scholarly journals Art in Science Competition invites artworks to the annual exhibition on ISMB 2018 in Chicago

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 337
Author(s):  
Lonnie Welch ◽  
Bruno Gaeta ◽  
Diane E. Kovats ◽  
Milana Frenkel Morgenstern
Keyword(s):  
Phylogenetic Trees ◽  
Visual Aids ◽  
Deep Insight ◽  
Art Form ◽  
Wide Range ◽  
Microscope Images ◽  
Scatter Plots ◽  
Flow Diagrams ◽  
Structural Formulae ◽  
Protein Models

The International Society of Computational Biology and Bioinformatics (ISCB) brings together scientists from a wide range of disciplines, including biology, medicine, computer science, mathematics and statistics. Practitioners in these fields are constantly dealing with information in visual form: from microscope images and photographs of gels to scatter plots, network graphs and phylogenetic trees, structural formulae and protein models to flow diagrams, visual aids for problem-solving are omnipresent. The ISCB Art in Science Competition 2017 at the ISCB/ECCB 2017 conference in Prague offered a way to show the beauty of science in art form. Past artworks in this annual exhibition at ISMB combined outstanding beauty and aesthetics with deep insight that perfectly validated the exhibit’s approach or went beyond the problem's solution. Others were surprising and inspiring through the transition from science to art, opening eyes and minds to reflect on the work being undertaken.

scholarly journals Assessing evidence for adaptive evolution in two hearing-related genes important for high-frequency hearing in echolocating mammals

2021 ◽  
Author(s):  
Hui Wang ◽  
Hanbo Zhao ◽  
Yujia Chu ◽  
Jiang Feng ◽  
Keping Sun
Keyword(s):  
Adaptive Evolution ◽  
Hair Cells ◽  
High Frequency ◽  
Phylogenetic Trees ◽  
Outer Hair Cells ◽  
Functional Domain ◽  
Coding Region ◽  
Selective Pressures ◽  
Wide Range ◽  
Different Parts

Abstract High-frequency hearing is particularly important for echolocating bats and toothed whales. Previously, studies of the hearing-related genes Prestin, KCNQ4, and TMC1 documented that adaptive evolution of high-frequency hearing has taken place in echolocating bats and toothed whales. In this study, we present two additional candidate hearing-related genes, Shh and SK2, that may also have contributed to the evolution of echolocation in mammals. Shh is a member of the vertebrate Hedgehog gene family and is required in the specification of the mammalian cochlea. SK2 is expressed in both inner and outer hair cells, and it plays an important role in the auditory system. The coding region sequences of Shh and SK2 were obtained from a wide range of mammals with and without echolocating ability. The topologies of phylogenetic trees constructed using Shh and SK2 were different; however, multiple molecular evolutionary analyses showed that those two genes experienced different selective pressures in echolocating bats and toothed whales compared to non-echolocating mammals. In addition, several nominally significant positively selected sites were detected in the non-functional domain of the SK2 gene, indicating that different selective pressures were acting on different parts of the SK2 gene. This study has expanded our knowledge of the adaptive evolution of high-frequency hearing in echolocating mammals.

scholarly journals Ceramics as the conveyance of art

2017 ◽  
Vol 6 (4) ◽  
pp. 133-139
Author(s):  
Olcay Boratav
Keyword(s):  
Time Perspective ◽  
Background Knowledge ◽  
Original Structure ◽  
The Arts ◽  
Art Form ◽  
Wide Range ◽  
Different Shapes ◽  
Different Cultures ◽  
Greek Pottery ◽  
Shed Light

AbstractThe concept of art has varied according to space and time perspective in each and every period and it has emerged in different forms in every culture. Artists or designers produce a wide range of forms with different materials representing the period and culture while creating their ceramics. Ceramics symbolizes a thousand-year-old endeavor as well as being considered as one of the arts. It has shed light on the history in different shapes and cultures in addition to undertaking the task of conveyance of art with original structure and formal style in the works of art. Ceramics makes identity differences thanks to background knowledge, form and decorative techniques and originality. Art is not for society’s sake; it aims to relieve the tension, to satisfy pleasure, to enable people to see and hear, to use and to evaluate. Different cultures have generated new styles in their ceramics by integrating creativity into their own traditions and techniques as well as interacting with Mayan vases and pots, Greek pottery, Anatolian ceramics and tiles. Some of these impacts have been so profound in ceramics that they have been passed on from generation to generation.This paper seeks to address to the following questions: How was ceramics used in different cultures and periods with composition features such as form, decoration, motif and figure; and how has it undertaken the task of conveyance of art by investigating what features they have. Keywords: ceramics, art, conveyance of art, form, figure.

scholarly journals Predicate logic as a modeling language: modeling and solving some machine learning and data mining problems withIDP3

2014 ◽  
Vol 15 (6) ◽  
pp. 783-817 ◽  
Author(s):  
MAURICE BRUYNOOGHE ◽  
HENDRIK BLOCKEEL ◽  
BART BOGAERTS ◽  
BROES DE CAT ◽  
STEF DE POOTER ◽  
...  
Keyword(s):  
Machine Learning ◽  
Data Mining ◽  
Phylogenetic Trees ◽  
Predicate Logic ◽  
Classical Problem ◽  
Modeling Language ◽  
Finite Model ◽  
Partial Functions ◽  
Inductive Definitions ◽  
Wide Range

AbstractThis paper provides a gentle introduction to problem-solving with the IDP3 system. The core of IDP3 is a finite model generator that supports first-order logic enriched with types, inductive definitions, aggregates and partial functions. It offers its users a modeling language that is a slight extension of predicate logic and allows them to solve a wide range of search problems. Apart from a small introductory example, applications are selected from problems that arose within machine learning and data mining research. These research areas have recently shown a strong interest in declarative modeling and constraint-solving as opposed to algorithmic approaches. The paper illustrates that the IDP3 system can be a valuable tool for researchers with such an interest. The first problem is in the domain of stemmatology, a domain of philology concerned with the relationship between surviving variant versions of text. The second problem is about a somewhat related problem within biology where phylogenetic trees are used to represent the evolution of species. The third and final problem concerns the classical problem of learning a minimal automaton consistent with a given set of strings. For this last problem, we show that the performance of our solution comes very close to that of the state-of-the art solution. For each of these applications, we analyze the problem, illustrate the development of a logic-based model and explore how alternatives can affect the performance.

Visualizing Speciation in Artificial Cichlid Fish

2006 ◽  
Vol 12 (2) ◽  
pp. 243-257 ◽  
Author(s):  
Ross Clement
Keyword(s):  
Phylogenetic Tree ◽  
Phylogenetic Trees ◽  
Cichlid Fish ◽  
Natural Consequence ◽  
Open Problems ◽  
Visualization System ◽  
Low Level ◽  
Wide Range ◽  
Level Information ◽  
History Of

The Cichlid Speciation Project (CSP) is an ALife simulation system for investigating open problems in the speciation of African cichlid fish. The CSP can be used to perform a wide range of experiments that show that speciation is a natural consequence of certain biological systems. A visualization system capable of extracting the history of speciation from low-level trace data and creating a phylogenetic tree has been implemented. Unlike previous approaches, this visualization system presents a concrete trace of speciation, rather than a summary of low-level information from which the viewer can make subjective decisions on how speciation progressed. The phylogenetic trees are a more objective visualization of speciation, and enable automated collection and summarization of the results of experiments. The visualization system is used to create a phylogenetic tree from an experiment that models sympatric speciation.

Variability of Echiniscus tristis Gąsiorek & Kristensen, 2018—is morphology sufficient for taxonomic differentiation of Echiniscidae?

Zootaxa ◽  
2019 ◽  
Vol 4701 (1) ◽  
pp. 1-24 ◽  
Author(s):  
TOMASZ BARTYLAK ◽  
ADAM KULPA ◽  
DARIA GROBYS ◽  
MARTA KEPEL ◽  
ANDRZEJ KEPEL ◽  
...  
Keyword(s):  
Dna Sequences ◽  
28S Rrna ◽  
Life Stages ◽  
Significant Genetic Differentiation ◽  
Wide Range ◽  
Microscope Images ◽  
Different Types ◽  
Taxonomic Confusion ◽  
Species Specific ◽  
Range Of Variation

The majority of species in the genus Echiniscus (Heterotardigrada) have been described based on differences in the chaetotaxy or dorsal sculpture. Dorsal sculpture is, in general, considered to be species-specific and not very variable; however, many problems have arisen due to various interpretations of microscope images, which has led to taxonomic confusion in the genus Echiniscus. Conversely, chaetotaxy is generally much easier to interpret, even using low-quality microscope optics. In this study, we emended the description of Madagascan population of Echiniscus tristis Gąsiorek & Kristensen, 2018 that exhibits several different types of chaetotaxy and dorsal sculpture. The analysed specimens were characterised by two types of chaetotaxy, A-C-Dd-E and A-Dd-E, but we also found a wide range of variation in appendage number, shape and length. The observed differences are partly correlated with life stages. Additionally, we analysed DNA sequences of 28S rRNA, ITS-2 and COI of the two main morphotypes, and did not find significant genetic differentiation of the two morphotypes. This highlights the importance of analysing the morphology of both immature stages and adults, as well as of DNA markers in tardigrade species identification. 

scholarly journals Demonstration of catecholamine and resorcinolamine derivatives as formaldehyde-induced fluorescence in protein models.

1988 ◽  
Vol 36 (6) ◽  
pp. 615-620
Author(s):  
L J Bryan ◽  
S R O'Donnell
Keyword(s):  
Fluorescence Intensity ◽  
Alkyl Chain ◽  
Emission Spectra ◽  
Ring Structure ◽  
Histochemical Demonstration ◽  
Wide Range ◽  
Protein Models ◽  
Fluorescence Microphotometry ◽  
Potential Use ◽  
Long Alkyl Chain

We assessed in protein droplet models the potential use of the formaldehyde condensation method for histochemical demonstration of a wide range of catecholamines and resorcinolamines. The experiments showed that all of the amines tested, except salbutamol and carbuterol, formed fluorophores, and that the fluorescence was specific [i.e., there was no fluorescence in the absence of formaldehyde, the fluorescence was quenched by water, and the fluorophores were subject to photodecomposition by the exciting (405-nm) light]. Peak wavelengths of the emission spectra were 480-485 nm for fluorophores of resorcinolamine derivatives. The fluorescence intensity of the catecholamines was greater than that of the resorcinolamines. Fluorophore formation was not hindered by substitution of t-butyl, phenylisoprophyl, or p-hydroxyphenylisopropyl on the amino-N in catecholamines (t-butylnorepinephrine, Cc24, Cc25, respectively) or resorcinolamines (terbutaline, Th1161, fenoterol, respectively), and fluorophores also formed for catecholamines with the amino-N in a ring structure (rimiterol) or with a long alkyl chain substituted on the amino-N (hexoprenaline). Our study showed that fluorescence microphotometry can be used to detect a range of drugs that are catecholamines or resorcinolamines, and hence it should be possible to use this technique to study the properties of dissipation of these amines in tissues.

Morphology and molecular studies on large Neidium species (Bacillariophyta) of North America, including an examination of Ehrenberg’s types

Phytotaxa ◽  
2015 ◽  
Vol 220 (3) ◽  
pp. 201 ◽  
Author(s):  
Keely E Lefebvre ◽  
Paul B Hamilton
Keyword(s):  
New York ◽  
North America ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
New York State ◽  
Central Area ◽  
Large Species ◽  
Sem Images ◽  
Wide Range ◽  
Future Work

The genus Neidium contains a large array of diatoms with a wide range in structural and morphological forms. Many of the larger species in this genus are old taxa dating back to the 1800s. However, there continues to be confusion over these large species including N. iridis, N. dilatatum, N. firma, and N. amphigomphus. In this study, selected Neidium taxa from North America were examined using LM and SEM images from both Ehrenberg’s original samples and present day samples from Ontario (Canada) and New York State (USA). As well, Neidium individuals were isolated from Adriondack Park, NY (USA) and Ontario (Canada), amplified using a nested PCR protocol and sequenced for rbcL and 18S barcoding genes. The sequence data was concatenated to construct phylogenetic trees using Maximum Likelihood and Bayesian Analysis techniques. Here we present emended species descriptions and sequence data of four previously named Neidium taxa: N. tumescens, N. hitchcockii, N. dilatatum and N. amphigomphus. In addition, we designate isolectotypes for N. hitchcockii, N. dilatatum and N. amphigomphus. A new species is also formally described—N. fossum, sp. nov.—with a designated holotype and sequence data. Neidium fossum is distinguished by its size, longitudinal canal structure, central area and proximal raphe ends. Future work combining traditional morphological methods and phylogenetic methods will allow for further delineation of Neidium species and other diatom taxa.

scholarly journals Phylogenetic Analysis Reveals Multiple Lateral Transfers of Adenosine-5′-Phosphosulfate Reductase Genes among Sulfate-Reducing Microorganisms

2002 ◽  
Vol 184 (1) ◽  
pp. 278-289 ◽  
Author(s):  
Michael W. Friedrich
Keyword(s):  
Phylogenetic Analysis ◽  
Gene Transfer ◽  
16S Rrna ◽  
Lateral Gene Transfer ◽  
Phylogenetic Trees ◽  
Gram Positive ◽  
Sulfate Reducing ◽  
Wide Range ◽  
Aps Reductase ◽  
Key Enzyme

ABSTRACT Lateral gene transfer affects the evolutionary path of key genes involved in ancient metabolic traits, such as sulfate respiration, even more than previously expected. In this study, the phylogeny of the adenosine-5′-phosphosulfate (APS) reductase was analyzed. APS reductase is a key enzyme in sulfate respiration present in all sulfate-respiring prokaryotes. A newly developed PCR assay was used to amplify and sequence a fragment (∼900 bp) of the APS reductase gene, apsA, from a taxonomically wide range of sulfate-reducing prokaryotes (n = 60). Comparative phylogenetic analysis of all obtained and available ApsA sequences indicated a high degree of sequence conservation in the region analyzed. However, a comparison of ApsA- and 16S rRNA-based phylogenetic trees revealed topological incongruences affecting seven members of the Syntrophobacteraceae and three members of the Nitrospinaceae, which were clearly monophyletic with gram-positive sulfate-reducing bacteria (SRB). In addition, Thermodesulfovibrio islandicus and Thermodesulfobacterium thermophilum, Thermodesulfobacterium commune, and Thermodesulfobacterium hveragerdense clearly branched off between the radiation of the δ-proteobacterial gram-negative SRB and the gram-positive SRB and not close to the root of the tree as expected from 16S rRNA phylogeny. The most parsimonious explanation for these discrepancies in tree topologies is lateral transfer of apsA genes across bacterial divisions. Similar patterns of insertions and deletions in ApsA sequences of donor and recipient lineages provide additional evidence for lateral gene transfer. From a subset of reference strains (n = 25), a fragment of the dissimilatory sulfite reductase genes (dsrAB), which have recently been proposed to have undergone multiple lateral gene transfers (M. Klein et al., J. Bacteriol. 183:6028–6035, 2001), was also amplified and sequenced. Phylogenetic comparison of DsrAB- and ApsA-based trees suggests a frequent involvement of gram-positive and thermophilic SRB in lateral gene transfer events among SRB.

scholarly journals TreeSwift: a massively scalable Python tree package

2018 ◽  
Author(s):  
N. Moshiri
Keyword(s):  
Evolutionary Biology ◽  
Phylogenetic Trees ◽  
Phylogenetic Information ◽  
Large Trees ◽  
Wide Range ◽  
User Friendly ◽  
Python Package

AbstractPhylogenetic trees are essential to evolutionary biology, and numerous methods exist that attempt to extract phylogenetic information applicable to a wide range of disciplines, such as epidemiology and metagenomics. Currently, the three main Python packages for trees are Bio.Phylo, DendroPy, and the ETE Toolkit, but as dataset sizes grow, parsing and manipulating ultra-large trees becomes impractical for these tools. To address this issue, we present TreeSwift, a user-friendly and massively scalable Python package for traversing and manipulating trees that is ideal for algorithms performed on ultra-large trees.

scholarly journals Taxonomic circumscription of melanconis-like fungi causing canker disease in China

MycoKeys ◽  
2018 ◽  
Vol 42 ◽  
pp. 89-124 ◽  
Author(s):  
Xinlei Fan ◽  
Zhuo Du ◽  
Jadson D.P. Bezerra ◽  
Chengming Tian
Keyword(s):  
Molecular Phylogeny ◽  
Species Distribution ◽  
Fungal Pathogens ◽  
Phylogenetic Trees ◽  
New Genus ◽  
Sequence Data ◽  
Canker Disease ◽  
Wide Range ◽  
Molecular Phylogenies

Melanconis-like species comprise latent fungal pathogens with a wide range of woody hosts. Taxonomy of these pathogens is difficult due to their uninformative descriptions and similar asexual morphology. Based on molecular phylogenies, many species of this group were placed in various families of Diaporthales. In this study, eight species of melanconis-like fungi were isolated from Betulaalbosinensis, B.platyphylla (Betulaceae), Cornuscontroversa (Cornaceae), Corylusmandshurica (Betulaceae) and Juglansregia (Juglandaceae) in China. These species were phylogenetically placed in three families of Diaporhthales, i.e. Juglanconisjuglandina, J.oblonga (Juglanconidaceae), Melanconiellabetulicolasp. nov., M.corylinasp. nov. (Melanconiellaceae), Melanconisbetulae, Ms.itoana, Ms.stilbostoma (Melanconidaceae) and one new genus, Sheathospora (Melanconiellaceae). Sheathospora is proposed to accommodate Melanconiellacornuta with conical and discrete pycnidia with aseptate, hyaline, cylindrical to ellipsoidal conidia with distinct hyaline sheath on branches of Cornuscontroversa. Combined analyses of ITS, LSU, CAL, RPB2 and TEF1-α sequence data were used to construct the molecular phylogeny. Additionally, we provided separate phylogenetic trees for three families (Juglanconidaceae, Melanconidaceae and Melanconiellaceae) to show the species distribution of melanconis-like fungi in China.

Sign in / Sign up

Export Citation Format

Share Document