Rapid detection of arbuscular mycorrhizae in roots and soil of an intensively managed turfgrass system by PCR amplification of small subunit rDNA

 Arbuscular mycorrhizal fungi (AMF) were detected in uninoculated soil and roots of turfgrass (Agrostis palustris) by direct extraction and PCR amplification of the small subunit rRNA gene. Sequence analysis of the cloned PCR product confirmed the identity of the amplified DNA as an AMF sequence having 95% identity to Glomus intraradices. The sensitivity of the method was gauged by comparison with the most probable number analysis of infective propagules in an intensively managed turfgrass system having 56 propagules per 100 g soil. In contrast to the heavily managed system, infective propagule numbers were high in systems under moderate and limited management. The method described may be useful for rapid investigations of genetic diversity and community structure of AMF. Accepted: 8 January 1999     

在韩国境内Potentilla fragarioides var.sprengeliana的遗传多样 …

根据２２个等位酶位点遗传变异,探讨了韩国境内委陵菜（Ｐｏｔｅｎｔｉｌｌａ ｆｒａｇａｒｉｏｉｄｅｓ Ｌ．ｖａｒ．ｓｐｒｅｎｇｅｌｉａｎａ）的遗传多样性和种群结构。酶位点的多态位点百分比为５９．１％。种和种群水平上的遗传多样性比较高,分别为Ｈｅｓ＝０．２１０,Ｈｅｐ＝０．１９９;而种群的分化水平则相对较低（ＧＳＴ＝０．０７４）。１９个种群中随机交配的偏差为ＦＩＳ＝０．３３１。每代迁移数的间接估计     

Nox4-dependent ROS modulation by amino endoperoxides to induce apoptosis in cancer cells

Tumor metastasis is the main cause of death in cancer patients. Anoikis resistance is one critical malefactor of metastatic cancer cells to resist current clinical chemotherapeutic treatments. Although endoperoxide-containing compounds have long been suggested as anticancer drugs, few have been clinically employed due to their instability, complex synthesis procedure or low tumor cell selectivity. Herein, we describe a one-pot strategy to synthesize novel amino endoperoxides and their derivatives with good yields and stabilities. In vitro cell-based assays revealed that 4 out of the 14 amino endoperoxides selectively induce metastatic breast carcinoma cells but not normal breast cells to undergo apoptosis, in a dose-dependent manner. Mechanistic studies showed that the most potent amino endoperoxide, 4-Me, is selective for cancer cells expressing a high level of Nox4. The anticancer effects are further shown to be associated with reduced O₂⁻:H₂O₂ ratio and increased ·OH level in the cancerous cells. Animal study showed that 4-Me impairs orthotopic breast tumor growth as well as tumor cell metastasis to lymph nodes. Altogether, our study suggests that anticancer strategies that focus on redox-based apoptosis induction in tumors are clinically viable.     

Molecular Phylogenetic Analysis of Archaea and Bacteria in Wind Cave,South Dakota

The diversity of bacteria and archaea was characterized from sediments collected from Wind Cave located in Wind Cave National Park in the Black Hills of South Dakota. Wind Cave is a limestone dissolution cave with strata that started forming over 300 million years ago, making it one of the oldest in the world. Previous work suggested that the cave was largely a detritus based system ultimately dependent upon allochthonous energy and carbon from photosynthesis of the overlying vegetation, and algae growing near lights along the tour routes. In this work, we used a molecular phylogenetic approach to characterize the microbial structure and infer a corresponding ecosystem function where appropriate. Four bacterial divisions and subdivisions were found in the culture collection, which represented 14 phylotypes, whereas 12 divisions and subdivisions were identified in the clonal analysis comprising 49 phylotypes. The predominant groups were the γ-Proteobacteria and Acidobacteria. Although a few of the clones resembled sequences from other cave and subterranean systems, no cave-specific bacterial community was evident in this work. Archaeal phylotypes (20 Crenarchaeota and 2 Euryarchaeota) were detected, with a large proportion of the Crenarchaeota resembling sequences from a South African gold mine. One archaeal cluster in particular appears to be specific to the subterranean environment. Most of the microbial sequences were not related to known chemolithoautotrophs, therefore we conclude that this particular community is likely detritus based where allochthonous energy and carbon are transported into the cave by infiltrating waters.     

Evolutionary divergence times in the Annonaceae: evidence of a late Miocene origin of Pseuduvaria in Sundaland with subsequent diversification in New Guinea

Background  

Phylogenetic analyses of the Annonaceae consistently identify four clades: a basal clade consisting of Anaxagorea, and a small 'ambavioid' clade that is sister to two main clades, the 'long branch clade' (LBC) and 'short branch clade' (SBC). Divergence times in the family have previously been estimated using non-parametric rate smoothing (NPRS) and penalized likelihood (PL). Here we use an uncorrelated lognormal (UCLD) relaxed molecular clock in BEAST to estimate diversification times of the main clades within the family with a focus on the Asian genus Pseuduvaria within the SBC. Two fossil calibration points are applied, including the first use of the recently discovered Annonaceae fossil Futabanthus. The taxonomy and morphology of Pseuduvaria have been well documented, although no previous dating or biogeographical studies have been undertaken. Ancestral areas at internal nodes within Pseuduvaria are determined using dispersal-vicariance analysis (DIVA) and weighted ancestral area analysis (WAAA).     

Phosphatidylcholine activation of human heart (R)-3-hydroxybutyrate dehydrogenase mutants lacking active center sulfhydryls: site-directed mutagenesis of a new recombinant fusion protein

(R)-3-Hydroxybutyrate dehydrogenase (BDH) is a lipid-requiring mitochondrial enzyme with a specific requirement of phosphatidylcholine (PC) for function. A plasmid has been constructed to express human heart (HH) BDH in Escherichia coli as a hexahistidine-tagged fusion protein (HH-Histag-BDH). A rapid two-step affinity purification yields active HH-Histag-BDH (and six mutants) with high specific activity ( approximately 130 micromol of NAD(+) reduced.min(-1).mg(-1)). HH-Histag-BDH has no activity in the absence of phospholipid and exhibits a specific requirement of PC for function. The HH-Histag-BDH-PC complex (and HH-BDH derived therefrom by enterokinase cleavage) has apparent Michaelis constants (K(m) values) for NAD(+), NADH, (R)-3-hydroxybutyrate (HOB), and acetoacetate (AcAc) similar to those for bovine heart or rat liver BDH. A computed structural model of HH-BDH predicts the two active center sulfhydryls to be C69 (near the adenosine moiety of NAD) and C242. With both sulfhydryls derivatized, BDH has minimal activity, but site-directed mutagenesis of C69 and/or C242 now shows that neither of these cysteines is required for PC activation or catalysis (the double mutant, C69A/C242A, is highly active with essentially normal kinetic parameters). Six cysteine mutants each have an increased K(m)(NADH) (2-6-fold) but an unchanged K(m)(NAD)+. The C242S and C69A/C242S enzymes (but not the analogous C242A mutants nor the C69A or C69S mutants) exhibit approximately 10-fold increases in K(m)(HOB) and K(m)(AcAc), reflecting an altered substrate binding site. Thus, although C242 (in the C-terminal lipid binding domain of BDH) is close to the active site, it appears to be in a hydrophobic environment and only indirectly defines the substrate binding site at the catalytic center of BDH.     

Territorial defense against various food competitors in the Tanganyikan benthophagous cichlid <Emphasis Type="Italic">Neolamprologus tetracanthus</Emphasis>

Territorial defense of nonbreeding female Neolamprologus tetracanthus, a shrimp-eating Tanganyikan cichlid, was investigated. Females defended territories (=home ranges, ca. 1m across) against a variety of intruding fishes. Conspecific females were usually attacked outside the territories, heterospecific benthivores (shrimp eaters) and omnivores near the border of the territories, and piscivores, algae and detritus feeders, and herbivores inside the territories. Females used some parts of the sandy substrate in the territories for foraging (foraging areas). Territorial defense prevented most of the conspecific females and benthivores from intruding into the foraging areas. In omnivores, piscivores, and algae and detritus feeders, about half the intruders were repelled from the foraging areas, although herbivores were infrequently repelled in the areas. Soon after removal of the resident females, many food competitors invaded the foraging areas and eagerly devoured prey, suggesting that the territories are maintained for food resource protection from these competitors. Females are likely to discriminate intruding fishes and change their territorial defense primarily on the basis of the degree of dietary overlap, resulting in monofunctional serial territories.     

Seahawk: moving beyond HTML in Web-based bioinformatics analysis

Background  

Traditional HTML interfaces for input to and output from Bioinformatics analysis on the Web are highly variable in style, content and data formats. Combining multiple analyses can therfore be an onerous task for biologists. Semantic Web Services allow automated discovery of conceptual links between remote data analysis servers. A shared data ontology and service discovery/execution framework is particularly attractive in Bioinformatics, where data and services are often both disparate and distributed. Instead of biologists copying, pasting and reformatting data between various Web sites, Semantic Web Service protocols such as MOBY-S hold out the promise of seamlessly integrating multi-step analysis.