Denver Papillae Protocol for Objective Analysis of Fungiform Papillae

The goal of the Denver Papillae Protocol is to use a dichotomous key to define and prioritize the characteristics of fungiform papillae (FP) to ensure consistent scoring between scorers. This protocol builds off of a need that has arisen from the last two decades of taste research using FP as a proxy for taste pore density. FP density has historically been analyzed using Miller & Reedy’s 1990 characterizations of their morphology: round, stained lighter, large, and elevated. In this work, the authors forewarned that stricter definitions of FP morphology needed to be outlined. Despite this call to action, follow up literature has been scarce, with most studies continuing to cite Miller & Reedy’s original work. Consequently, FP density reports have been highly variable and, combined with small sample sizes, may contribute to the discrepant conclusions on the role of FP in taste sensitivity. The Genetics of Taste Lab explored this apparent inconsistency in counting and found that scorers were individually prioritizing the importance of these characteristics differently and had no guidance for when a papilla had some, but not all, of the reported qualities of FP. The result of this subjectivity is highly variable FP counts of the same tongue image. The Denver Papillae Protocol has been developed to remedy this consequence through use of a dichotomous key that further defines and prioritizes the importance of the characteristics put forth by Miller & Reedy. The proposed method could help create a standard way to quantify FP for researchers in the field of taste and nutritional studies.     

FIM Imaging and FIMtrack: Two New Tools Allowing High-throughput and Cost Effective Locomotion Analysis

The analysis of neuronal network function requires a reliable measurement of behavioral traits. Since the behavior of freely moving animals is variable to a certain degree, many animals have to be analyzed, to obtain statistically significant data. This in turn requires a computer assisted automated quantification of locomotion patterns. To obtain high contrast images of almost translucent and small moving objects, a novel imaging technique based on frustrated total internal reflection called FIM was developed. In this setup, animals are only illuminated with infrared light at the very specific position of contact with the underlying crawling surface. This methodology results in very high contrast images. Subsequently, these high contrast images are processed using established contour tracking algorithms. Based on this, we developed the FIMTrack software, which serves to extract a number of features needed to quantitatively describe a large variety of locomotion characteristics. During the development of this software package, we focused our efforts on an open source architecture allowing the easy addition of further modules. The program operates platform independent and is accompanied by an intuitive GUI guiding the user through data analysis. All locomotion parameter values are given in form of csv files allowing further data analyses. In addition, a Results Viewer integrated into the tracking software provides the opportunity to interactively review and adjust the output, as might be needed during stimulus integration. The power of FIM and FIMTrack is demonstrated by studying the locomotion of Drosophila larvae.     

Biogeographic area relationships of lowland Neotropical rainforest based on raw distributions of vertebrate groups

Hypotheses of the historic biogeography of Neotropical anurans inhabiting lowland forests were generated using Parsimony Analysis of Endemicity. In order to establish comparisons with the biogeographical patterns of other vertebrates, previous cladistic analyses reported in the literature (for lizards and primates) were extended and reanalysed to match the geographical scope of the anuran analysis. Cladistic analysis of the distribution of 335 anuran species at 14 localities showed two regions that form a basal dichotomy: (1) Central America + Choco and (2) Amazon Basin + Brazilian Atlantic Forest. This result is interpreted as the first vicariance event that separated lowland Neotropical rainforests into Cis-Andean (east from the Andes) and Trans-Andean (west from the Andes) areas. Within the Cis-Andean localities, the earliest separation occurred between the Amazon Basin and the Brazilian Atlantic Forest. Within the Amazon Basin, three distinctive clusters are defined: (1) Belem, (2) Guianan Region, and (3) Upper Amazon Basin. Data sets on the distribution of anurans, lizards, and mammals have strong cladistic signal. Strong congruence exists among the area cladograms of anurans, lizards, and primates. All of them have, or at least did not conflict with: (1) a basal separation between Cis- and Trans-Andean regions, (2) a Central American clade, (3) the Choco Region is sister to the Central American clade, (4) an Amazon Basin clade, (5) an Upper Amazon Basin clade, and (6) a Guianan clade. The area cladograms are dichotomous and therefore do not support biogeographic theories that hypothesize simultaneous isolations of biotas in the Neotropics.     

Simultaneous parsimony jackknife analysis of 2538rbcL DNA sequences reveals support for major clades of green plants, land plants, seed plants and flowering plants

The ever-larger data matrices resulting from continuing improvements in DNA sequencing techniques require faster and more efficient methods of phylogenetic analysis. Here we explore a promising new method, parsimony jackknifing, by analyzing a matrix comprising 2538 sequences of the chloroplast generbcL. The sequences included cover a broad taxonomic range, from cyanobacteria to flowering plants. Several parsimony jackknife analyses were performed, both with and without branch-swapping and multiple random addition sequences: 1) including all positions; 2) including only first and second codon positions; 3) including only third positions; and 4) using only transversions. The best resolution was obtained using all positions. Removal of third positions or transitions led to massive loss of resolution, although using only transversions somewhat improved basal resolution. While branch-swapping improved both resolution and the support found for several groups, most of the groups could be recovered by faster simple analyses. Designed to eliminate groups poorly supported by the data, parsimony jackknifing recognizes 1400 groups on the basis of allrbcL positions. These include major taxa such as green plants, land plants, flowering plants, monocots and eudicots. We include appendices of supported angiosperm families, as well as larger groups.     

A model of the plant-to-plant movement of aphids II. Estimation of parameters and the application

1. It was shown in the previous report that the statistical model of the plant-to-plant movement of aphids could be fitted well to the actual population of barley aphids (Shiyomi , 1967). To examine validity of the model, results of the further experiments were analysed and the methods of estimation of parameters were given in this paper.
2. Comparing the estimates of the parameters obtained by the moment method with those obtained by the maximum likelihood method, the estimates from the latter method were somewhat precise.
3. The theoretical frequency distributions calculated from the model were fitted very well to the observed ones.
4. The model was reexamined with reference to the results obtained byItô (1954, 1960). When the distance between plants was less than 4.5 cm, the farther was the distance between plants, the smaller was the rate of the plant-to-plant movement of aphids. When the distance was greater than 4.5 cm, however, the rate of the plant-to-plant movement was independent of the distance. This result is similar to that ofItô .

     

Comparative phylogeography of the western Indian Ocean reef fauna

Assessing patterns of connectivity at the community and population levels is relevant to marine resource management and conservation. The present study reviews this issue with a focus on the western Indian Ocean (WIO) biogeographic province. This part of the Indian Ocean holds more species than expected from current models of global reef fish species richness. In this study, checklists of reef fish species were examined to determine levels of endemism in each of 10 biogeographic provinces of the Indian Ocean. Results showed that the number of endemic species was higher in the WIO than in any other region of the Indian Ocean. Endemic species from the WIO on the average had a larger body size than elsewhere in the tropical Indian Ocean. This suggests an effect of peripheral speciation, as previously documented in the Hawaiian reef fish fauna, relative to other sites in the tropical western Pacific. To explore evolutionary dynamics of species across biogeographic provinces and infer mechanisms of speciation, we present and compare the results of phylogeographic surveys based on compilations of published and unpublished mitochondrial DNA sequences for 19 Indo-Pacific reef-associated fishes (rainbow grouper Cephalopholis argus, scrawled butterflyfish Chaetodon meyeri, bluespot mullet Crenimugil sp. A, humbug damselfish Dascyllus abudafur/Dascyllus aruanus, areolate grouper Epinephelus areolatus, blacktip grouper Epinephelus fasciatus, honeycomb grouper Epinephelus merra, bluespotted cornetfish Fistularia commersonii, cleaner wrasse Labroides sp. 1, longface emperor Lethrinus sp. A, bluestripe snapper Lutjanus kasmira, unicornfishes Naso brevirosris, Naso unicornis and Naso vlamingii, blue-spotted maskray Neotrygon kuhlii, largescale mullet Planiliza macrolepis, common parrotfish Scarus psicattus, crescent grunter Terapon jarbua, whitetip reef shark Triaenodon obesus) and three coastal Indo-West Pacific invertebrates (blue seastar Linckia laevigata, spiny lobster Panulirus homarus, small giant clam Tridacna maxima). Heterogeneous and often unbalanced sampling design, paucity of data in a number of cases, and among-species discrepancy in phylogeographic structure precluded any generalization regarding phylogeographic patterns. Nevertheless, the WIO might have been a source of haplotypes in some cases and it also harboured an endemic clade in at least one case. The present survey also highlighted likely cryptic species. This may eventually affect the accuracy of the current checklists of species, which form the basis of some of the recent advances in Indo-West Pacific marine ecology and biogeography.     

Formative Assessment and Increased Student Involvement Increase Grades in an Upper Secondary School Biology Course

This study shows that formative methods and increased student participation has a positive influence on learning measured as grades. The study was conducted during the course Biology A in a Swedish Upper Secondary School. The students constructed grade criteria and defined working methods and type of examination within a given topic, Gene technology. The procedure resulted in variation within teaching and examination carried out as an oral test in small groups. In the analysis, students’ grades on Gene technology were analysed in comparison with grades on other topics within the course, and the results show that mean grade is significantly higher on Gene technology. Based on the results and student course evaluations, I discuss the reasons behind the good results and the relation to participation, student interest, teacher and type of examination.     

An Algorithm for Cladistics—Method of Minimal Parallel Evolution

The paper presented here is Concerned with the numerical cladisties. In consideration of the fact that the parallel evolution has close relation to the length of evolution graph, a new method of reconstructing evolutionary tree has been developed for the application and practice of cladistics. The procedure of the algorithm of the new method presented in Table I is similar to the method described in paper "An algorithm for cladistics method of maximal same step length". An essential step of the algorithm is how to decide the coefficient between two cladistic units (CTUs). A coefficient called parallel evolutionary coefficient between CTUp and CTUq is defined as follows: where the j is code of CTU and the i is code of character; E(p, q, i, j) is a function given by following expression: min (X_ij, Xpj)+(X_ij, Xqj)-2min(Xpj, Xqj) as Xij>min (Xpj, Xqj) E(p,q, i,j ) = 0 otherwise. where the X_ij is the ith row (CTU) jth colunm (Character) element of the data matrix. Because the method of minimal parallel evolution is closely related to the length of evolutionary graph, it is superior to the method of maximal same step length. A simple datum as an example for comparison shows that the method of minimal parallel evolution can arrive at a better result. But in some cases, we may combine one method with another and thus the coefficient should take following form: S(S_ij)=M·S (C) _ij-N·S(P) _ij in which S (C) _ij and S (P) _ij are the same step coefficients and the parallel evolution coefficient respectively, and the M and N are positive integers as a weightnumber being given in advance.     

杭州西湖山区植被的分类

用Braun-B1anquet法对西湖山区植被的132个样地进行了群落的分类。初步确定了2个 群丛(木荷群丛与黄连木群丛)、7个亚群丛和6个变型;并对28个鉴别种组进行了分析,它们都较好地反映了群落分类单位的特征和生境条件特点以及植被在空间分布上的连续性变异。