植物功能生态学研究进展

植物功能生态学是研究植物种类间或环境梯度内植物某一功能性状变化,阐释其进化意义或生态意义的生态学分支学科;围绕3个主题开展工作:(1)利用功能性状作为研究解释的变量,(2)在种类间,清晰地进行性状比较,表述一般趋势,(3)在环境梯度内,清晰或模糊地比较性状的变化.性状是指从细胞到整个有机体个体水平的可测度的任何形态、生理、物候特点,不包括任何其它生物层次和环境因素.性状一般分为功能性状、表现性状等;功能性状是指对有机体表现产生强烈影响的性状,表现性状为反应功能性状作用和变化、并指示植物适合度的性状.功能性状研究不限于个体水平,现在已广泛联系了群落和生态系统过程与功能,正在开创植物生态学研究的一个崭新领域.比较是功能生态学的研究手段和途径.中国植物和植被研究基础丰富,开展中国植物区系的植物功能性状研究将积极贡献于功能生态学发展,种系发生途径和地理分布途径可能是功能生态学研究的全新视角.     

Functional impact of transposable elements using bioinformatic analysis and a comparative genomic approach

A dual coding event, which is the translation of different isoforms from a single gene, is one of the special patterns among the alternative splicing events. This is an important mechanism for the regulation of protein diversity in human and mouse genomes. Although the regulation for dual coding events has been characterized in a few genes, the individual mechanism remains unclear. Numerous studies have described the exonization of transposable elements, which is the splicing mediated insertion of transposable element sequence fragments into mature mRNAs. Therefore, in this study, we investigated the number of transposable element (TE)-derived dual coding genes in human, chimpanzee and mouse genomes. TE fusion exons appeared in the dual coding regions of 309 human genes. Functional protein domain alterations by TE-derived dual coding events were observed in 129 human genes. Comparative TE-derived dual coding events were also analyzed in chimpanzee and mouse orthologs. Seventy chimpanzee orthologs had TE-derived dual coding events, but mouse orthologs did not have any TE-derived dual coding events. Taken together, our analyses listed the number of TE-derived dual coding genes which could be investigated by experimental analysis and suggested that TE-derived dual coding events were major sources for the functional diversity of human genes, but not mouse genes.     

Species residency status affects model selection and hypothesis testing in freshwater community ecology

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Turn prediction in proteins using a pattern-matching approach

We extend the use of amino acid sequence patterns [Cohen, F.E., Abarbanel, R. M., Kuntz, I. D., & Fletterick, R. J. (1983) Biochemistry 22, 4894-4904] to the identification of turns in globular proteins. The approach uses a conservative strategy, combined with a hierarchical search (strongest patterns first) and length-dependent masking, to achieve high accuracy (95%) on a test set of proteins of known structure. Applying the same procedure to homologous families gives a 90% success rate. Straightforward changes are suggested to improve the predictive power. The computer program, written in Lisp, provides a general pattern-recognition language well suited for a number of investigations of protein and nucleic acid sequences.     

Sweat loss prediction using a multi-model approach

A new multi-model approach (MMA) for sweat loss prediction is proposed to improve prediction accuracy. MMA was computed as the average of sweat loss predicted by two existing thermoregulation models: i.e., the rational model SCENARIO and the empirical model Heat Strain Decision Aid (HSDA). Three independent physiological datasets, a total of 44 trials, were used to compare predictions by MMA, SCENARIO, and HSDA. The observed sweat losses were collected under different combinations of uniform ensembles, environmental conditions (15–40°C, RH 25–75%), and exercise intensities (250–600 W). Root mean square deviation (RMSD), residual plots, and paired t tests were used to compare predictions with observations. Overall, MMA reduced RMSD by 30–39% in comparison with either SCENARIO or HSDA, and increased the prediction accuracy to 66% from 34% or 55%. Of the MMA predictions, 70% fell within the range of mean observed value ± SD, while only 43% of SCENARIO and 50% of HSDA predictions fell within the same range. Paired t tests showed that differences between observations and MMA predictions were not significant, but differences between observations and SCENARIO or HSDA predictions were significantly different for two datasets. Thus, MMA predicted sweat loss more accurately than either of the two single models for the three datasets used. Future work will be to evaluate MMA using additional physiological data to expand the scope of populations and conditions.     

Geographical and taxonomic biases in invasion ecology

Invasive alien species come from most taxonomic groups, and invasion biology is searching for robust cross-taxon generalizations and principles. An analysis of 2,670 papers dealing with 892 invasive species showed that all major groups of invaders are well studied, but that most information on the mechanisms of invasion has emerged from work on a limited number of the most harmful invaders. A strong geographical bias, with Africa and Asia understudied, inhibits a balanced understanding of invasion, because we might be lacking knowledge of specific invasion mechanisms from poorly studied, regionally specific habitats. International cooperation is required to achieve a more geographically balanced picture of biological invasions. Invasive species with the greatest impact are best studied, but more studies of species that are naturalized but not (yet) invasive are needed to improve understanding of the mechanisms acting during the naturalization phase of invasions and leading to successful invasion.     

Integrative data analysis for functional prediction: a multi-objective optimization approach

SUMMARY: An integrative classification system for functional genomics is introduced. A comparison with a previous study of the yeast mitochondrial proteome is presented. AVAILABILITY: A demonstration prototype, interSearch, is available on request. SUPPLEMENTARY INFORMATION: http://ijsr32.infj.ulster.ac.uk/~e10110731/interSearch.     

A comparison of the predatory impacts of an invasive and native crab species using a functional response approach

The European green crab (Carcinus maenas) is invasive on the West coast of North America, but the ecological consequences of this invasion remain poorly understood. Comparative functional response analysis has arisen as a method of elucidating ecological consequences of invasive species by comparing the impact of these species to native analogues. Through comparative functional response experiments of green crabs and native red rock crabs (Cancer productus) we found that green crab predation increased asymptotically (Type II functional response) when fed increasing densities of Pacific oysters (Magallana gigas), while red rock crab predation displayed a sigmoidal (Type III) response. At high oyster densities red rock crabs consume more Pacific oysters than green crabs do, due to their reduced handling time, though green crabs consume more Pacific oysters relative to their size than red rock crabs. However, compared to red rock crabs, green crabs consume more oysters at low prey densities, which implies that they have a larger, potentially destabilizing impact on low densities of Pacific oysters. As green crabs continue to spread across the West coast of North America, Pacific oysters will face increased predation pressure. Our results show the advantage of using functional response analysis to compare density dependent predation between an invasive species and a native species to predict the ecological consequences of invasions.

     

Biomechanical characterization of cartilages by a novel approach of blunt impact testing

The present article introduces a novel method of characterizing the macromechanical cartilage properties based on dynamic testing. The proposed approach of instrumented impact testing shows the possibility of more detailed investigation of the acting dynamic forces and corresponding deformations within the wide range of strain rates and loads, including the unloading part of stress-strain curves and hysteresis loops. The presented results of the unconfined compression testing of both the native joint cartilage tissues and potential substitute materials outlined the opportunity to measure the dissipation energy and thus to identify the initial mechanical deterioration symptoms and to introduce a better definition of material damage. Based on the analysis of measured specimen deformation, the intact and pathologically changed cartilage tissue can be distinguished and the differences revealed.     

Characterization of cervical lymph-nodes using a multi-parametric and multi-modal approach for an early prediction of tumor response to chemo-radiotherapy

PurposeIn the treatment of Head-and-Neck Squamous Cell Carcinoma (HNSCC), the early prediction of residual malignant lymph nodes (LNs) is currently required. Here, we investigated the potential of a multi-modal characterization (combination of CT, T2w-MRI and DW-MRI) at baseline and at mid-treatment, based on texture analysis (TA), for the early prediction of LNs response to chemo-radiotherapy (CRT).Methods30 patients with pathologically confirmed HNSCC treated with CRT were considered. All patients underwent a planning CT and two serial MR examinations (including T2w and DW images), one before and one at mid-CRT. For each patient the largest malignant LN was selected and within each LN, morphological and textural features were estimated from T2w-MRI and CT, besides a quantification of the apparent diffusion coefficient (ADC) from DW-MRI. After a median follow-up time of 26.6 months, 19 LNs showed regional control, while 11 LNs showed regional failure at a median time of 4.6 months. Linear discriminant analysis was used to test the accuracy of the image-based features in predicting the final response.ResultsPre-treatment features showed higher predictive power than mid-CRT features, the ADC having the highest accuracy (80%); CT-based indices were found not predictive. When ADC was combined with TA, the classification performance increased (accuracy = 82.8%). If only T2w-MRI features were considered, the best combination of pre-CRT indices and their variation reached an equivalent accuracy (81.8%).ConclusionOur results may suggest that TA on T2w-MRI and ADC can be combined together to obtain a more accurate prediction of response to CRT.     

Physical modeling of the batocrinid anal tube: functional analysis and multiple hypothesis testing

Baumiller, T. K. 1990 10 15: Physical modeling of the batocrinid anal tube: functional analysis and multiple hypothesis testing. Lethaia , VOL 23, pp. 399–408. Oslo. ISSN 0024–1164.
Three hypotheses related to the function of the batocrinid anal tube were tested using physical models: (1) the anal tube served as a 'rudder', allowing the crinoid to passively maintain an effective feeding posture in moving water, (2) the tube served as a splitter 'plate', reducing the drag on the organism while it was in its feeding posture, and (3) the anal tube functioned as a 'chimney' by moving the anus downstream of the arms and thus reducing the risk of the organism ingesting its own wastes and/or gametes. Results of experiments performed in a recirculating flow tank suggested that the tube was well suited for the 'chimney' function: it reduced the concentrations of excreted matter in the proximity of the feeding appendages. Differences in rotational torques between models with a tube versus those without a tube implied that a large tube may have increased the rotational stability of the feeding posture in environments with variable current directions. No differences were detected between drag measurements on models with and without the anal tube; thus the 'splitter-plate' function of the tube was rejected. ▭ Batocrinid anal tube, functional morphology, physical modeling .     

Ion channels and schizophrenia: a gene set-based analytic approach to GWAS data for biological hypothesis testing

Schizophrenia is a complex genetic disorder. Gene set-based analytic (GSA) methods have been widely applied for exploratory analyses of large, high-throughput datasets, but less commonly employed for biological hypothesis testing. Our primary hypothesis is that variation in ion channel genes contribute to the genetic susceptibility to schizophrenia. We applied Exploratory Visual Analysis (EVA), one GSA application, to analyze European-American (EA) and African-American (AA) schizophrenia genome-wide association study datasets for statistical enrichment of ion channel gene sets, comparing GSA results derived under three SNP-to-gene mapping strategies: (1) GENIC; (2) 500-Kb; (3) 2.5-Mb and three complimentary SNP-to-gene statistical reduction methods: (1) minimum p value (pMIN); (2) a novel method, proportion of SNPs per Gene with p values below a pre-defined α-threshold (PROP); and (3) the truncated product method (TPM). In the EA analyses, ion channel gene set(s) were enriched under all mapping and statistical approaches. In the AA analysis, ion channel gene set(s) were significantly enriched under pMIN for all mapping strategies and under PROP for broader mapping strategies. Less extensive enrichment in the AA sample may reflect true ethnic differences in susceptibility, sampling or case ascertainment differences, or higher dimensionality relative to sample size of the AA data. More consistent findings under broader mapping strategies may reflect enhanced power due to increased SNP inclusion, enhanced capture of effects over extended haplotypes or significant contributions from regulatory regions. While extensive pMIN findings may reflect gene size bias, the extent and significance of PROP and TPM findings suggest that common variation at ion channel genes may capture some of the heritability of schizophrenia.