Isolation of β-Tocopherol from the Root Bark of the Mulberry Tree

Kluyvera citrophila KY7844 enzymatically catalyzed N-acylation of 7-amino-desacetoxycephalosporanic acid with 1-(1H)-tetrazolylacetate methylester to produce 7-[1-(1H)-tetrazolylacetamido]-desacetoxycephalosporanic acid. The product was purified and characterized.     

What Is the Tree of Life?

A universal Tree of Life (TOL) has long been a goal of molecular phylogeneticists, but reticulation at the level of genes and possibly at the levels of cells and species renders any simple interpretation of such a TOL, especially as applied to prokaryotes, problematic.One of the several ways in which microbiology puts the neo-Darwinian synthesis in jeopardy is by the threatening to “uproot the Tree of Life (TOL)” [1]. Lateral gene transfer (LGT) is much more frequent than most biologists would have imagined up until about 20 years ago, so phylogenetic trees based on sequences of different prokaryotic genes are often different. How to tease out from such conflicting data something that might correspond to a single, universal Tree of Life becomes problematic. Moreover, since many important evolutionary transitions involve lineage fusions at one level or another, the aptness of a tree (a pattern of successive bifurcations) as a summary of life’s history is uncertain [2–4].     

Up in the Tree – The Overlooked Richness of Bryophytes and Lichens in Tree Crowns

Assessing diversity is among the major tasks in ecology and conservation science. In ecological and conservation studies, epiphytic cryptogams are usually sampled up to accessible heights in forests. Thus, their diversity, especially of canopy specialists, likely is underestimated. If the proportion of those species differs among forest types, plot-based diversity assessments are biased and may result in misleading conservation recommendations. We sampled bryophytes and lichens in 30 forest plots of 20 m × 20 m in three German regions, considering all substrates, and including epiphytic litter fall. First, the sampling of epiphytic species was restricted to the lower 2 m of trees and shrubs. Then, on one representative tree per plot, we additionally recorded epiphytic species in the crown, using tree climbing techniques. Per tree, on average 54% of lichen and 20% of bryophyte species were overlooked if the crown was not been included. After sampling all substrates per plot, including the bark of all shrubs and trees, still 38% of the lichen and 4% of the bryophyte species were overlooked if the tree crown of the sampled tree was not included. The number of overlooked lichen species varied strongly among regions. Furthermore, the number of overlooked bryophyte and lichen species per plot was higher in European beech than in coniferous stands and increased with increasing diameter at breast height of the sampled tree. Thus, our results indicate a bias of comparative studies which might have led to misleading conservation recommendations of plot-based diversity assessments.     

Root traits of maize seedlings—indicators of nitrogen efficiency?

Due to the high price of fertilizer the input of N for grain maize production must be kept low in many parts of the world. Low input cultivars have been suggested to meet this requirement. Screening of a group of tropical cultivars revealed two high input, two low input and two intermediate cultivars with regard to N utilization. One of the causes of an interaction between genotype and N fertilization might be differences in root morphology. Screening for such differences at an early seedling stage would facilitate the selection for low input varieties. This hypothesis was tested by growing seedlings of the six varieties at different levels of N until the fourth leaf stage. There was no significant interaction between genotypes and N supply. At low and medium N supply, the total seedling biomass was the same but at low N a higher proportion of dry weight was found in the roots. Total biomass was reduced at high N. Low input and intermediate cultivars had higher shoot and root dry weights than did high input cultivars but no significant differences in root surface area were found. Root surface area was greatest at low N. Number and total length of seminal roots were significantly lower for high input varieties which, in combination with a relatively high root surface area, points to an intensive root type.     

Nitrate Assimilation Function of Yellow Lupine Root Nodules?

Low nitrate assimilation activity of the root nodules was demonstrated by assaying the activities of nitrate reductase, glutamate synthetase, glutamate dehydrogenase, and asparagine synthetase as well as the kinetics of ¹⁴C-labeled sucrose incorporation in the amino acids and amides of the cortex and the bacteroid-containing root nodule zones. Irrespective of the exogenous nitrogen concentration (0, 11.2, or 25 mM NO^- ₃), nitrate concentration in the nodules was low as compared to the plant roots, leaves, and stems. This allowed us to propose the presence of structural and/or metabolic barriers in the nodules limiting nitrate transport and assimilation in the nodule.     

Three-dimensional Microorganization of the Soil–Root–Microbe System

Soils contain the greatest reservoir of biodiversity on Earth, and the functionality of the soil ecosystem sustains the rest of the terrestrial biosphere. This functionality results from complex interactions between biological and physical processes that are strongly modulated by the soil physical structure. Using a novel combination of biochemical and biophysical indicators and synchrotron microtomography, we have discovered that soil microbes and plant roots microengineer their habitats by changing the porosity and clustering properties (i.e., spatial correlation) of the soil pores. Our results indicate that biota act to significantly alter their habitat toward a more porous, ordered, and aggregated structure that has important consequences for functional properties, including transport processes. These observations support the hypothesis that the soil–plant–microbe complex is self-organized.     

Is The Amphibian Tree of Life really fatally flawed?

Wiens (2007 , Q. Rev. Biol. 82, 55–56) recently published a severe critique of Frost et al.'s (2006, Bull. Am. Mus. Nat. Hist. 297, 1–370) monographic study of amphibian systematics, concluding that it is “a disaster” and recommending that readers “simply ignore this study”. Beyond the hyperbole, Wiens raised four general objections that he regarded as “fatal flaws”: (1) the sampling design was insufficient for the generic changes made and taxonomic changes were made without including all type species; (2) the nuclear gene most commonly used in amphibian phylogenetics, RAG‐1, was not included, nor were the morphological characters that had justified the older taxonomy; (3) the analytical method employed is questionable because equally weighted parsimony “assumes that all characters are evolving at equal rates”; and (4) the results were at times “clearly erroneous”, as evidenced by the inferred non‐monophyly of marsupial frogs. In this paper we respond to these criticisms. In brief: (1) the study of Frost et al. did not exist in a vacuum and we discussed our evidence and evidence previously obtained by others that documented the non‐monophyletic taxa that we corrected. Beyond that, we agree that all type species should ideally be included, but inclusion of all potentially relevant type species is not feasible in a study of the magnitude of Frost et al. and we contend that this should not prevent progress in the formulation of phylogenetic hypotheses or their application outside of systematics. (2) Rhodopsin, a gene included by Frost et al. is the nuclear gene that is most commonly used in amphibian systematics, not RAG‐1. Regardless, ignoring a study because of the absence of a single locus strikes us as unsound practice. With respect to previously hypothesized morphological synapomorphies, Frost et al. provided a lengthy review of the published evidence for all groups, and this was used to inform taxonomic decisions. We noted that confirming and reconciling all morphological transformation series published among previous studies needed to be done, and we included evidence from the only published data set at that time to explicitly code morphological characters (including a number of traditionally applied synapomorphies from adult morphology) across the bulk of the diversity of amphibians (Haas, 2003, Cladistics 19, 23–90). Moreover, the phylogenetic results of the Frost et al. study were largely consistent with previous morphological and molecular studies and where they differed, this was discussed with reference to the weight of evidence. (3) The claim that equally weighted parsimony assumes that all characters are evolving at equal rates has been shown to be false in both analytical and simulation studies. (4) The claimed “strong support” for marsupial frog monophyly is questionable. Several studies have also found marsupial frogs to be non‐monophyletic. Wiens et al. (2005, Syst. Biol. 54, 719–748) recovered marsupial frogs as monophyletic, but that result was strongly supported only by Bayesian clade confidence values (which are known to overestimate support) and bootstrap support in his parsimony analysis was < 50%. Further, in a more recent parsimony analysis of an expanded data set that included RAG‐1 and the three traditional morphological synapomorphies of marsupial frogs, Wiens et al. (2006, Am. Nat. 168, 579–596) also found them to be non‐monophyletic. Although we attempted to apply the rule of monophyly to the naming of taxonomic groups, our phylogenetic results are largely consistent with conventional views even if not with the taxonomy current at the time of our writing. Most of our taxonomic changes addressed examples of non‐monophyly that had previously been known or suspected (e.g., the non‐monophyly of traditional Hyperoliidae, Microhylidae, Hemiphractinae, Leptodactylidae, Phrynobatrachus, Ranidae, Rana, Bufo; and the placement of Brachycephalus within “Eleutherodactylus”, and Lineatriton within “Pseudoeurycea”), and it is troubling that Wiens and others, as evidenced by recent publications, continue to perpetuate recognition of non‐monophyletic taxonomic groups that so profoundly misrepresent what is known about amphibian phylogeny. © The Willi Hennig Society 2007.     

Activity of β-glucuronidase in Root Tips of Different Types of Transgenic Sugar Beet Plants

Expression of the -glucuronidase (GUS) reporter gene driven by the CaMV 35S, rolC, nos and mas promoters was assessed in the tips of 12 independent clones of transgenic sugar beet (Beta vulgaris) roots. Three questions were addressed: 1) expression pattern specific for a given promoter, 2) expression pattern variability, and 3) relationship between gene expression and cell differentiation. Characteristic patterns of tissue-specific expression were distinguished for each promoter. Striking differences, however, were found between some clones, bearing the same construct. Statistical analysis of the pattern variability proved that the variability is significantly lower within the construct than between constructs. rolC-GUS clones exhibited the lowest and CaMV 35S clones the highest pattern variability. Comparisons between the four promoters showed consistent GUS activity in areas playing a key role in tissue determination (the elongation zone) where cells switch from frequent mitosis and mostly isodiametrical growth, typical for the promeristem, to rapid elongation and differentiation. All of the clones were highly GUS-positive in the elongation zone of stele. Activity was commonly localised in the stele of the maturation zone for CaMV 35S, rolC and mas-GUS clones. CaMV 35S-GUS clones were highly active in the promeristem.     

Evidence of Tree Species’ Range Shifts in a Complex Landscape

Climate change is expected to change the distribution of species. For long-lived, sessile species such as trees, tracking the warming climate depends on seedling colonization of newly favorable areas. We compare the distribution of seedlings and mature trees for all but the rarest tree species in California, Oregon and Washington, United States of America, a large, environmentally diverse region. Across 46 species, the mean annual temperature of the range of seedlings was 0.120°C colder than that of the range of trees (95% confidence interval from 0.096 to 0.144°C). The extremes of the seedling distributions also shifted towards colder temperature than those of mature trees, but the change was less pronounced. Although the mean elevation and mean latitude of the range of seedlings was higher than and north of those of the range of mature trees, elevational and latitudinal shifts run in opposite directions for the majority of the species, reflecting the lack of a direct biological relationship between species’ distributions and those variables. The broad scale, environmental diversity and variety of disturbance regimes and land uses of the study area, the large number and exhaustive sampling of tree species, and the direct causal relationship between the temperature response and a warming climate, provide strong evidence to attribute the observed shifts to climate change.     

Seasonal Variation of δ13C of Four Tree Species: A Biological Integrator of Environmental Variables

Foliar δ13C values, an indicator of long-term intercellular carbon dioxide concentration and, thus,of long-term water use efficiency (WUE) in plants, were measured for Pinus massoniana Lamb., P. elliottii Engelm., Cunninghamia laceolata (Lamb.) Hook., and Schima superba Gardn. et Champ. in a restored forest ecosystem in the Jiazhu River Basin. Seasonal variation and the relationship between the foliar δ13Cvalues of the four species and environmental factors (monthly total precipitation, monthly average air temperature, relative humidity, atmospheric pressure, and monthly total solar radiation and evaporation)were investigated. The monthly δ13C values and WUE of the four species increased with increasing precipitation, air temperature, solar radiation, and evaporation, whereas δ13C values of the four species decreased with increasing relative humidity and atmospheric pressure. Despite significant differences in δ13C seasonal means for the four species, our results demonstrate a significant convergence in the responses of δ13C values and WUE to seasonal variations in environmental factors among the species investigated and that the δ13C signature for each species gives a strong indication of environmental variables.     

Seasonal Variation of δ^13C of Four Tree Species： A Biological Integrator of Environmental Variables

Foliar δ^13C values, an indicator of long-term intercellular carbon dioxide concentration and, thus, of long-term water use efficiency （WUE） in plants, were measured for Pinus massoniana Lamb., P. elliottii Engelm., Cunninghamia laceolata （Lamb.） Hook., and Schima superba Gardn. et Champ. in a restored forest ecosystem in the Jiazhu River Basin. Seasonal variation and the relationship between the foliar δ^13C values of the four species and environmental factors （monthly total precipitation, monthly average air temperature, relative humidity, atmospheric pressure, and monthly total solar radiation and evaporation） were investigated. The monthly δ^13C values and WUE of the four species increased with increasing precipitation, air temperature, solar radiation, and evaporation, whereas δ^13C values of the four species decreased with increasing relative humidity and atmospheric pressure. Despite significant differences in δ^13C seasonal means for the four species, our results demonstrate a significant convergence in the responses of δ^13C values and WUE to seasonal variations in environmental factors among the species investigated and that the δ^13C signature for each species gives a strong indication of environmental variables.     

Gas Transport through the Root–shoot Transition Zone of Rice Tillers

Rice plants (Oryza sativa L.) are mainly cultivated in flooded paddy fields and are thus dependent on oxygen transport through the plant to maintain aerobic root metabolism. This gas transport is effectuated through the aerenchyma of roots and shoots. However, the efficiency of gas transport through the root–shoot transition zone is disputed and there are indications that the root–shoot transition zone may represent one of the largest resistances for gas transport. Therefore, we present gas conductance measurements of the root–shoot transition of individual rice tillers measured using SF₆. SF₆ was detected with a highly advanced laser based photoacoustic detection scheme allowing sensitive, high resolution measurements. In conjunction with these measurements, various plant morphological parameters were quantified. These measurements indeed indicate that the conductance at the root–shoot transition may be much smaller than the conductance of root and shoot aerenchyma within the rice plant. Conductance was strongly correlated to tiller transverse area. After elimination of tiller area from the conductance equation, the resulting permeance coefficient was still correlated to tiller area, but negatively and related to the process of radial tiller expansion. In addition, a decrease in the permeance coefficient was also observed for increasing distance from the plant centre. No correlation was found with tiller type or age of the mother tiller. Incorporation of estimates of the conductance of the root–shoot transition zone coupled to plant morphological parameters will allow considerable improvement of understanding and models on gas transport through plants.     

Complementary Models of Tree Species–Soil Relationships in Old-Growth Temperate Forests

Ecosystem-level studies identify plant–soil feedbacks as important controls on soil nutrient availability, particularly for nitrogen and phosphorus. Although site- and species-specific studies of tree species–soil relationships are relatively common, comparatively fewer studies consider multiple co-existing species in old-growth forests across a range of sites that vary in underlying soil fertility. We characterized patterns in forest floor and mineral soil nutrients associated with four common tree species across eight undisturbed old-growth forests in Oregon, USA, and used two complementary conceptual models to assess tree species–soil relationships. Plant–soil feedbacks that could reinforce site-level differences in nutrient availability were assessed using the context-dependent relationships model, whereby relative species-based differences in each soil nutrient diverged or converged as nutrient status changed across sites. Tree species–soil relationships that did not reflect strong feedbacks were evaluated using a site-independent relationships model, whereby forest floor and surface mineral soil nutrient pools differed consistently by tree species across sites, without variation in deeper mineral soils. We found that the organically cycled elements carbon, nitrogen, and phosphorus exhibited context-dependent differences among species in both forest floor and mineral soil, and most often followed a divergence model, whereby species differences were greatest at high-nutrient sites. These patterns are consistent with theory emphasizing biotic control of these elements through plant–soil feedback mechanisms. Site-independent species differences were strongest for pools of the weatherable cations calcium, magnesium, potassium, as well as phosphorus, in mineral soils. Site-independent species differences in forest floor nutrients were attributable to one species that displayed significantly greater forest floor mass accumulation. Our findings confirm that site-independent and context-dependent tree species-soil relationships occur simultaneously in old-growth temperate forests, with context-dependent relationships strongest for organically cycled elements, and site-independent relationships strongest for weatherable elements with inorganic cycling phases. These models provide complementary explanations for patterns of nutrient accumulation and cycling in mixed-species old-growth temperate forests.     

Genetic Diversity of ‘Ubá’ Mango Tree Using ISSR Markers

In this study, the genetic diversity of ‘Ubá’ mango trees cultivated at the Zona da Mata of Minas Gerais State, Brazil, was assessed, to identify whether there is variability in the plants grown in the region, justifying the mass selection as a breeding method. We used 102 accessions. Leaves were collected for extraction of genomic DNA, which was amplified with nine ISSR primers. The data obtained by the analysis of electrophoretic patterns were arranged in a binary matrix, considering 0 for the absence and 1 for the presence of bands. Based on these data, we performed the analysis of genetic dissimilarity and carried out the cluster analysis by the methods of Tocher and graphical dispersion. The most similar accessions are 144 and 150, both coming from Ubá, while the most divergent ones are 29 and 97, from Visconde do Rio Branco. The grouping by the Tocher method separated the accessions into six groups, 94.1% of which were allocated in the first group and showed that there is no separation of accessions depending on the sampling sites. The 3D scatter plot reinforces this conclusion. There is genetic variability among the accessions of ‘Ubá’ mango tree evaluated. Therefore, it is possible to make mass selection in open-pollinated populations.     

Cross-validation of Non-linear Growth Functions for Modelling Tree Height–Diameter Relationships

Six non-linear growth functions were fitted to tree height–diameter data of ten conifer species collected in the inland Northwest of the United States. The data sets represented a wide range of tree sizes, especially large-sized trees. According to the model statistics, the six growth functions fitted the data equally well, but resulted in different asymptote estimates. The model prediction performance was evaluated using Monte Carlo cross-validation or data splitting for 25-cm diameter classes. All six growth functions yielded similar mean prediction errors for small- and middle-sized trees. For large-sized trees [e.g. DBH (diameter at breast height)>100 cm], however, five of the six growth functions (except the Gompertz function) overestimated tree heights for western white pine, western larch, Douglas-fir, subalpine fir, and ponderosa pine, but underestimated tree heights for western hemlock and Engelmann spruce. Among these five functions, the Korf/Lundqvist and Exponential functions produced larger overestimations. The Schnute, Weibull, and Richards functions were superior in prediction performance to others. The Gompertz function seemed always to underestimate tree heights for large-sized trees.     

Root specific elicitation and exudation of fluorescent β-carbolines in transformed root cultures of Oxalis tuberosa

Stable transformation was achieved in oca (Oxalis tuberosa L.) using an Agrobacterium rhizogenes-mediated system. Transformation frequencies varied with the use of different types of strains of A. rhizogenes and the age of explants. The transfer of rol A gene into the oca genome was confirmed by PCR analysis. In vitro transformed root cultures of oca grown in sterile liquid media induced purplish-blue fluorescence of the culture flask medium when irradiated with UV light. We have previously observed a similar phenomenon, the exudation of fluorescent compounds by the roots of in vitro and field-grown oca plants. Hairy root cultures of O. tuberosa transformed with A. rhizogenes (ATCC-15834) exuded constitutive levels of harmine (7-methoxy-1-methyl-β-carboline) and harmaline (3,4-dihydroharmine), the main fluorescent compounds detected from oca’s root exudates. Transformed roots showed better growth and exudation of harmine and harmaline compared to the untransformed normal roots. Upon elicitation with fungal cell wall elicitors from Phytophthora cinnamoni, the production and exudation of harmine/harmaline was enhanced in both transformed and non-transformed roots. Harmine and harmaline showed a wide range of antimicrobial activity against soil-borne microorganisms. Biologically, these findings suggest that in nature β-carbolines are constitutive antimicrobial compounds released into the rhizosphere upon microbial challenge. Transformed root cultures of oca make a simple, reliable and well-defined model system to investigate the molecular and metabolic exudation of fluorescent β-carboline biosynthesis, and to evaluate the biological significance of the phenomenon of root exudation of fluorescent metabolites.     

Root Morphology and Zn^2＋ Uptake Kinetics of the Zn Hyperaccumulator of Sedum alfredii Hance

Root morphology and Zn^2＋ uptake kinetics of the hyperaccumulating ecotype （HE） and nonhyperaccumulating ecotype （NHE） of Sedum alfredii Hance were investigated using hydroponic methods and the radiotracer flux technique. The results indicate that root length, root surface area, and root volume of NHE decreased significantly with increasing Zn^2＋ concentration in growth media, whereas the root growth of HE was not adversely affected, and was even promoted, by 500μmol/L Zn^2＋. The concentrations of Zn^2＋ in both ecotypes of S. alfredii were positively correlated with root length, root surface area and root volumes, but no such correlation was found for root diameter. The uptake kinetics for ^65Zn^2＋ in roots of both ecotypes of S. alfredii were characterized by a rapid linear phase during the first 6 h and a slower linear phase during the subsequent period of investigation. The concentration-dependent uptake kinetics of the two ecotypes of S. alfredii could be characterized by the Michaelis-Menten equation, with the Vmax for ^65Zn^2＋ influx being threefold greater in HE compared with NHE, indicating that enhanced absorption into the root was one of the mechanisms involved in Zn hyperaccumulation. A significantly larger Vmax value suggested that there was a higher density of Zn transporters per unit membrane area in HE roots.     

Neuroprotective Role of Withania somnifera Root Extract in Maneb–Paraquat Induced Mouse Model of Parkinsonism

Parkinson’s disease (PD) is a neurodegenerative disorder and these days a lot of emphasis is given on the treatment of this disease using herbal medicines. The present study evaluates the neuroprotective effect of Withania somnifera (Ws) root extract on Parkinsonian mice. The mice were divided into three groups; the first group served as control, the second group was given maneb (MB) and paraquat (PQ) and the last group was administered MB–PQ along with Ws root extract for 3, 6 and 9 weeks. The behavioral studies showed a significant improvement in the motor movement patterns and gripping ability of Ws root extract exposed Parkinsonian mice. Tyrosine hydroxylase (TH) immunostaining was reduced in the substantia nigra of MB–PQ exposed mice, while Ws co-exposure restored TH immunostaining significantly. Additionally, our results also demonstrate generation of oxidative stress in the nigrostriatal region of MB–PQ exposed mice. There was a marked decline in the level of catalase and a simultaneous increase in the level of nitrite and lipid peroxidation in Parkinsonian mice. Thus, the Ws root extract have shown to counteract the pro-oxidants and their associated oxidative stress in the PD model studied here. Our results clearly indicate the usefulness of Ws root extract in providing protection against MB–PQ induced nigrostriatal dopaminergic neurodegeneration and marked improvement in the behavioral, anatomical and the biochemical deformities.     

Ameloblastin in Hertwig’s Epithelial Root Sheath Regulates Tooth Root Formation and Development

Tooth root formation begins after the completion of crown morphogenesis. At the end edge of the tooth crown, inner and outer enamel epithelia form Hertwig’s epithelial root sheath (HERS). HERS extends along with dental follicular tissue for root formation. Ameloblastin (AMBN) is an enamel matrix protein secreted by ameloblasts and HERS derived cells. A number of enamel proteins are eliminated in root formation, except for AMBN. AMBN may be related to tooth root formation; however, its role in this process remains unclear. In this study, we found AMBN in the basal portion of HERS of lower first molar in mice, but not at the tip. We designed and synthesized small interfering RNA (siRNA) targeting AMBN based on the mouse sequence. When AMBN siRNA was injected into a prospective mandibular first molar of postnatal day 10 mice, the root became shorter 10 days later. Furthermore, HERS in these mice revealed a multilayered appearance and 5-bromo-2′-deoxyuridine (BrdU) positive cells increased in the outer layers. In vitro experiments, when cells were compared with and without transiently expressing AMBN mRNA, expression of growth suppressor genes such as p21^Cip1 and p27^Kip1 was enhanced without AMBN and BrdU incorporation increased. Thus, AMBN may regulate differentiation state of HERS derived cells. Moreover, our results suggest that the expression of AMBN in HERS functions as a trigger for normal root formation.