Should congruence between intra- and interspecific ecomorphological relationships be expected? A case study with the great tit,Parus major

We studied the relationship between leg morphology and posture while feeding in a population of great tits (Parus major) under controlled conditions to investigate to what extent morphology and ecology are linked at the individual level. From predictions generated at the interspecific level within the genus Parus (Moreno and Carrascal 1993), we tested whether intra- and interspecific ecomorphological relationships are consistent. Within our population, neither leg bone lengths nor leg muscle morphology were related to the feeding posture of individuals. However, differences in body weight were correlated with inter-individual differences in time spent hanging. These results demonstrate that the association between intra- and interspecific ecomorphological relationships is not uniform. We argue that, at the intraspecific level, body weight overrides the significance of other traits that have a functional meaning at the interspecific level (i.e. leg segment lengths, muscular morphology), due to isometric variation of morphological traits (muscular and skeletal) with body mass. Thus, the discrepancy between the ecomorphological associations at intra- and interspecific levels is the result of a problem of scale (morphological changes in evolutionary time and isometric variation of morphological traits with body mass in ecological time).     

Validated biomechanical model for efficiency and speed of rowing

The speed of a competitive rowing crew depends on the number of crew members, their body mass, sex and the type of rowing—sweep rowing or sculling. The time-averaged speed is proportional to the rower?s body mass to the 1/36^th power, to the number of crew members to the1/9^th power and to the physiological efficiency (accounted for by the rower?s sex) to the 1/3^rd power. The quality of the rowing shell and propulsion system is captured by one dimensionless parameter that takes the mechanical efficiency, the shape and drag coefficient of the shell and the Froude propulsion efficiency into account. We derive the biomechanical equation for the speed of rowing by two independent methods and further validate it by successfully predicting race times. We derive the theoretical upper limit of the Froude propulsion efficiency for low viscous flows. This upper limit is shown to be a function solely of the velocity ratio of blade to boat speed (i.e., it is completely independent of the blade shape), a result that may also be of interest for other repetitive propulsion systems.     

Ranking and clustering of Drosophila olfactory receptors using mathematical morphology

This article introduces an alignment-free clustering method in order to cluster all the 66 DORs sequentially diverse protein sequences. Two different methods are discussed: one is utilizing twenty standard amino acids (without grouping) and another one is using chemical grouping of amino acids (with grouping). Two grayscale images (representing two protein sequences by order pair frequency matrices) are compared to find the similarity index using morphology technique. We could achieve the correlation coefficients of 0.9734 and 0.9403 for without and with grouping methods respectively with the ClustalW result in the ND5 dataset, which are much better than some of the existing alignment-free methods. Based on the similarity index, the 66 DORs are clustered into three classes - Highest, Moderate and Lowest - which are seen to be best fitted for 66 DORs protein sequences. OR83b is the distinguished olfactory receptor expressed in divergent insect population which is substantiated through our investigation.     

On A Six-Dimensional Representation of RNA Secondary Structures

Abstract

In this paper, we proposed a 6-D representation of RNA secondary structures. The use of the 6-D representation is illustrated by constructing structure invariants. Comparisons with the similarity/dissimilarity results based on 6-D representation for a set of RNA secondary structures, are considered to illustrate the use of our structure invariants based on the entries in derived sequence matrices restricted to a selected width of a band along the main diagonal.     

Fire,aridity and seed banks. What does seed bank composition reveal about community processes in fire‐prone desert?

Questions: The relationship between fire, aridity and seed banks is poorly understood in plant community ecology. We tested whether there was a close correspondence between the seed bank and standing vegetation composition with time‐since‐fire in a desert. We also examined whether longer‐lived species showed seed limitation relative to more ephemeral species, as this could influence grass‐woody ratios in a major biome. Location: Dune hummock grasslands/shrublands of central Australia. Methods: The effects of time‐since‐fire on floristic and functional group composition were examined by comparing plots unburned since 1984 against plots that had been burned in 2002. Three methods were used to quantify seed abundances: a germination trial using heat and smoke application, a flotation method, and a sieving method. Results: Seed bank densities were very low (<3000 m^?2). Species similarity between the seed bank and standing vegetation was high at sites recently burned (0.86) and low in sites long‐since burned (0.52). The relative abundance of ephemeral species in the seed bank peaked in recently burned plots, but the relative abundance of seeds of woody species did not match the pattern of abundance in the standing vegetation. Remarkably, the dominant perennial grasses and woody species were either absent from the seed bank or present at extremely low abundances. Discussion: Differences in the relative abundance of ephemeral species between standing vegetation and seed bank relate to the post‐fire succession process. The small soil pool of seed from woody species may be explained by allocation to belowground carbohydrate storage over seed production. Field observations suggest, however, that production of strongly dormant seed can be prolific and that high levels of seed predation make this system strongly seed‐limited. The discovery of this seed bank syndrome indicates that shifts in grass‐woody ratios can be driven by the juxtaposition of unpredictable seed rain and fire events in these desert dunes. However, estimates of grass‐woody ratios due to changing fire regimes will be difficult to predict.     

Similarity analysis for DNA sequences based on chaos game representation. Case study: The albumin

Using chaos game representation we introduce a novel and straightforward method for identifying similarities/dissimilarities between DNA sequences of the same type, from different organisms. A matrix is associated to each CGR pattern and the similarities result from the comparison between the matrices of the sequences of interest. Three different methods of analysis of the resulting difference matrix are considered: a 3-dimensional representation giving both local and global information, a numerical characterization by defining an n-letter word similarity measure and a statistical evaluation. The method is illustrated by implementation to the study of albumin nucleotides sequences from eight mammal species taking as reference the human albumin.     

广东南岭自然保护区堇菜属植物垂直分布格局的研究

在南岭自然保护区核心区选择海拔高度为500—600m、600—800m、800—1000m、1000—1200m、1200—1400m、1400—1600m、1600—1800m、1800—1902m共8个连续的海拔梯度,分别对植物群落中的堇菜属植物进行普查。结果表明,随着海拔升高,各海拔段有堇菜属植物5、8、9、10、9、7、3、1种,以中海拔段的物种多样性较高。两海拔段间距离越近,物种相似性系数越大;距离越远,相似性系数越小。在中海拔段,堇菜属植物种类的多度最大,两端较小。南岭自然保护区堇菜属植物的垂直分布格局呈“中间膨胀型”或“单峰型”,与普遍的木本植物一致,这种格局可能是与沿海拔水热梯度的变化相关。     

Sub-epitopic dissection of HCV E1<Subscript>315–328</Subscript>HRMAWDMMMNWSPT sequence by similarity analysis

Summary. Our labs are focused on identifying amino acid sequences having the ability to react specifically with the functional binding site of a complementary antibody. Our epitopic definition is based on the analysis of the similarity level of antigenic amino acid sequences to the host proteome. Here, the similarity profile to the human proteome of an HCV E1 immunodominant epitope, i.e. the HCV E1_315–328HRMAWDMMMNWSPT sequence, led to i) characterizing the immunoreactive HCV E1 315–328 region as a sequence endowed with a low level of similarity to human proteins; ii) defining 2 contiguous immunodominant linear determinants respectively located at the NH₂ and COOH terminus of the conserved viral antigenic sequence. This study supports the hypothesis that low sequence similarity to the host’s proteome modulates the pool of epitopic amino acid sequences in a viral antigen, and appears of potential value in defining immunogenic viral peptide sequences to be used in immunotherapeutic approaches for HCV treatment. Authors’ address: D. Kanduc, Department of Biochemistry and Molecular Biology, University of Bari, Via Orabona 4, Bari 70125, Italy     

Comparison of protein secondary structures based on backbone dihedral angles

In this article, we propose a relatively similar measure to compare protein secondary structures. We first transform a protein secondary structure into a special sequence representation (angle sequence) based on a partition of the backbone φ,ψ-space. Then, pairwise sequence distance is evaluated on the basis of a symbolic sequence complexity. To illustrate our approach, we construct the similarity tree of 24 proteins from PDB.