Similarities and Differences in Genome-Wide Expression Data of Six Organisms

Comparing genomic properties of different organisms is of fundamental importance in the study of biological and evolutionary principles. Although differences among organisms are often attributed to differential gene expression, genome-wide comparative analysis thus far has been based primarily on genomic sequence information. We present a comparative study of large datasets of expression profiles from six evolutionarily distant organisms: S. cerevisiae, C. elegans, E. coli, A. thaliana, D. melanogaster, and H. sapiens. We use genomic sequence information to connect these data and compare global and modular properties of the transcription programs. Linking genes whose expression profiles are similar, we find that for all organisms the connectivity distribution follows a power-law, highly connected genes tend to be essential and conserved, and the expression program is highly modular. We reveal the modular structure by decomposing each set of expression data into coexpressed modules. Functionally related sets of genes are frequently coexpressed in multiple organisms. Yet their relative importance to the transcription program and their regulatory relationships vary among organisms. Our results demonstrate the potential of combining sequence and expression data for improving functional gene annotation and expanding our understanding of how gene expression and diversity evolved

Effect of Perch Height and Position on the Usage in Enriched Colony Housing Systems for Laying Hens

In order to determine the utility of different perches in enriched colony housing systems for laying hens, the use of perches and an effect of the type and location in the system was examined in this behavioral study. Laying hens of the line Lohmann Selected Leghorn were housed in four different enriched colony housing systems which differed particularly in the alignment and arrangement of the functional areas. For analysis, perches were grouped into three types: low, low underneath the drinking trough and high. To evaluate the use of the perch types, video recordings were taken for 48 hours during three observation periods. These recordings were analyzed hourly at daytime and twice at nighttime. Through scan sampling, the overall number of hens using the perches and the fraction of hens per meter on a specific perch type were assessed. At nighttime, an average 62% of the laying hens used the perches. On average, 24% of the laying hens used the perches at daytime, with no significant difference between the different systems. Low perches that were not installed underneath the drinking trough were less commonly used than high perches. However, the hens used low perches that were positioned underneath the drinking trough more than other perch types during the day. At nighttime, high perches were used frequently and, depending on the system, more than the low perches. It should be considered that the hens used the low perches underneath the drinking trough during the day not to rest but rather to have better access to the drinking trough. It can be recommended that a sufficient number of high perches should be offered, so that all hens have access to these obviously preferred perches. If perches are installed underneath the drinking trough, it should be considered if additional perch space should be offered

Effect of Perch Height and Position on the Usage in Enriched Colony Housing Systems for Laying Hens

In order to determine the utility of different perches in enriched colony housing systems for laying hens, the use of perches and an effect of the type and location in the system was examined in this behavioral study. Laying hens of the line Lohmann Selected Leghorn were housed in four different enriched colony housing systems which differed particularly in the alignment and arrangement of the functional areas. For analysis, perches were grouped into three types: low, low underneath the drinking trough and high. To evaluate the use of the perch types, video recordings were taken for 48 hours during three observation periods. These recordings were analyzed hourly at daytime and twice at nighttime. Through scan sampling, the overall number of hens using the perches and the fraction of hens per meter on a specific perch type were assessed. At nighttime, an average 62% of the laying hens used the perches. On average, 24% of the laying hens used the perches at daytime, with no significant difference between the different systems. Low perches that were not installed underneath the drinking trough were less commonly used than high perches. However, the hens used low perches that were positioned underneath the drinking trough more than other perch types during the day. At nighttime, high perches were used frequently and, depending on the system, more than the low perches. It should be considered that the hens used the low perches underneath the drinking trough during the day not to rest but rather to have better access to the drinking trough. It can be recommended that a sufficient number of high perches should be offered, so that all hens have access to these obviously preferred perches. If perches are installed underneath the drinking trough, it should be considered if additional perch space should be offered

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

Background: The increasing use of computational simulation experiments to inform modern biological research creates new challenges to annotate, archive, share and reproduce such experiments. The recently published Minimum Information About a Simulation Experiment (MIASE) proposes a minimal set of information that should be provided to allow the reproduction of simulation experiments among users and software tools. Results: In this article, we present the Simulation Experiment Description Markup Language (SED-ML). SED-ML encodes in a computer-readable exchange format the information required by MIASE to enable reproduction of simulation experiments. It has been developed as a community project and it is defined in a detailed technical specification and additionally provides an XML schema. The version of SED-ML described in this publication is Level 1 Version 1. It covers the description of the most frequent type of simulation experiments in the area, namely time course simulations. SED-ML documents specify which models to use in an experiment, modifications to apply on the models before using them, which simulation procedures to run on each model, what analysis results to output, and how the results should be presented. These descriptions are independent of the underlying model implementation. SED-ML is a software-independent format for encoding the description of simulation experiments; it is not specific to particular simulation tools. Here, we demonstrate that with the growing software support for SED-ML we can effectively exchange executable simulation descriptions. Conclusions: With SED-ML, software can exchange simulation experiment descriptions, enabling the validation and reuse of simulation experiments in different tools. Authors of papers reporting simulation experiments can make their simulation protocols available for other scientists to reproduce the results. Because SED-ML is agnostic about exact modeling language(s) used, experiments covering models from different fields of research can be accurately described and combined

Individual plumage and integument scoring of laying hens on commercial farms: correlation with severe feather pecking and prognosis by visual scoring on flock level

Various plumage and integument scoring methods are commonly used to deduce the occurrence of severe feather pecking and cannibalism in laying hens. The aim of our study was to provide evidence of correlations between the occurrence of severe feather pecking and our individual plumage scoring system used under practical conditions on commercial farms with non–beak-trimmed and beak-trimmed layers (study I). In second step, we aimed to verify whether the results of the elaborate individual scoring may be predicted with a visual scoring method based on the total body scores of groups of birds (study II). For study I we observed the pecking behavior and performed an individual plumage scoring at the beginning, in the middle, and at the end of a laying period on 8 commercial farms. For study II we performed both an individual and a visual plumage scoring on 49 flocks on 45 farms at the beginning of the laying period and on 43 flocks on 41 farms at the end of the laying period. Spearman's Rho revealed a correlation of the mean feather pecking rate with the total plumage score, the neck–back plumage score, and the total cannibalism score in all observation periods. A high feather pecking rate was correlated with severe plumage damage and the frequent occurrence of skin injuries. We conclude that both the total plumage score and the neck–back plumage score constitute a reliable indicator of the occurrence of severe feather pecking in the flocks assessed in this study. The results of study II suggest that the percental assessment of plumage damage on flock level in 3 categories (“visual score”) leads to a good prognosis of the actual, individually assessed plumage score. Therefore, the application (and documentation) of the visual score on a regular basis can provide a good evaluation of the development of the plumage condition of the flock. The visual score presented in this study is suggested as a suitable instrument for self-evaluation programs on farms

Risk Factors for the Occurrence of Feather Pecking in Non-Beak-Trimmed Pullets and Laying Hens on Commercial Farms

Severe feather pecking (SFP) is a behavioral disorder, for which there are multifactorial reasons. Various aspects of pullet and laying-hen husbandry—including housing conditions, management, feeding, and genetics—must be considered, to prevent negative outcomes, such as severe plumage damage, skin injuries, and high mortality rates due to SFP. The aim of this study was to identify housing and management factors in the occurrence of feather pecking, so as to reduce the risk of this behavioral disorder in non-beak-trimmed laying hens on commercial farms with aviaries. Beak trimming may reduce the extent of plumage damage, but it does not prevent feather pecking and cannibalism. Thirty non-beak-trimmed flocks (16 in the first, and 14 in the second laying period) were investigated on 16 commercial farms in Germany. Each flock was visited twice during rearing, and three times during the laying period. During each visit, individual plumage and integument scoring were performed, and data were collected, regarding the housing and management conditions of the flocks. To analyze the influence of management and housing on the plumage condition of the rearing and laying flocks, models were calculated, using univariate multifactorial analysis. In the rearing period, high stocking density and poor litter quality were significant risk factors in plumage damage due to SFP. In the laying period, a lack of free range, poor litter quality, insufficient enrichment, and plumage damage during rearing were significant risk factors for the development of SFP. An individual risk analysis of pullet and layer farms is therefore strongly recommended, to prevent outbreaks of SFP and cannibalism, especially in non-beak-trimmed birds

A new age in AquaMedicine: unconventional approach in studying aquatic diseases

Background Marine and aquaculture industries are important sectors of the food production and global trade. Unfortunately, the fish food industry is challenged with a plethora of infectious pathogens. The freshwater and marine fish communities are rapidly incorporating novel and most up to date techniques for detection, characterization and treatment strategies. Rapid detection of infectious diseases is important in preventing large disease outbreaks. Main text One hundred forty-six articles including reviews papers were analyzed and their conclusions evaluated in the present paper. This allowed us to describe the most recent development research regarding the control of diseases in the aquatic environment as well as promising avenues that may result in beneficial developments. For the characterization of diseases, traditional sequencing and histological based methods have been augmented with transcriptional and proteomic studies. Recent studies have demonstrated that transcriptional based approaches using qPCR are often synergistic to expression based studies that rely on proteomic-based techniques to better understand pathogen-host interactions. Preventative therapies that rely on prophylactics such as vaccination with protein antigens or attenuated viruses are not always feasible and therefore, the development of therapies based on small nucleotide based medicine is on the horizon. Of those, RNAi or CRISPR/Cas- based therapies show great promise in combating various types of diseases caused by viral and parasitic agents that effect aquatic and fish medicine. Conclusions In our modern times, when the marine industry has become so vital for feed and economic stability, even the most extreme alternative treatment strategies such as the use of small molecules or even the use of disease to control invasive species populations should be considered

Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 2 Core Release 2

Computational models can help researchers to interpret data, understand biological functions, and make quantitative predictions. The Systems Biology Markup Language (SBML) is a file format for representing computational models in a declarative form that different software systems can exchange. SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. By supporting SBML as an input/output format, different tools can all operate on an identical representation of a model, removing opportunities for translation errors and assuring a common starting point for analyses and simulations. This document provides the specification for Release 2 of Version 2 of SBML Level 3 Core. The specification defines the data structures prescribed by SBML as well as their encoding in XML, the eXtensible Markup Language. Release 2 corrects some errors and clarifies some ambiguities discovered in Release 1. This specification also defines validation rules that determine the validity of an SBML document, and provides many examples of models in SBML form. Other materials and software are available from the SBML project website at http://sbml.org/