Stridulation of the clear-wing meadow katydid <i>Xiphelimum amplipennis</i>, adaptive bandwidth

Rubbed wings, analysed calls and peculiar sound generator structure in males of a conocephaline katydid, Xiphelimum amplipennis, give insight into the making of broadband spectra. High shear forces are indicated by a robust forewing morphology. Intensity is high for frequencies in a 20-60 kHz ultrasonic band. Besides a typical katydid sound-radiating mirror and harp, this insect has a long costal series of semitransparent specular sound radiators. These wing cells are loaded behind by an enlarged and partitioned subwing air space. Calls repeat steadily with five different time-domain sound elements. Distinctive spectra are associated with two of these, giving stepwise frequency modulation that combines to create the exceptionally wide spectral breadth. Broadcast sound levels at 10 cm dorsal, right and left, are near 100 dB. Costal wing-cell sound radiation was explored by loading the costal ‘speculae’ with wax. This produced almost no decrease in lateral sound levels, but did alter spectral content. Apparently this insect’s costal region both baffles and radiates. The species lives at high densities in cluttered vegetation and sound signal attenuation should code via spectral shape for distance ranging.Facultad de Ciencias Naturales y Muse

TableButler – a Windows based tool for processing large data tables generated with high-throughput methods

<p>Abstract</p> <p>Background</p> <p>High-throughput "omics" based data analysis play emerging roles in life sciences and molecular diagnostics. This emphasizes the urgent need for user-friendly windows-based software interfaces that could process the diversity of large tab-delimited raw data files generated by these methods. Depending on the study, dozens to hundreds of these data tables are generated. Before the actual statistical or cluster analysis, these data tables have to be combined and merged to expression matrices (e.g., in case of gene expression analysis). Gene annotations as well as information concerning the samples analyzed may be appended, renewed or extended. Often additional data values shall be computed or certain features must be filtered out.</p> <p>Results</p> <p>In order to perform these tasks, we have developed a Microsoft Windows based application, "<b><it>TableButler</it></b>", which allows biologists or clinicians without substantial bioinformatics background to perform a plethora of data processing tasks required to analyze the large-scale data.</p> <p>Conclusion</p> <p><b><it>TableButler </it></b>is a monolithic Windows application. It is implemented to handle, join and preprocess large tab delimited ASCII data files. The intuitive user interface enables scientists (e.g. biologists, clinicians or others) to setup workflows for their specific problems by simple drag-and drop like operations.</p> <p>For more details about <b><it>TableButler</it></b>, visit <url>http://www.OncoExpress.org/software/tablebutler</url>.</p

Investigation of tumor hypoxia using a two-enzyme system for in vitro generation of oxygen deficiency

<p>Abstract</p> <p>Background</p> <p>Oxygen deficiency in tumor tissue is associated with a malign phenotype, characterized by high invasiveness, increased metastatic potential and poor prognosis. Hypoxia chambers are the established standard model for <it>in vitro </it>studies on tumor hypoxia. An enzymatic hypoxia system (GOX/CAT) based on the use of glucose oxidase (GOX) and catalase (CAT) that allows induction of stable hypoxia for <it>in vitro </it>approaches more rapidly and with less operating expense has been introduced recently. Aim of this work is to compare the enzymatic system with the established technique of hypoxia chamber in respect of gene expression, glucose metabolism and radioresistance, prior to its application for <it>in vitro </it>investigation of oxygen deficiency.</p> <p>Methods</p> <p>Human head and neck squamous cell carcinoma HNO97 cells were incubated under normoxic and hypoxic conditions using both hypoxia chamber and the enzymatic model. Gene expression was investigated using Agilent microarray chips and real time PCR analysis. ¹⁴C-fluoro-deoxy-glucose uptake experiments were performed in order to evaluate cellular metabolism. Cell proliferation after photon irradiation was investigated for evaluation of radioresistance under normoxia and hypoxia using both a hypoxia chamber and the enzymatic system.</p> <p>Results</p> <p>The microarray analysis revealed a similar trend in the expression of known HIF-1 target genes between the two hypoxia systems for HNO97 cells. Quantitative RT-PCR demonstrated different kinetic patterns in the expression of carbonic anhydrase IX and lysyl oxidase, which might be due to the faster induction of hypoxia by the enzymatic system. ¹⁴C-fluoro-deoxy-glucose uptake assays showed a higher glucose metabolism under hypoxic conditions, especially for the enzymatic system. Proliferation experiments after photon irradiation revealed increased survival rates for the enzymatic model compared to hypoxia chamber and normoxia, indicating enhanced resistance to irradiation. While the GOX/CAT system allows independent investigation of hypoxia and oxidative stress, care must be taken to prevent acidification during longer incubation.</p> <p>Conclusion</p> <p>The results of our study indicate that the enzymatic model can find application for <it>in vitro </it>investigation of tumor hypoxia, despite limitations that need to be considered in the experimental design.</p

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

Finding Our Way through Phenotypes

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility

The hemolymph vascular system in Araneus diadematuswith special focus on intraspecific variability in artery systems

Volume: 44Start Page: 153End Page: 16

Morphological description, character conceptualization and the reconstruction of ancestral states exemplified by the evolution of arthropod hearts.

Arthropods are the most species-rich taxon within Metazoa and have gone through major evolutionary changes with regard to body organization. Arthropod hearts and their associated vascular systems are thus morphologically highly disparate: while some arthropods exhibit very powerful hearts and complex vascular systems, other arthropods do not possess any kind of vascular system or heart at all. A comprehensive study investigating the structure of arthropods hearts has never been undertaken. In this study, we therefore investigate the hearts of 34 species from all major arthropod groups using various imaging techniques (confocal laser scanning microscopy, micro-computed tomography, histology) and describe them by addressing different aspects of heart morphology, e.g. the structure of the myocard or the composition of ostia. In a next step, we conceptualize 18 characters related to heart morphology and their respective character states and-using additional data from the literature-score a matrix for a total of 45 species from 38 supraspecific taxa. We map the characters onto prevailing phylogenetic hypotheses and perform parsimony-based ancestral state reconstruction to trace the evolutionary transformations undergone by arthropod hearts. An exploration of the character concepts (as explanatory hypotheses) reveals ontological peculiarities of character statements that clearly distinguish them in terms of ontological status from descriptive statements (i.e. descriptions of morphemes). The implications of these findings influence the interpretation of ground patterns as explanations. This first phylogenetic approach to heart morphology in the arthropod ground pattern reveals numerous new putative synapomorphies and leads to a reconsideration of the morphology of circulatory systems in early arthropods. Hypotheses on the evolution of hearts in (Pan-) Arthropoda are illustrated and discussed