Allometric analysis of Sitka spruce branches: mechanical versus hydraulic design principles

The geometry of tree branches can have considerable effect on their efficiency in terms of carbon export per unit carbon investment in structure. The purpose of this study was to evaluate different design criteria using data describing the form of Picea sitchensis branches. Allometric analysis of the data suggests that resources are distributed to favour shoots with the greatest opportunity for extension into new space, with priority to the extension of the leader. The distribution of allometric relations of links (branch elements) was tested against two models: the pipe model, based on hydraulic transport requirements, and a static load model based on the requirement of shoots to provide mechanical resistance to static loads. Static load resistance required the load parameter to be proportional to the link radius raised to the power of 4. This was shown to be true within a 95% statistical confidence limit. The pipe model would require total distal length to be proportional to link radius squared but the measured branches did not conform well to this model. The comparison suggests that the diameters of branch elements were more related to the requirements for mechanical load. The cost of following a hydraulic design principle (the pipe model) in terms of mechanical efficiency was estimated and suggested that the pipe model branch would not be mechanically compromised but would use structural resources inefficiently. Resource allocation among branch elements was found to be consistent with mechanical stability criteria but also indicated the possibility of allocation based on other criteria, such as potential light interception by shoots. The evidence suggests that whilst branch topology increments by reiteration of units of morphogenesis, the geometry follows a functional design pattern.     

Isolation and purification of functional total RNA from blue-grained wheat endosperm tissues containing high levels of starches and flavonoids

Isolation of intact, functional total RNA from blue-grained wheat endosperms containing high levels of starches, polysaccharides, and flavonoids was extremely difficult using traditional methods. We describe here a modified SDS/phenol method that can be used to isolate total RNA from blue-grained wheat endosperms. This method solved the problems of RNA degradation, contamination, and low yield due to binding and/or co-precipitation with starches, polysaccharides, and flavonoids. The isolated total RNA was of high quality and undegraded as determined by spectrophotometric readings and denaturing agarose gel analysis. Quality of the total RNA isolated using our protocol was further assessed by RT-PCR and northern blot hybridization. Using this efficient procedure, 350–400 μg of total RNA was routinely obtained from 1 g of blue-grained wheat seeds.     

Isolation of high-quality RNA from white spruce tissue using a three-stage purification method and subsequent cloning of a transcript from the PR-10 gene family

Isolation of PinmIII cDNA homologues from white spruce tissues required a rigorous RNA extraction protocol developed following assessment of three previously reported conifer RNA extraction protocols. Total RNA was extracted via several purification steps designed to minimize binding of phenolics to nucleic acids and was then subjected to caesium chloride ultra-centrifugation. This procedure produced consistently high-quality, intact RNA from both needles and roots with spectrophotometric ratios of approximately 2.0 for both 260/280 nm and 260/230 nm. Total RNA was obtained from the roots of cold-hardened white spruce seedlings for cDNA library construction. More than 2 million recombinant phage particles were generated from 5 microg of a poly(A)+RNA fraction, and ca. 1.3 million cDNA particles were amplified for storage. Approximately 500,000 primary recombinant clones were screened with an heterologous PinmIII cDNA sequence yielding a unique clone, picgl, that was very similar to members of the PR10 gene family.     

The measurement of woody root decomposition using two methodologies in a Sitka spruce forest ecosystem

Background and aims

The decomposition of roots is an important process in the loss of carbon (C) and the mineralization of nitrogen (N) in forest ecosystems. The early stage decomposition rate of Sitka spruce (Picea sitchensis (Bong.) Carr.) roots was determined using trenched plots and decomposition bags.

Methods

Stumps of known age were trenched and quadrants (50?cm by 50?cm) excavated from randomly selected stumps every 6?months over 4?years, while the mass loss from buried roots in decomposition bags, divided among four diameter categories (ranging from fine roots <2?mm to large roots >50?mm), was monitored for 27?months. The C and N concentrations of excavated samples at different time points were analysed.

Results

The change in total root necromass per quadrant showed a higher decomposition rate-constant (k) of 0.24?±?0.068?year^?1 than the k-value of roots in decomposition bags (0.07?±?0.005?year^?1). The C concentration (47.24?±?0.609?%) did not significantly change with decomposition. There was a significant increase in the C:N ratio of roots in all diameter categories (fine: 48.92?%, small: 38.53?%, medium 11.71?%, large: 76.25?%) after 4?years of decomposition, driven by N loss. Root diameter accounted for 78?% of the variation in the N concentration of roots as decomposition progressed.

Conclusion

Though the trenched plot approach offered an alternative to the more common decomposition bag method for estimating root decomposition, high spatial variation and sampling difficulties may lead to an overestimation of the mass loss from trenched roots, thus, the decomposition bag method gives a more reliable decomposition rate-constant.     

Simple isolation of functional RNA from woody stems of gymnosperms

Stems of woody conifers contain high levels of polysaccharides and phenolic compounds that complicate the isolation of functional RNA from this highly lignified tissue. These difficulties were overcome by pulverizing the frozen tissue with a stainless-steel mortar and by effectively sequestering interfering phenolic compounds with vinylpyrrolidone polymers, thereby minimizing damage to nucleic acids during extraction. RNases were inhibited by aurintricarboxylic acid, and gelatinous polysaccharides were removed by inclusion of a 10% ethanol precipitation step. RNA was then isolated by precipitation with 33% isopropanol and ultracentrifugation onto a cushion of 5.7 M CsCl. Yields of 10 to 20 μg RNA/g FW were obtained from woody stems of several different gymnosperm species, including grand fir (Abies grandis), lodgepole pine (Pinus contorta), loblolly pine (Pinus taeda), Douglas fir (Pseudotsuga menziesii) and Pacific yew (Taxus brevifolia). The high quality of the RNA obtained was determined by UV-spectrophotometry, denaturing agarose gel electrophoresis, andin-vitro translation, and this material was used to construct cDNA libraries.     

Isolation of total RNA from pollens.

Isolation of total RNA from plant materials has been difficult, due to the presence of complex organic substances and the associated pigmentation. In fact, there is a dearth of standardized protocols for isolating total RNA from pollens. To find a simple and reliable method for isolating total RNA from pollen, four methods, viz. phenol/SDS (PS), guanidine HCl (GH), tri-reagent (TR), and modified SDS-betaME (SB) were tested with fresh pollen of Ricinus communis (procured at -70 degrees C) and pollen dried at 30-37 degrees C. The quality and quantity of RNA was superior for the material processed at -70 degrees C. SB gave the highest RNA yield (2.35 mg/g, OD260/280 >2.0), compared to other methods. The results obtained by the SB method were found to be comparable with the widely used tri-reagent method. This was validated with other pollens of Imperata cylindrica and Xanthium strumarium. The yield obtained from graded amounts of pollen was consistent with SB, compared to the TR method. The RNA isolated by SB gave good quality mRNA for synthesizing cDNA. The SDS-betaME method is simple, efficient, and uses less expensive reagents. Hence, we recommend the modified SDS-betaME method for isolating total RNA from pollens.     

Isolation of total RNA from baker's yeast

A simple method of production of total RNA from baker's yeast was developed. Total RNA was isolated from yeast (Saccharomyces cerevisiae) biomass using lysis with sodium dodecyl sulfate at 100 degrees C for 40-60 min and subsequent precipitation of the target product with 3 M NaCl. The preparation obtained was characterized in detail: yield of total RNA from 1 kg of pressed yeast, 9.25 g; optical density at 260 nm of 1 mg of RNA dissolved in 1 ml of water, 20.2 U; content of the acid-soluble fraction, 2.02%; and protein content, 1.8%. Total tRNA was isolated from total RNA by fractional precipitation with ethanol followed by gel filtration.     

Isolation of functional RNA from cactus fruit

Isolating RNA from cactus fruit is notoriously difficult because the fruit contains high amounts of secondary metabolites and polysaccharides. These form insoluble complexes with nucleic acids during extraction and can inhibit enzyme action. Our procedure allows for the extraction of RNA from finely ground tissue. The RNA we isolated was of high quality and undegraded, as gauged by spectrophotometry and electrophoresis in agarose gels. Quality was further assessed through use of the RNA in RT-PCR and northern blot analysis, indicating that it could be used to construct cDNA libraries. Using this modified protocol, 90μg of RNA was routinely obtained from 1 g of dried cactus fruit. Isolating RNA from other polysaccharide-rich fruits was also possible.     

Rooting of Sitka spruce cuttings from hedges,and after chilling

Summary Four clones of Sitka spruce (Picea sitchensis (Bong.) Carr.) were established from cuttings of two and four-year old material in 1968. Within each clone half the trees were randomly hedged at 1 m in 1977. Cuttings from hedges rooted more freely than cuttings from the lower crown which, in turn, rooted more readily than upper crown cuttings. Rooting occurred most readily during January and early February. Concentrations of sugars in stems and foliage showed little correlation with rooting.Chilling must be completed for most rapid rooting of dormant Sitka spruce cuttings and this requirement can be satisfied by 10 weeks at 2°C.     

Methods to extract NAD+-malate dehydrogenase efficiently from white spruce needles

The spectrophotometrically-determined activity of NAD⁺-malate dehydrogenase (MDH, EC 1.1.1.37) from white spruce [ Picea glauca (Moench) Voss] needles was assayed with NADH and oxaloacetate. Activity was very low when extracted with only acetate buffer (pH 5.4), phosphate buffer (pH 6.8), or Tris-HCl buffer (pH 8.0). However, activity increased from 1 to over 200 μmol (g dry weight)^-1 min^-1 with the addition of polymers such as polyvinylpyrrolidone (PVP) and polyethylene glycol (PEG) and the detergents, Tween 80, Tergitol 15-S-9 and Triton X-100. Best activity was observed when extracted in a buffer at pH 6.8 and with 1% (v/v) for the three detergents and PEG, and 6% (w/v) for PVP.
MDH activity decreased with age of the needles on the tree. Six-year-old needles contained only about one-fifth of the activity of current year, fully-expanded needles. The main decrease in enzyme activity was observed in one-year-old needles. Protein content obtained from needles extracted with just phosphate buffer (pH 6.8) was very low, but increased greatly when the above chemicals were added to the buffer. In contrast with needles, extracts of vegetative buds contained much higher levels of MDH and protein when extracted with only phosphate buffer (pH 6.8). Although MDH activity in needle extracts declined with storage of the extracts at 4°C in the dark for 6 days, the decrease was least for buffers containing a combination of different protective agents.     

Phytoliths of six woody species important in the Carpathians: characteristic phytoliths in Norway spruce needles

Vegetation History and Archaeobotany - Phytoliths—also known as plant opals—are preserved in soils and sediments and have taxonomical relevance, therefore phytoliths can be fingerprints...     

Isolation and partial purification of ceruloplasmin messenger RNA from rat liver

Partially purified ceruloplasmin mRNA was isolated using indirect immunoprecipitation of rat liver polysomes and poly(U)-Sepharose chromatography of polysomal RNA. This RNA programmed the synthesis of ceruloplasmin polypeptides in a cell-free system from mitochondria. Immunochemical analysis of the translation products revealed a 40-fold enrichment of the ceruloplasmin mRNA activity. The purified ceruloplasmin mRNA migrated as a major homogeneous component with an apparent molecular weight about 1×10⁶ daltons in polyacrylamide gels containing sodium dodecyl sulfate. The immunoprecipitated products of the cell-free translation had molecular weights in the range 4.5–5.4×10⁴ daltons as estimated by gel-electrophoresis under denaturating conditions. These values approach the weight of the half-molecule of native ceruloplasmin.     

Specific polyadenylation and purification of total messenger RNA from Escherichia coli.

Obtaining pure mRNA preparations from prokaryotes has been difficult, if not impossible, for want of a poly(A) tail on these messages. We have used poly(A) polymerase from yeast to effect specific polyadenylation of Escherichia coli polysomal mRNA in the presence of magnesium and manganese. The polyadenylated total mRNA, which could be subsequently purified by binding to and elution from oligo(dT) beads, had a size range of 0.4-4.0 kb. We have used hybridization to a specific plasmid-encoded gene to further confirm that the polyadenylated species represented mRNA. Withdrawal of Mg2+ from the polyadenylation reaction resulted in addition of poly(A) to 16S rRNA despite the presence of Mn2+, indicating the vital role of Mg2+ in maintaining the native structure of polysomes. Complete dissociation of polysomes into ribosomal subunits resulted in quantitative polyadenylation of both 16S and 23S rRNA species. Chromosomal lacZ gene-derived messages were quantitatively recovered in the oligo(dT)-bound fraction, as demonstrated by RT-PCR analysis. Potential advantages that accrue from the availability of pure total mRNA from prokaryotes is discussed.     

Negative stain in wax tubes from the surface of Sitka spruce leaves

Summary Carbon replicas and scanning electron micrographs of wax outgrowths on some leaf surfaces have not shown conclusively whether the outgrowths are tubes or solid rods. Some workers have suggested that they are solid rods. We find that negative stains will penetrate into a cavity in the centre of wax outgrowths on leaves of Sitka spruce (Picea sitchensis Bong. Carr) and Tulipa kaufmanniana Elliot. Thus these outgrowths appear to be tubes.