Molecular Analysis of the Microbial Diversity Present in the Colonic Wall, Colonic Lumen, and Cecal Lumen of a Pig

Random clones of 16S ribosomal DNA gene sequences were isolated after PCR amplification with eubacterial primers from total genomic DNA recovered from samples of the colonic lumen, colonic wall, and cecal lumen from a pig. Sequences were also obtained for cultures isolated anaerobically from the same colonic-wall sample. Phylogenetic analysis showed that many sequences were related to those of Lactobacillus or Streptococcus spp. or fell into clusters IX, XIVa, and XI of gram-positive bacteria. In addition, 59% of randomly cloned sequences showed less than 95% similarity to database entries or sequences from cultivated organisms. Cultivation bias is also suggested by the fact that the majority of isolates (54%) recovered from the colon wall by culturing were related to Lactobacillus and Streptococcus, whereas this group accounted for only one-third of the sequence variation for the same sample from random cloning. The remaining cultured isolates were mainly Selenomonas related. A higher proportion of Lactobacillus reuteri-related sequences than of Lactobacillus acidophilus- and Lactobacillus amylovorus-related sequences were present in the colonic-wall sample. Since the majority of bacterial ribosomal sequences recovered from the colon wall are less than 95% related to known organisms, the roles of many of the predominant wall-associated bacteria remain to be defined.     

Foliar nutrients explain goldspotted oak borer,Agrilus auroguttatus,adult feeding preference among four California oak species

Adults of the invasive goldspotted oak borer, Agrilus auroguttatus Schaeffer (Coleoptera: Buprestidae), consumed foliar weight in no‐choice feeding tests of, in descending order, California black oak Quercus kelloggii Newb., Engelmann oak, Quercus engelmannii Greene, coast live oak, Quercus agrifolia Née, and canyon live oak, Quercus chrysolepis Liebm. (Fagaceae). Furthermore, significantly more foliar area was consumed of Q. kelloggii than of Q. chrysolepis. In dual‐choice feeding tests with isolated leaf disks, A. auroguttatus consumed significantly more foliar weight and area of Q. kelloggii relative to the other three oak species, and more foliar weight of Q. agrifolia than of Q. chrysolepis. In dual‐choice feeding tests with leaves on small branches, A. auroguttatus consumed more foliar weight of Q. kelloggii than of Q. engelmannii and Q. agrifolia. Thus, multiple experiments suggested that adults of A. auroguttatus preferred the foliage of Q. kelloggii over that of the other three oak species, and among the other three species they did not appear to have a strong feeding preference. Factor analysis reduced the quantities of 13 foliar nutrients into two new variables (factor 1 and factor 2). Factor 1 was weighted heavily on the quantities of nitrogen, sulfur, phosphorus, potassium, zinc, and copper, whereas factor 2 was weighted heavily on the quantities of zinc, iron, and aluminum. Factor 1 varied by oak species, with Q. kelloggii having a higher factor 1 nutrient content than the other three species. Factor 2 response was higher in Q. kelloggii, Q. agrifolia, and Q. engelmannii than in Q. chrysolepis. The collective effects of four macronutrients (nitrogen, sulfur, phosphorus, and potassium) and two micronutrients (zinc and copper) suggest that these might be the nutrients directing preferential feeding of A. auroguttatus adults on the foliage of Q. kelloggii. Leaf toughness might also play an important role in feeding preference. Female A. auroguttatus did not show an ovipositional preference among the four oak species.     

Revisiting the use of Iprodione and Trichoderma in the integrated management of onion white rot

The biocontrol properties of Trichoderma species are well documented, but their effectiveness in antagonism of the problematic Sclerotium cepivorum, the causal agent of white rot in Allium species, appears limited with reports of significant control only relating to deliberately-mutated strains of Trichoderma. Our previous studies have indicated the possibility of using selected naturally-occurring strains of the antagonist in the suppression of other diseases; now in vitro and controlled environment in vivo studies have indicated that a degree of control of Onion White Rot is possible, and that the selected antagonist strains can be used in integrated treatments with Iprodione to good effect. The possible value of such treatments is considered in light of other approaches to the suppression of this continuing problem.     

Molecular interactions in the insulin-like growth factor (IGF) axis: a surface plasmon resonance (SPR) based biosensor study

This review describes a comprehensive analysis of a surface plasmon resonance (SPR)-based biosensor study of molecular interactions in the insulin-like growth factor (IGF) molecular axis. In this study, we focus on the interaction between the polypeptide growth factors IGF-I and IGF-II with six soluble IGF binding proteins (IGFBP 1-6), which occur naturally in various biological fluids. We have describe the conditions required for the accurate determination of kinetic rate constants for these interactions and highlight the experimental and theoretical pitfalls, which may be encountered in the early stages of such a study. We focus on IGFBP-5 and describe a site-directed mutagenesis study, which examines the contribution of various residues in the protein to high affinity interaction with IGF-I and -II. We analyse the interaction of IGFBP-5 (and IGFBP-3) with heparin and other biomolecules and describe experiments, which were designed to monitor multi-protein complex formation in this molecular axis.     

Environmental and Biotic Controls over Aboveground Biomass Throughout a Tropical Rain Forest

The environmental and biotic factors affecting spatial variation in canopy three-dimensional (3-D) structure and aboveground tree biomass (AGB) are poorly understood in tropical rain forests. We combined field measurements and airborne light detection and ranging (lidar) to quantify 3-D structure and AGB across a 5,016 ha rain forest reserve on the northeastern flank of Mauna Kea volcano, Hawaii Island. We compared AGB among native stands dominated by Metrosideros polymorpha found along a 600–1800 m elevation/climate gradient, and on three substrate-age classes of 5, 20, and 65 kyr. We also analyzed how alien tree invasion, canopy species dominance and topographic relief influence AGB levels. Canopy vertical profiles derived from lidar measurements were strong predictors (r ² = 0.78) of AGB across sites and species. Mean AGB ranged from 48 to 363 Mg ha⁻¹ in native forest stands. Increasing elevation corresponded to a 53–84% decrease in AGB levels, depending upon substrate age. Holding climate constant, changes in substrate age from 5 to 65 kyr corresponded to a 23–53% decline in biomass. Invasion by Psidium cattleianum and Ficus rubiginosa trees resulted in a 19–38% decrease in AGB, with these carbon losses mediated by substrate age. In contrast, the spread of former plantation tree species Fraxinus uhdei corresponded to a 7- to 10-fold increase in biomass. The effects of topographic relief at both local and regional scales were evident in the AGB maps, with poorly drained terrain harboring 76% lower biomass than forests on well-drained relief. Our results quantify the absolute and relative importance of environmental factors controlling spatial variation in tree biomass across a rain forest landscape, and highlight the rapid changes in carbon storage incurred following biological invasion. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. Author Contributions  GPA and RFH conceived of or designed the study. GPA, RFH, TAV, DEK, and TKB performed research and analyzed data. GPA, RFH, DEK, and TKB contributed new methods or models. GPA wrote the article.     

Ruminococcus bromii is a keystone species for the degradation of resistant starch in the human colon

The release of energy from particulate substrates such as dietary fiber and resistant starch (RS) in the human colon may depend on the presence of specialist primary degraders (or ‘keystone species'') within the microbial community. We have explored the roles of four dominant amylolytic bacteria found in the human colon in the degradation and utilization of resistant starches. Eubacterium rectale and Bacteroides thetaiotaomicron showed limited ability to utilize RS2- and RS3-resistant starches by comparison with Bifidobacterium adolescentis and Ruminococcus bromii. In co-culture, however, R. bromii proved unique in stimulating RS2 and RS3 utilization by the other three bacterial species, even in a medium that does not permit growth of R. bromii itself. Having previously demonstrated low RS3 fermentation in vivo in two individuals with undetectable populations of R. bromii-related bacteria, we show here that supplementation of mixed fecal bacteria from one of these volunteers with R. bromii, but not with the other three species, greatly enhanced the extent of RS3 fermentation in vitro. This argues strongly that R. bromii has a pivotal role in fermentation of RS3 in the human large intestine, and that variation in the occurrence of this species and its close relatives may be a primary cause of variable energy recovery from this important component of the diet. This work also indicates that R. bromii possesses an exceptional ability to colonize and degrade starch particles when compared with previously studied amylolytic bacteria from the human colon.     

Galanin-Like Immunoreactivity Is Unchanged in Alzheimer''s Disease and Parkinson''s Disease Dementia Cerebral Cortex

Galanin is a recently isolated neuropeptide that is of particular interest in dementing disorders because of its known colocalization with choline acetyltransferase in magnocellular neurons of the basal nucleus of Meynert. These neurons degenerate in Alzheimer's disease, and there is a corresponding deficiency of cortical choline acetyltransferase activity. In the present study, galanin-like immunoreactivity was measured in the postmortem cerebral cortex and hippocampus of 10 controls and 14 patients who had had Alzheimer's disease. Significant reductions of choline acetyltransferase activity (50-60%) were found in all regions examined; however, there was no significant effect on concentrations of galanin-like immunoreactivity. Similar measurements were made in postmortem tissues of 12 control and 13 demented Parkinsonian patients who had had Alzheimer-type cortical pathology. Choline acetyltransferase activity was again significantly decreased in all regions examined but there were no significant reductions in galanin-like immunoreactivity. Experimental lesions of the fornix in rats produced parallel significantly correlated reductions of both choline acetyltransferase activity and galanin-like immunoreactivity in the hippocampus. Galanin-like immunoreactivity in the human hypothalamus consisted of two molecular-weight species on gel-permeation chromatography, and two forms were resolved by reverse-phase HPLC. The paradoxical preservation of galanin-like immunoreactivity, despite depletion of the activity of choline acetyltransferase, with which it is colocalized, is as yet unexplained. Recent studies have shown that galanin inhibits both acetylcholine release in the hippocampus and memory acquisition; therefore, preserved galanin may exacerbate the cholinergic and cognitive deficits that accompany dementia.     

Reduced-median-network analysis of complete mitochondrial DNA coding-region sequences for the major African, Asian, and European haplogroups

The evolution of the human mitochondrial genome is characterized by the emergence of ethnically distinct lineages or haplogroups. Nine European, seven Asian (including Native American), and three African mitochondrial DNA (mtDNA) haplogroups have been identified previously on the basis of the presence or absence of a relatively small number of restriction-enzyme recognition sites or on the basis of nucleotide sequences of the D-loop region. We have used reduced-median-network approaches to analyze 560 complete European, Asian, and African mtDNA coding-region sequences from unrelated individuals to develop a more complete understanding of sequence diversity both within and between haplogroups. A total of 497 haplogroup-associated polymorphisms were identified, 323 (65%) of which were associated with one haplogroup and 174 (35%) of which were associated with two or more haplogroups. Approximately one-half of these polymorphisms are reported for the first time here. Our results confirm and substantially extend the phylogenetic relationships among mitochondrial genomes described elsewhere from the major human ethnic groups. Another important result is that there were numerous instances both of parallel mutations at the same site and of reversion (i.e., homoplasy). It is likely that homoplasy in the coding region will confound evolutionary analysis of small sequence sets. By a linkage-disequilibrium approach, additional evidence for the absence of human mtDNA recombination is presented here.