Vertical distribution of bacterial community structure in the sediments of two eutrophic lakes revealed by denaturing gradient gel electrophoresis (DGGE) and multivariate analysis techniques

Vertical distribution of bacterial community structure was investigated in the sediments of two eutrophic lakes of China, Lake Taihu and Lake Xuanwu. Profiles of bacterial communities were generated using a molecular fingerprinting technique, denaturing gradient gel electrophoresis (DGGE) followed by DNA sequence analysis, and the results were interpreted with multivariate statistical analysis. To assess changes in the genetic diversity of bacterial communities with changing depth, DGGE banding patterns were analysed by cluster analysis. Distinct clusters were recognized in different sampling stations of Lake Taihu. Canonical correspondence analysis (CCA) was carried out to infer the relationship between environmental variables and bacterial community structure. DGGE samples collected at the same sampling site clustered together in both lakes. Total phosphorus, organic matter and pH were considered to be the key factors driving the changes in bacterial community composition.     

Influence of ethanol concentration of extraction solvent on metabolite profiling for Salviae Miltiorrhizae Radix et Rhizoma extract by 1H NMR spectroscopy and multivariate data analysis

Salviae Miltiorrhizae Radix et Rhizoma (Danshen in China) and its related preparations are widely used in clinical practice due to its high medicinal value. In recent years, ¹H NMR technology has made great progress and demonstrated its unique advantages in the field of botanical metabolomics. In this study, ¹H NMR-based metabolomics was used to investigate the dissolution of various metabolites in Danshen as a function of ethanol concentration. ¹H NMR spectroscopy of Danshen extract identified 28 metabolites including 6 sugars, 11 amino acids, 3 organic acids, 4 salvianolic acids, and 4 tanshinones. Multivariate statistical analysis was used to classify and compare various Danshen extracts. PCA and HCA were used to obtain a global overview of the similarity in the samples and two-class OPLS-DA models were established for identifying characteristic metabolites. Then, ¹H-qNMR method was used to estimate the concentration of 22 metabolites, which is helpful to further describe the changes in metabolite ratios of various Danshen extracts. The result of this study laid the foundation for further biological activity research, and also provided an important reference for subsequent process research and quality control of Danshen related preparations.     

Codon Bias and Mutability in HIV Sequences

A survey of the patterns of synonymous codon preference in the HIV env gene reveals a correlation between the codon bias and the mutability requirements of different regions of the protein. At hypervariable regions in gp120 one finds a greater proportion of codons that tend to mutate nonsynonymously, but to a target that is similar in hydrophobicity and volume. We argue that this strategy results from a compromise between the selective pressure placed on the virus by the induced immune response, which favors amino acid substitutions in the complementarity determining regions, and the negative selection against missense mutations that violate structural constraints of the env protein. Received: 9 June 1997 / Accepted: 25 May 1998     

Data partitioning and correction for ascertainment bias reduce the uncertainty of placental mammal divergence times inferred from the morphological clock

Bayesian estimates of divergence times based on the molecular clock yield uncertainty of parameter estimates measured by the width of posterior distributions of node ages. For the relaxed molecular clock, previous works have reported that some of the uncertainty inherent to the variation of rates among lineages may be reduced by partitioning data. Here we test this effect for the purely morphological clock, using placental mammals as a case study. We applied the uncorrelated lognormal relaxed clock to morphological data of 40 extant mammalian taxa and 4,533 characters, taken from the largest published matrix of discrete phenotypic characters. The morphologically derived timescale was compared to divergence times inferred from molecular and combined data. We show that partitioning data into anatomical units significantly reduced the uncertainty of divergence time estimates for morphological data. For the first time, we demonstrate that ascertainment bias has an impact on the precision of morphological clock estimates. While analyses including molecular data suggested most divergences between placental orders occurred near the K‐Pg boundary, the partitioned morphological clock recovered older interordinal splits and some younger intraordinal ones, including significantly later dates for the radiation of bats and rodents, which accord to the short‐fuse hypothesis.     

Invasive plants negatively impact native,but not exotic,animals

Despite our growing understanding of the impacts of invasive plants on ecosystem structure and function, important gaps remain, including whether native and exotic species respond differently to plant invasion. This would elucidate basic ecological interactions and inform management. We performed a meta‐analytic review of the effects of invasive plants on native and exotic resident animals. We found that invasive plants reduced the abundance of native, but not exotic, animals. This varied by animal phyla, with invasive plants reducing the abundance of native annelids and chordates, but not mollusks or arthropods. We found dissimilar impacts among “wet” and “dry” ecosystems, but not among animal trophic levels. Additionally, the impact of invasive plants increased over time, but this did not vary with animal nativity. Our review found that no studies considered resident nativity differences, and most did not identify animals to species. We call for more rigorous studies of invaded community impacts across taxa, and most importantly, explicit consideration of resident biogeographic origin. We provide an important first insight into how native and exotic species respond differently to invasion, the consequences of which may facilitate cascading trophic disruptions further exacerbating global change consequences to ecosystem structure and function.     

Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations.

We present an approach which can be used to identify native-like folds in a data base of protein conformations in the absence of any sequence homology to proteins in the data base. The method is based on a knowledge-based force field derived from a set of known protein conformations. A given sequence is mounted on all conformations in the data base and the associated energies are calculated. Using several conformations and sequences from the globin family we show that the native conformation is identified correctly. In fact the resolution of the force field is high enough to discriminate between a native fold and several closely related conformations. We then apply the procedure to several globins of known sequence but unknown three dimensional structure. The homology of these sequences to globins of known structures in the data base ranges from 49 to 17%. With one exception we find that for all globin sequences one of the known globin folds is identified as the most favorable conformation. These results are obtained using a force field derived from a data base devoid of globins of known structure. We briefly discuss useful applications in protein structural research and future development of our approach.     

Improving Risk Assessment: Priorities for Epidemiologic Research

The Epidemiology Work Group at the Workshop on Future Research for Improving Risk Assessment Methods, Of Mice, Men, and Models, held August 16 to 18, 2000, at Snowmass Village, Aspen, Colorado, concluded that in order to improve the utility of epidemiologic studies for risk assessment, methodologic research is needed in the following areas: (1) aspects of epidemiologic study designs that affect doseresponse estimation; (2) alternative methods for estimating dose in human studies; and (3) refined methods for dose-response modeling for epidemiologic data. Needed research in aspects of epidemiologic study design includes recognition and control of study biases, identification of susceptible subpopulations, choice of exposure metrics, and choice of epidemiologic risk parameters. Much of this research can be done with existing data. Research needed to improve determinants of dose in human studies includes additional individual-level data (e.g., diet, co-morbidity), development of more extensive human data for physiologically based pharmacokinetic (PBPK) dose modeling, tissue registries to increase the availability of tissue for studies of exposure/dose and susceptibility biomarkers, and biomarker data to assess exposures in humans and animals. Research needed on dose-response modeling of human studies includes more widespread application of flexible statistical methods (e.g., general additive models), development of methods to compensate for epidemiologic bias in dose-response models, improved biological models using human data, and evaluation of the benchmark dose using human data. There was consensus among the Work Group that, whereas most prior risk assessments have focused on cancer, there is a growing need for applications to other health outcomes. Developmental and reproductive effects, injuries, respiratory disease, and cardiovascular disease were identified as especially high priorities for research. It was also a consensus view that epidemiologists, industrial hygienists, and other scientists focusing on human data need to play a stronger role throughout the risk assessment process. Finally, the group agreed that there was a need to improve risk communication, particularly on uncertainty inherent in risk assessments that use epidemiologic data.     

Isolation and introgression in the Intermountain West: contrasting gene genealogies reveal the complex biogeographic history of the American pika (Ochotona princeps)

Aim We studied the history of colonization, diversification and introgression among major phylogroups in the American pika, Ochotona princeps (Lagomorpha), using comparative and statistical phylogeographic methods. Our goal was to understand how Pleistocene climatic fluctuations have shaped the distribution of diversity at mitochondrial DNA (mtDNA) and nuclear DNA (nDNA) loci in this alpine specialist. Location North America’s Intermountain West. Methods We accumulated mtDNA sequence data (c. 560–1700 bp) from 232 pikas representing 64 localities, and sequenced two nuclear introns (mast cell growth factor, c. 550 bp, n = 148; protein kinase C iota, c. 660 bp, n = 139) from a subset of individuals. To determine the distribution of major mtDNA lineages, we conducted a phylogenetic analysis on the mtDNA sequence data, and we calculated divergence times among the lineages using a Bayesian Markov chain Monte Carlo approach. Relationships among nuclear alleles were explored with minimum spanning networks. Finally, we conducted coalescent simulations of alternative models of population history to test for congruence between nDNA and mtDNA responses to Pleistocene glacial cycles. Results We found that: (1) all individuals could be assigned to one of five allopatric mtDNA lineages; (2) lineages are associated with separate mountain provinces; (3) lineages originated from at least two rounds of differentiation; (4) nDNA and mtDNA markers exhibited overall phylogeographic congruence; and (5) introgression among phylogroups has occurred at nuclear loci since their initial isolation. Main conclusions Pika populations associated with different mountain systems have followed separate but not completely independent evolutionary trajectories through multiple glacial cycles. Range expansion associated with climate cooling (i.e. glaciations) promoted genetic admixture among populations within mountain ranges. It also permitted periodic contact and introgression between phylogroups associated with different mountain systems, the record of which is retained at nDNA but not mtDNA loci. Evidence for different histories at nuclear and mtDNA loci (i.e. periodic introgression versus deep isolation, respectively) emphasizes the importance of multilocus perspectives for reconstructing complete population histories.     

Microsatellite analysis of genetic diversity in the Chinese alligator (<Emphasis Type="Italic">Alligator sinensis</Emphasis>) Changxing captive population

Chinese alligator (Alligator sinensis) is a critically endangered species endemic to China. In this study, the extent of genetic variation in the captive alligators of the Changxing Reserve Center was investigated using microsatellite markers derived from American alligators. Out of 22 loci employed, 21 were successfully amplified in the Chinese alligator. Sequence analysis showed loci in American alligators had a bigger average size than that of the Chinese alligators and the longest allele of an individual locus almost always existed in the species with longer stretch of repeat units. Eight of the 22 loci were found to be polymorphic with a total of 26 alleles present among 32 animals scored, yielding an average of 3.25 alleles per polymorphic locus. The expected heterozygosity (H _E) ranged at a moderate level from 0.4385 to 0.7163 in this population. Compared to that in the American alligators, a lower level of microsatellite diversity existed in the Changxing population as revealed by about 46% fewer alleles per locus and smaller H _E at the homologous loci. The average exclusion power and the ability to detect shared genotypes and multiple paternity were evaluated for those markers. Results suggested that when the polymorphic loci were combined, they could be sensitive markers in genetic diversity study and relatedness inference within the Chinese alligator populations. The level of genetic diversity present in the current Changxing population indicated an important resource to complement reintroductions based on the individuals from the other population. In addition, the microsatellite markers and their associated diversity characterized in this population could be utilized to further investigate the genetic status of this species.