinin-free medium multiple shoots elongated from the buds. These shoots were excised and transferred to root initiation medium (RIM2.1), consisting of full-stregth SH macro- and micro-salts, 1000 mg l^–1 myo-inositol, 0.4 mg l^–1 thiamine-HCl, 2% sucrose and a combination of naphthaleneacetic acid (NAA), IBA and BAP at concentrations of 2.69, 4.93 and 0.11 M, respectively. After 5–15 days, root meristems were initiated on the stem bases. The highest rooting frequency was achieved when shoots were treated for 10 days on RIM2.1 medium, before being transferred to half-strength Schenk and Hildebrandt medium with 1% sucrose and without growth regulators for root growth.     

Evaluation of major genetic loci contributing to inbreeding depression for survival and early growth in a selfed family of Pinus taeda

The magnitude of fitness effects at genetic loci causing inbreeding depression at various life stages has been an important question in plant evolution. We used genetic mapping in a selfed family of loblolly pine (Pinus taeda L.) to gain insights on inbreeding depression for early growth and viability. Two quantitative trait loci (QTLs) were identified that explain much of the phenotypic variation in height growth through age 3 and may account for more than 13% inbreeding depression in this family. One of these QTLs maps to the location of cad-nl, a lignin biosynthesis mutation. Both QTLs show evidence of overdominance, although evidence for true versus pseudo-overdominance is inconclusive. Evidence of directional dominance for height growth was noted throughout the genome, suggesting that additional loci may contribute to inbreeding depression. A chlorophyll-deficiency mutation, spf did not appear to be associated with growth effects, but had significant effects on survival through age 3. Previously identified embryonic viability loci had little or no overall effect on germination, survival, or growth. Our results challenge, at least in part, the prevailing hypothesis that inbreeding depression for growth is due to alleles of small effect. However, our data support predictions that loci affecting inbreeding depression are largely stage specific.     

Phosphorus compartmentation in Pinus serotina Michx. (pond pine); observations from in vivo nuclear magnetic resonance spectroscopy

³¹P nuclear magnetic resonance (NMR) spectroscopy was used to estimate the amount of inorganic phosphate (Pi) present in the cytoplasm and vacuole of root tips and subapical root segments of pond pine ( Pinus serotina Michx.). In root tips of seedlings grown with 100 mmol m^–3P (HP) the cytoplasmic Pi content, on a root volume basis, was ≈ 1·5 μ mol cm^–3 and the vacuolar Pi content, on a root volume basis, was ≈ 3·4 μ mol cm^–3. In root tips from Pi starved seedlings the cytoplasmic Pi content, on a root volume basis, was ≈ 0·75 μ mol cm^–3; vacuolar Pi was too low to be reliably estimated. Similar results were obtained with subapical root segments; the Pi concentration in the cytoplasm was maintained at around 2 mol m^–3 while that in the vacuole varied with Pi supply. This work demonstrates for the first time that quantitative measurements of the subcellular compartmentation of Pi can be made in young tissues of a woody species. The results indicate that cytoplasmic Pi levels are maintained across a range of external Pi supplies probably by withdrawing Pi stored in the vacuole.     

长白山自然保护区阔叶红松林林隙干扰状况的研究

 本文研究了长白山自然保护区阔叶红松林林隙干扰的基本规律,得到了描述林隙干扰状况的一些重要参数。结果表明扩展林隙在阔叶红松林中所占的面积比例是27.36％,而实际林隙所占的面积比例为13.05％,林隙干扰的频率每年约为0.15％;林隙的分布格局是均匀式的。形成林隙最重要的方式是掘根风倒,其次为干基折断;大多数的林隙都是由1～4株形成木形成的,林隙形成木主要是由红松、水曲柳、蒙古栎和紫椴组成;阔叶红松林的主林层乔木在直径为40～60cm和高度为25～30m时,形成林隙的可能性最大。     

EVALUATING THE IMPACT OF INSECT COMMUNITY ON PINE CATERPILLAR DENSITY IN DIFFERENT STAND CONDITIONS

Abstract  Natural enemies play an important role in inhibiting population growth of pine caterpillar, but they are difficult to be used in systematic management models. This paper attempts to use some forest stand factors to substitute the effect of natural enemies, which could be used in management models. Through the studies from more than 200 stand plots with different stand conditions in Qu County, Changshan County, and Longyou County of Zhejiang Province, 16 predominant species groups from insect community were selected, and the canonical correlation coefficient between the diversity index, species number, individual number of predominant species and the stand factors was analyzed. The results indicated that the canopy density and ground vegetation were the key stand factors for characterizing the function of insect community. The forest area was divided into four types according to the variation of canopy and vegetation conditions by using cluster analysis. The regression models between the rate of variation of pine caterpillar density and the forest factors including canopy density and vegetation covers were developed in each type of forests. There were significant differences in diversity index, species number, individual number of insect community and population density of pine caterpillar among four types of forests, and correlation coefficients of the four regression models were rather high ( r =0. 924 — 0. 964). This means that the classification of the forest stands is reasonable and the stand factors can characterize the effect of natural enemies in practice.     

Immunoaffinity columns for isolation of abscisic acid in conifer seedlings

Spleen cells of mice immunized with cis, trans (±) abscisic acid (ABA) conjugated to bovine serum albumin (BSA) were fused with myeloma cells to produce hybridomas. Hybridomas secreting antibodies to cis, trans (+) ABA were detected by enzyme-linked immunoassay and injected into the peritoneal cavity of mice to produce ascites fluid. Antibodies purified by size-exclusion chromatography were linked to cyanogen bromide-activated Sepharose beads and used to prepare immunoaffinity columns (IAC). Semi-purified conifer seedling (Douglas-fir [ Pseudotsuga menziesii (Mirb) Franco] lodgepole pine ( Pinus contorta Dougl), cedar ( Thuja plicata D. Don), and spruce [ Picea glauca (Moench) Voss)]) extracts were passed through IAC, washed thoroughly with water and then eluted with methanol. ABA in the methanol eluate was analysed by high performance liquid chromatography with UV detection. UV absorption of extracts before and after purification through IAC indicated an excellent purification of extract by IAC. The identity of the ABA peak was confirmed by gas chromatography-mass spectrometry.     

Avian top predator and the landscape of fear: responses of mammalian mesopredators to risk imposed by the golden eagle

Top predators may induce extensive cascading effects on lower trophic levels, for example, through intraguild predation (IGP). The impacts of both mammalian and avian top predators on species of the same class have been extensively studied, but the effects of the latter upon mammalian mesopredators are not yet as well known. We examined the impact of the predation risk imposed by a large avian predator, the golden eagle (Aquila chrysaetos, L.), on its potential mammalian mesopredator prey, the red fox (Vulpes vulpes, L.), and the pine marten (Martes martes, L.). The study combined 23 years of countrywide data from nesting records of eagles and wildlife track counts of mesopredators in Finland, northern Europe. The predation risk of the golden eagle was modeled as a function of territory density, density of fledglings produced, and distance to nearest active eagle territory, with the expectation that a high predation risk would reduce the abundances of smaller sized pine martens in particular. Red foxes appeared not to suffer from eagle predation, being in fact most numerous close to eagle nests and in areas with more eagle territories. This is likely due to similar prey preferences of the two predators and the larger size of foxes enabling them to escape eagle predation risk. Somewhat contrary to our prediction, the abundance of pine martens increased from low to intermediate territory density and at close proximity to eagle nests, possibly because of similar habitat preferences of martens and eagles. We found a slightly decreasing trend of marten abundance at high territory density, which could indicate that the response in marten populations is dependent on eagle density. However, more research is needed to better establish whether mesopredators are intimidated or predated by golden eagles, and whether such effects could in turn cascade to lower trophic levels, benefitting herbivorous species.     

Effects of pine wilt disease invasion on soil properties and Masson pine forest communities in the Three Gorges reservoir region,China

Pine wilt disease (PWD) has caused significant Masson pine mortality in the Three Gorges reservoir region in central China. In this study, five uniform Masson pine stand types infected by PWD were selected and surveyed on slopes and aspects with similar environmental conditions. In sites that had been infected, soil bulk density was reduced, and the difference among the groups was statistically significant (P < 0.05) at the 0–10 cm and 10–20 cm soil layers, but not at 20–40 cm. Other soil water‐related physical properties, excluding noncapillary porosity, significantly differed among the groups in all soil layers. Additionally, the values of available phosphorus, sodium, potassium, calcium, and magnesium were higher in the invaded stands, but the total nitrogen and organic matter contents were lower. Masson pine does not become reestablished following PWD‐induced mortality but is instead replaced by broad‐leaved tree species. Among the 19 examined environmental variables, five were found to be significantly related with the ordination of plant community structure: Masson pine stumps (MPS), K⁺, capillary water holding capacity (CWHC), capillary porosity (CP), and soil water content (SWC). Among these factors, the plant community structure was principally related to MPS and K⁺. The findings of this study show that the outbreak of PWD has impacted Masson pine forest soil properties and altered forest community composition. The disease is negatively related with the presence of Masson pine and positively associated with that of broad‐leaved tree species.