Amplification of intermethylated sites experimental design and results analysis with <Emphasis Type="Italic">AIMS in silico</Emphasis> computer software

Amplification of intermethylated sites (AIMS) is a powerful tool for differential methylation screening of genomes. Its applications have nevertheless been limited until recently for the absence of systemic approach to AIMS experimental design and of appropriate computer software for the analysis of AIMS results. We have developed AIMS in silico computer suggestion tool capable of predicting possible experimental outcomes, which assists in designing AIMS experiments depending on the research aims and available instrumentation, and in analyzing experimental results from the point of view of genomic locations of the DNA fragments under study. With AIMS in silico we have characterized qualitatively and quantitatively AIMS products obtainable under different conditions; to ease experimental design we demonstrate AIMS products hierarchical structure. We discuss examples of designing AIMS experiments and of results analysis as well as possible relative to AIMS alternative approaches to differential methylation screening. AIMS in silico computer software is intended to standardize AIMS applications and to turn it into one of the principal approaches towards cancer epigenomes studies as well as towards diagnostics in oncology, including early screening.     

Mikrocomputer-unterstützte prozeßkontrolle in der fermentationstechnik

Nowadays computer control is an effective and well established tool in optimizing fermentation processes. Based on recent development in microelectronics, especially in the field of personal computers, cost effective applications of this technology are now possible, even on laboratory- and pilot scale. In this paper the application of a personal computer (CBM 3032), controlling various types of fermentations, is described. In more detail the availability of physiologically relevant sensors, especially the respiration and the dynamic calorimetry, are discussed. Finally some examples of practical realisations are presented.     

A novel nest‐monitoring camera system using a Raspberry Pi micro‐computer

The utility, availability, cost‐effectiveness, and reliability of prefabricated video systems designed to monitor wildlife have lagged behind the unique and varied needs of many researchers. Many systems are limited by inflexible video settings, lack of adequate data storage, and cannot be programmed by the user. More sophisticated systems can be cost prohibitive, and the literature describing remote wildlife video monitoring has, for the most part, not incorporated advances in camera and computer technology. Here, we present details of a pilot study to design and construct a lower cost (US $340) nest camera system to record the behavior of Acorn Woodpeckers (Melanerpes formicivorus) in artificial tree cavity nests. This system incorporates a Raspberry Pi micro‐computer, Pi NoIR infrared camera, a wireless adapter to transmit video over the Internet, and Deka rechargeable gel batteries for power. We programmed the system to motion‐sense, to record exclusively during daylight hours, and to automatically upload videos to the cloud over wireless Internet. The Raspberry Pi micro‐computer does not require advanced programming or electrical engineering skills to build and configure and, because it is programmable, provides unprecedented flexibility for field researchers who wish to configure the system to the specific needs of their study.     

Schärfentiefe nach Maß

“Focus stacking” in biology: Depth of field as large as required As the shooting distance gets more narrow in photographing, the depth of field shrinks remarkably, making macro and especially microscope photography increasingly difficult. The focus stacking technique solves this problem by producing a series of photographs with different planes of sharpness, which are then combined into a photograph with extremely large depth of field with the help of a computer.     

hw‐quickcheck: an easy‐to‐use computer program for checking genotypes for agreement with Hardy–Weinberg expectations

Deviations from Hardy–Weinberg expectations are frequently a sign of genotyping error. hw‐quickcheck is an easy‐to‐use computer program for detecting departures from Hardy–Weinberg equilibrium. hw‐quickcheck uses exact tests for all of its calculations. These tests include a global test for heterozygote excess/deficiency and genotype‐specific tests.     

The use of reference gene selection programs to study the silvering transformation in a freshwater eel <Emphasis Type="Italic">Anguilla australis</Emphasis>: a cautionary tale

Background  

Quantitative real-time PCR (qPCR) has been the method of choice for the quantification of mRNA. Due to the various artifactual factors that may affect the accuracy of qPCR, internal reference genes are most often used to normalize qPCR data. Recently, many studies have employed computer programs such as GeNorm, BestKeeper and NormFinder in selecting reference genes, but very few statistically validate the outcomes of these programs. Thus, in this study, we selected reference genes for qPCR of liver and ovary samples of yellow (juvenile), migratory (silver) and 11-KT treated juveniles of New Zealand shortfinned eels (Anguilla australis) using the three computer programs and validate the selected genes statistically using REST 2009 software and the Mann-Whitney test. We also tested for the repeatability of use for the best reference genes by applying them to a data set obtained in a similar experiment conducted the previous year.     

Morphology of Nurse Cell Nuclei Induced by Meloidodera floridensis: A Graphics Application

The highly irregular distribution of nuclear material in the host nurse cell induced by Meloidodera floridensis has made it difficult to interpret the number of nuclei from two-dimensional micrographs alone. The primary goal of this investigation was to determine the distribution of nuclear material from a three-dimensional solid surface model of the nurse cell nucleus. This model demonstrated the continuity of nuclear material as a single highly irregular nucleus. Custom computer graphics programs were written to accept digitized tracings of nuclear material. From these digitized tracings, a wireframe or polygonalized mesh model was generated. The model was shaded, colored, rotated, and analyzed. This technique provides controlled transparency of the model to display nucleoli within the nucleus. Photographs of the computer screen, color printouts, and video recordings were used to record final results. These refined computer graphic tools have a range of applications in nematode host-parasite relationships, ontogeny, and morphology.     

Low concordance of short‐term and long‐term selection responses in experimental Drosophila populations

Experimental evolution is becoming a popular approach to study the genomic selection response of evolving populations. Computer simulation studies suggest that the accuracy of the signature increases with the duration of the experiment. Since some assumptions of the computer simulations may be violated, it is important to scrutinize the influence of the experimental duration with real data. Here, we use a highly replicated Evolve and Resequence study in Drosophila simulans to compare the selection targets inferred at different time points. At each time point, approximately the same number of SNPs deviates from neutral expectations, but only 10% of the selected haplotype blocks identified from the full data set can be detected after 20 generations. Those haplotype blocks that emerge already after 20 generations differ from the others by being strongly selected at the beginning of the experiment and display a more parallel selection response. Consistent with previous computer simulations, our results demonstrate that only Evolve and Resequence experiments with a sufficient number of generations can characterize complex adaptive architectures.     

Computer-manipulated stimuli as a research tool in Mozambique tilapia <Emphasis Type="Italic">Oreochromis mossambicus</Emphasis>

Multimodal communication is essential in social interactions in cichlid fish, including conspecifics’ recognition, agonistic interactions and courtship behaviour. Computer-manipulated image stimuli and sound playback offer powerful tools to assess the relative relevance of visual and acoustic stimuli in fish behavioural studies, but these techniques require validation for each taxon. The aim of the present study was to investigate whether Mozambique tilapia Oreochromis mossambicus responds to computer-manipulated visual stimuli and acoustic playback. Six experiments were conducted: computer animation playback, video playback, interaction with a mirror, presentation of a live male in a jar alone and combined with courting sound playback or with white noise playback. Individual agonistic interactions (lateral displays, up and down swimming, butting) and courting behaviours (tilting leading, digging) were tallied for each experiment. Our results suggest that non-interactive computer-manipulated visual stimuli is not a suitable tool in behavioural research with Mozambique tilapia. In contrast, interaction with a live male in a jar seems to remain the best visual research instrument inducing significant strong behavioural responses. Although none or only a few agonistic interactions were observed towards video playbacks or computer animations, such interactions significantly increased towards a male in jar and were modulated by courtship sound playback, suggesting the additional relevance of sound playback as a tool in behavioural research with Mozambique tilapia, including the study of multimodal signalling.     

A Digital Image Analysis System for Comparing Groups of Small Nematodes

A digital imaging system was developed for measuring various physical characteristics of individual nematodes and for comparing groups of nematodes. The equipment consists of a microscope, a video camera, a video digitizer, interactive displays, and a computer. Various physical and mathematical methods were incorporated, algorithms devised, and computer software written for image acquisition, editing, and analysis. To test the system, four populations of an isolate of the pinewood nematode, Bursaphelenchus xylophilus, subjected to 100% relative humidity at 22 C for 0, 12, 24, or 48 hours were compared. The results showed that the system can be used to measure physical parameters of individual nematodes and to differentiate groups of nematodes.     

Computer‐automated bird detection and counts in high‐resolution aerial images: a review

Bird surveys conducted using aerial images can be more accurate than those using airborne observers, but can also be more time‐consuming if images must be analyzed manually. Recent advances in digital cameras and image‐analysis software offer unprecedented potential for computer‐automated bird detection and counts in high‐resolution aerial images. We review the literature on this subject and provide an overview of the main image‐analysis techniques. Birds that contrast sharply with image backgrounds (e.g., bright birds on dark ground) are generally the most amenable to automated detection, in some cases requiring only basic image‐analysis software. However, the sophisticated analysis capabilities of modern object‐based image analysis software provide ways to detect birds in more challenging situations based on a variety of attributes including color, size, shape, texture, and spatial context. Some techniques developed to detect mammals may also be applicable to birds, although the prevalent use of aerial thermal‐infrared images for detecting large mammals is of limited applicability to birds because of the low pixel resolution of thermal cameras and the smaller size of birds. However, the increasingly high resolution of true‐color cameras and availability of small unmanned aircraft systems (drones) that can fly at very low altitude now make it feasible to detect even small shorebirds in aerial images. Continued advances in camera and drone technology, in combination with increasingly sophisticated image analysis software, now make it possible for investigators involved in monitoring bird populations to save time and resources by increasing their use of automated bird detection and counts in aerial images. We recommend close collaboration between wildlife‐monitoring practitioners and experts in the fields of remote sensing and computer science to help generate relevant, accessible, and readily applicable computer‐automated aerial photographic census techniques.     

Comments on “the interpretation of the EPR and Mössbauer spectra of two-iron,one-electron iron-sulfur proteins”

Evidence is presented indicating that the note mentioned in the title is incorrect in two important aspects. 1.) According to our results of ENDOR spectroscopy and computer simulations of Mössbauer spectra, the conclusions drawn are based on an erroneous interpretation of the Mössbauer spectra. 2.) According to quotations from the literature, previous interpretations of experimental data on iron-sulfur proteins are incorrectly represented.     

Three-dimensional structure determination of capsid of<Emphasis Type="Italic">Aedes albopictus</Emphasis> C6/36 cell densovirus

The three-dimensional structure of capsid ofAedes albopictus C6/36 densovirus was determined to 14-Å resolution by electron cryomicroscopy and computer reconstruction. The triangulation number of the capsid is 1. There are 12 holes in each triangular face and a spike on each 5-fold vertex. The validity of the capsid and nucleic acid densities in the reconstructions was discussed.     

Das Autoselect-System – ein Automatensystem zur Selektion von Antibiotikaproduzenten,VII. Hemmhofmeßautomat

The zone reader of the Autoselect-system enables to measure the 64 inhibition zones of a quadratic bioassay plate with an accuracy of 0,1 mm within 3 minutes. A carriage moves each zone in the light beam. With a special photometrical device 3 defined areas of the inhibition zone can be measured quantitatively by 2 receivers. The indicated values of the diameters result from the analog treatment of the signals. By coupling to a computer the datas of the measuring and other desired informations are printed out.     

Individual fates of mesenchymal stem cells <Emphasis Type="Italic">in vitro</Emphasis>

Background  

In vitro cultivated stem cell populations are in general heterogeneous with respect to their expression of differentiation markers. In hematopoietic progenitor populations, this heterogeneity has been shown to regenerate within days from isolated subpopulations defined by high or low marker expression. This kind of plasticity has been suggested to be a fundamental feature of mesenchymal stem cells (MSCs) as well. Here, we study MSC plasticity on the level of individual cells applying a multi-scale computer model that is based on the concept of noise-driven stem cell differentiation.     

A multiscale model of the cardiovascular system that regulates arterial pressure via closed loop baroreflex control of chronotropism,cell-level contractility,and vascular tone

Biomechanics and Modeling in Mechanobiology - Multiscale models of the cardiovascular system can provide new insights into physiological and pathological processes. PyMyoVent is a computer model...     

Thoracic musculature of <Emphasis Type="Italic">Sericoderus lateralis</Emphasis> (Coleoptera,Corylophidae): Miniaturization effects and flight muscle degeneration related to development of reproductive system

The thoracic musculature of adult Sericoderus lateralis is described based on histological sectioning and 3D computer reconstruction. The thoracic musculature of Corylophidae is not strongly affected by miniaturization: S. lateralis has an almost complete set of muscles found in large Cucuiformia beetles. The intravital flight muscle degeneration related to the development of the reproductive system is described.