The perception of inferred action

Our actions, and those of others, are often partly obscured from view. This complicates the sensory inputs that guide motor actions. In this issue of Neuron, Umilità and colleagues demonstrate that "mirror neurons" in ventral premotor cortex respond when monkeys observe hidden, but inferred, actions.     

Trends in protein evolution inferred from sequence and structure analysis

Complementary developments in comparative genomics, protein structure determination and in-depth comparison of protein sequences and structures have provided a better understanding of the prevailing trends in the emergence and diversification of protein domains. The investigation of deep relationships among different classes of proteins involved in key cellular functions, such as nucleic acid polymerases and other nucleotide-dependent enzymes, indicates that a substantial set of diverse protein domains evolved within the primordial, ribozyme-dominated RNA world.     

A muscle controlled finite-element model of laryngeal abduction and adduction

A three-dimensional finite-element model was developed to simulate the complex movement of the laryngeal cartilages during vocal fold abduction and adduction. The model consists of cricoid and arytenoid cartilages, as well as the intralaryngeal muscles and vocal folds. The active and passive properties of the muscles were idealised by one-dimensional elements based on the Hill theory. Its controlling input value is a time dependent stimulation rate. Optimisation loops have been carried out for the arrangement of the individual stimulation rates. Since in vivo measurements are not feasible, the developed biomechanical model shall be used to analyse the force distribution within the laryngeal muscles during phonatory manoeuvres. Simulations of abduction and adduction in different pitches of voice lead to realistic tensions of the vocal folds. The model is a first step to analyse motional vocal fold diseases and to predict the consequences of phonosurgical interventions.     

A muscle controlled finite-element model of laryngeal abduction and adduction

A three-dimensional finite-element model was developed to simulate the complex movement of the laryngeal cartilages during vocal fold abduction and adduction. The model consists of cricoid and arytenoid cartilages, as well as the intralaryngeal muscles and vocal folds. The active and passive properties of the muscles were idealised by one-dimensional elements based on the Hill theory. Its controlling input value is a time dependent stimulation rate. Optimisation loops have been carried out for the arrangement of the individual stimulation rates. Since in vivo measurements are not feasible, the developed biomechanical model shall be used to analyse the force distribution within the laryngeal muscles during phonatory manoeuvres. Simulations of abduction and adduction in different pitches of voice lead to realistic tensions of the vocal folds. The model is a first step to analyse motional vocal fold diseases and to predict the consequences of phonosurgical interventions.     

On the origin of photosynthesis as inferred from sequence analysis

Sequence alignments between membrane-spanning segments of pheophytin-quinone-type photosynthetic reaction centers, FeS-type photosynthetic reaction centers, core chlorophyll-proteins of PS II, chlorophyll t a/t b-containing antenna proteins of plants and light-harvesting complexes of purple bacteria led us to postulate a large common ancestral pigment-carrying protein with more than 10 membrane spans. Its original function as a UV-protector of the primordial cell is discussed. It is conceivable that a purely dissipative photochemistry started still in the context of the UV-protection. We suggest that mutations causing the t loss of certain porphyrin-type pigments led to the acquisition of redox cofactors and paved the way for a gradual transition from dissipative to productive photochemistry.     

Speciation in Pyricularia inferred from multilocus phylogenetic analysis

Pyricularia isolates from various host plants were subjected to a multilocus phylogenetic analysis based on rDNA-ITS, actin, β-tubulin, and calmodulin loci. A combined gene tree resolved seven groups with 100 % BS support, suggesting that they are monophyletic groups supported concordantly by all four loci. By incorporating biological and morphological species criteria, each of the seven groups was considered to be a current species. However, phylogenetic relationships among these species were unresolved in the single-gene trees and in the combined tree. Furthermore, the transition from concordance to conflict occurred more than once in the combined gene tree. They were interpreted by assuming that Pyricularia has evolved through repeated species radiation. The transition point other than the current species limit was considered to be the limit of the former species.     

Applications of finite-element scaling analysis in primatology

The study of biological shape in three dimensions using landmark data can now be accomplished using several alternative methods. This report focuses on the use of finite-element scaling analysis in primate craniofacial morphology. The method is particularly useful in its ability to localize the differences between forms, thereby indicating those loci that differ most between specimens. Several examples of this feature are provided from primatological research. Particulars of the methods are also discussed in an attempt to provide the reader with cautionary knowledge for prudent application of the method in future research.     

MRI-based finite-element analysis of left ventricular aneurysm

Tagged MRI and finite-element (FE) analysis are valuable tools in analyzing cardiac mechanics. To determine systolic material parameters in three-dimensional stress-strain relationships, we used tagged MRI to validate FE models of left ventricular (LV) aneurysm. Five sheep underwent anteroapical myocardial infarction (25% of LV mass) and 22 wk later underwent tagged MRI. Asymmetric FE models of the LV were formed to in vivo geometry from MRI and included aneurysm material properties measured with biaxial stretching, LV pressure measurements, and myofiber helix angles measured with diffusion tensor MRI. Systolic material parameters were determined that enabled FE models to reproduce midwall, systolic myocardial strains from tagged MRI (630 +/- 187 strain comparisons/animal). When contractile stress equal to 40% of the myofiber stress was added transverse to the muscle fiber, myocardial strain agreement improved by 27% between FE model predictions and experimental measurements (RMS error decreased from 0.074 +/- 0.016 to 0.054 +/- 0.011, P < 0.05). In infarct border zone (BZ), end-systolic midwall stress was elevated in both fiber (24.2 +/- 2.7 to 29.9 +/- 2.4 kPa, P < 0.01) and cross-fiber (5.5 +/- 0.7 to 11.7 +/- 1.3 kPa, P = 0.02) directions relative to noninfarct regions. Contrary to previous hypotheses but consistent with biaxial stretching experiments, active cross-fiber stress development is an integral part of LV systole; FE analysis with only uniaxial contracting stress is insufficient. Stress calculations from these validated models show 24% increase in fiber stress and 115% increase in cross-fiber stress at the BZ relative to remote regions, which may contribute to LV remodeling.     

Insulin action in skeletal muscle from patients with NIDDM

Insulin resistance in peripheral tissues is a common feature of non insulin-dependent diabetes mellitus (NIDDM). The decrease in insulin-mediated peripheral glucose uptake in NIDDM patients can be localized to defects in insulin action on glucose transport in skeletal muscle. Following short term in vitro exposure to both submaximal and maximal concentrations of insulin, 3-O-methylglucose transport rates are 40-50% lower in isolated skeletal muscle strips from NIDDM patients when compared to muscle strips from nondiabetic subjects. In addition, we have shown that physiological levels of insulin induce a 1.6-2.0 fold increase in GLUT4 content in skeletal muscle plasma membranes from control subjects, whereas no significant increase was noted in NIDDM skeletal muscle. Impaired insulin-stimulated GLUT4 translocation and glucose transport in NIDDM skeletal muscle is associated with reduced insulin-stimulated IRS-1 tyrosine phosphorylation and PI3-kinase activity. The reduced IRS-1 phosphorylation cannot be attributed to decreased protein expression, since the IRS-1 protein content is similar between NIDDM subjects and controls. Altered glycemia may contribute to decreased insulin-mediated glucose transport in skeletal muscle from NIDDM patients. We have shown that insulin-stimulated glucose transport is normalized in vitro in the presence of euglycemia, but not in the presence of hyperglycemia. Thus, the circulating level of glucose may independently regulate insulin stimulated glucose transport in skeletal muscle from NIDDM patients via a down regulation of the insulin signaling cascade.     

Genetic control ofH-2 alloantigens as inferred from analysis of mutations

A number of studies of phenotypic effects of anH-2D mutant, B10.D2(M504), have been reported by different laboratories. Their results show that lymphocyte-defined (LD) and serologically-defined (SD) functions of an antigenic molecule can both be controlled by a single gene,H-2D. Possible explanations of the observed phenotypic effects of 504 and other knownH-2 mutations are also discussed.     

A worldwide analysis of AG molecular diversity inferred from serology.

Ten population samples from different geographic origins were tested serologically for the AG polymorphism of human beta-lipoproteins. Their haplotype frequencies were used with previously published data to perform a wide analysis of AG genetic differentiations throughout the world. Coancestry coefficients were computed from weighted F(ST)s among populations by using a matrix of molecular distances among AG haplotypes, which is here determined on the basis of DNA studies. Coancestry coefficients derived from unweighted F(ST)s and more classical Prevosti distances were computed on the same data and used for a comparison. In all cases a highly significant correlation was found between genetics and geography on a worldwide scale, while the significance of the correlation with linguistics differed. A test of significance of the pairwise F(ST)s among populations also gave different results depending on whether the molecular distance matrix among AG haplotypes was included. Globally, this study shows that in spite of being highly significantly correlated to each other, different genetic distance measures can lead to different interpretations of the same data set. Moreover, the elucidation of the molecular models related to the presently known serological polymorphisms may represent an additional tool for analyzing such polymorphisms in human population genetics studies.     

Molecular phylogenetic analysis of ant subfamily relationship inferred from rDNA sequences

The relationships among ant subfamilies were studied by phylogenetic analysis of rDNA sequences of 15 species from seven subfamilies. PCR primers were designed on the basis of the rDNA sequence of the Australian bulldog ant, Myrmecia croslandi, previously determined. Phylogenetic trees were constructed using sequences of a fragment of 18S rDNA (1.8 kb), a fragment of 28S rDNA (0.7 kb excluding variable regions) and a combination of the 18S and 28S rDNAs, by neighbor-joining (NJ), maximum parsimony (MP) and maximum likelihood (ML). rDNA sequences corresponding to the same fragments from three non-ant hymenopteran species (a sawfly, a bee and a wasp) were employed as outgroups. These trees indicated that the ant subfamilies were clustered singly, and, among the seven subfamilies examined, Ponerinae and six other subfamilies are in a sister-groups relationship. The relationship among the six subfamilies, however, was not clarified. The phylogenetic trees constructed in the present study are not in contradiction to the tree from cladistic analysis of morphological data by Baroni Urbani et al. (1992) and the tree from morphological and molecular data (Ward and Brady, 2003), but are inconsistent with the traditional phylogeny. The present results thus raise a question as to the status of some traditionally employed "key" morphological characters. The present results also call for a reexamination of Amblyopone traditionally treated as a member of Ponerinae as belonging to a new subfamily.     

Modular arrangement of proteins as inferred from analysis of homology.

The structure of many proteins consists of a combination of discrete modules that have been shuffled during evolution. Such modules can frequently be recognized from the analysis of homology. Here we present a systematic analysis of the modular organization of all sequenced proteins. To achieve this we have developed an automatic method to identify protein domains from sequence comparisons. Homologous domains can then be clustered into consistent families. The method was applied to all 21,098 nonfragment protein sequences in SWISS-PROT 21.0, which was automatically reorganized into a comprehensive protein domain database, ProDom. We have constructed multiple sequence alignments for each domain family in ProDom, from which consensus sequences were generated. These nonreduntant domain consensuses are useful for fast homology searches. Domain organization in ProDom is exemplified for proteins of the phosphoenolpyruvate:sugar phosphotransferase system (PEP:PTS) and for bacterial 2-component regulators. We provide 2 examples of previously unrecognized domain arrangements discovered with the help of ProDom.     

Biogeography and ecological niche evolution in Diapensiaceae inferred from phylogenetic analysis

Diapensiaceae (Ericales) are a small family of about 15 species. Within this clade, two species are broadly distributed throughout the Northern Hemisphere, whereas the remaining species have a disjunct distribution between eastern North America and eastern Asia. To address patterns and processes of diversification in Diapensiaceae, we conducted biogeographic analyses and inferred shifts in the ecological niche across the phylogeny of the clade. Although Diapensiaceae have been the focus of multiple phylogenetic and biogeographic studies, previous studies have been taxonomically limited. This study has greatly improved the phylogenetic underpinning for Diapensiaceae with the most inclusive taxonomic sampling thus far, employing both nuclear and plastid gene sequence data for at least one sample per species in the family. Our estimates indicate that genera of Diapensiaceae variously diverged in the Eocene, Oligocene, and early to mid‐Miocene. The biogeographic analysis suggests that the probable ancestor of the Diapensiaceae crown clade originated in the Nearctic, with vicariance events contributing to the current distribution of the disjunct taxa. Ecological niche, when considered in a phylogenetic context, was observed to be clustered on the basis of biogeographic realm. In general, a greater ecological overlap was found at younger nodes and a greater niche divergence was found among distantly related species. Diversification in Diapensiaceae appears to have been shaped by both large‐scale biogeographic factors, such as vicariance, and divergence in an ecological niche among closely related species.     

Genetic differentiation of hexaploid wheat inferred from analysis of microsatellite loci

Landraces of wheat can serve as important potential sources for extending the genetic basis of selection cultivars. Analysis of microsatellites and typing of polymorphism in a representative sample of 347 genotypes, including landraces and selection cultivars, was performed using a set of 38 selected oligonucleotide primer pairs. Each genotype had a unique allele combination at 39 microsatellite loci examined. Classification of genotypes with respect to the level of their similarity was performed using cluster analysis. The data obtained pointed to genetic differentiation of hexaploid wheat. The groups of cultivars, the formation of which was thought to be associated with the main old areas of wheat cultivation in Europe and Asia, were identified. The basis of each of the groups was formed by landraces of common wheat. The differences between the groups identified were associated with multiple changes in the wheat genome and were expressed as quantitative differences in the allele frequencies of microsatellite loci. The results of the study are of interest in terms of understanding the structure of wheat genetic diversity and revealing the pathways of evolution of this culture.     

Genetic differentiation in the squid Moroteuthis ingens inferred from RAPD analysis

Randomly amplified polymorphic DNA markers (RAPDs) were applied in a cephalopod population study. Samples of the squid Moroteuthis ingens taken from around the Falkland Islands and Macquarie Island were used to test a null hypothesis that M. ingens forms a single, panmictic population in the Southern Ocean. Six of the 8 arbitrary RAPD primers screened produced a total of 30 reproducible polymorphic bands. Analysis of RAPD allele frequencies demonstrated high levels of variation between individuals but little variation between two sample sites. Although the differentiation between the two sites was low, subtle population structure was detected and the null hypothesis was rejected. The implications of low genetic differentiation between the two sites are briefly discussed in terms of possible egg and paralarval drift facilitated via the circumpolar current.     

Composition of carrageenan blends inferred from C-NMR and infrared spectroscopic analysis

Carrageenan blends mainly composed of kappa, iota and lambda carrageenan were investigated by ¹³C-NMR and infrared (IR) spectroscopy. ¹³C-NMR was shown to be a powerful tool for quantifying the kappa-iota ratio in a carrageenan blend. The technique, however, was not helpful for identifying lambda carrageenan. Consequently, IR spectroscopy was used to achieve a semi-quantitative determination of lambda carrageenan. By combining both techniques, the carrageenan composition of several commercial samples was established.     

Phylogenetic relationships of someMicrosporum andArthroderma species inferred from mitochondrial DNA analysis

Thirty-eight strains of 12Microsporum and 10Arthroderma (Nannizzia) species were investigated by analysis of mitochondrial DNA with 6 restriction enzymes, and classified into 13 genetic groups. The phylogenetic tree of the 13 groups thus established was constructed. On the tree,M. audouinii, M. langeronii, M. rivalieri, M. distortum, M. equinum, M. ferrugineum andA. otae comprise one genetic group and are suggested to be the same species.A. gypseum, A. fulvum, M. duboisii, M. ripariae, A. incurvatum, A. persicolor andA. obtusum are clustered on one of five boughs of the tree indicating their close relation.A. racemosum andA. cajetani are also closely related.