DNALinux Virtual Desktop Edition

The new version of DNALinux (VDE) is presented. DNALinux VDE is a departure from traditional distributions since it uses a virtual machine to bundle together the operating system and bioinformatics applications. The main advantage of this approach is that a virtualized environment doesn't affect a installed system. With a virtual machine a Linux system can be run under a Windows system, provided that the virtual machine player is installed. The included programs are listed and specifications to add more programs are explained. We believe that DNALinux could be used as a standardized virtual machine for learning, using, developing and testing bioinformatics applications

Use of Biostimulants for Organic Apple Production: Effects on Tree Growth, Yield, and Fruit Quality at Harvest and During Storage

The experiment was conducted during two consecutive seasons (years 2016 and 2017) in an organic apple orchard of the cultivar Jonathan. Several biostimulants were tested (10 in total), including humic acids, macro and micro seaweed extracts, alfalfa protein hydrolysate, amino acids alone or in combination with zinc, B-group vitamins, chitosan and a commercial product containing silicon. Treatments were performed at weekly intervals, starting from the end of May until mid-August. The macroseaweed extract was effective in stimulate tree growth potential in both years, as shown by a significantly larger leaf area (+20% as compared to control) and by an higher chlorophyll content and leaf photosynthetic rate in year 2016. As for the yield performances and apples quality traits at harvest (average fruit weight, soluble solids content, titratable acidity, and flesh firmness), they were generally affected by the different climatic conditions that characterized the two growing seasons (year 2017 being characterized by higher maximal and average temperatures and by limited rainfalls at the beginning of the season). Treatments with macroseaweed extract, B-group vitamins and alfalfa protein hydrolysate were able to significantly improve the intensity and extension of the red coloration of apples at harvest. Correspondingly, the anthocyanin content in the skin of apples treated with the same biostimulants resulted significantly higher than control, highlighting the potential influence of these substances on the synthesis of secondary metabolites in apple. The incidence of physiological disorders was also monitored during apple storage period. Amino acids plus zinc application was effective in reducing (more than 50%) the incidence of the “Jonathan spot,” the main post-harvest disorder for this cultivar

Development of a model for anemia of inflammation that is relevant to critical care

Background: Anemia of inflammation (AI) is common in critically ill patients. Although this syndrome negatively impacts the outcome of critical illness, understanding of its pathophysiology is limited. Also, new therapies that increase iron availability for erythropoiesis during AI are upcoming. A model of AI induced by bacterial infections that are relevant for the critically ill is currently not available. This paper describes the development of an animal model for AI that is relevant for critical care research. Results: In experiments with rats, the rats were inoculated either repeatedly or with a slow release of Streptococcus pneumoniae or Pseudomonas aeruginosa. Rats became ill, but their hemoglobin levels remained stable. The use of a higher dose of bacteria resulted in a lethal model. Then, we turned to a model with longer disease duration, using pigs that were supported by mechanical ventilation after inoculation with P. aeruginosa. The pigs became septic 12 to 24 h after inoculation, with a statistically significant decrease in mean arterial pressure and base excess, while heart rate tended to increase. Pigs needed resuscitation and vasopressor therapy to maintain a mean arterial pressure > 60 mmHg. After 72 h, the pigs developed anemia (baseline 9.9 g/dl vs. 72 h, 7.6 g/dl, p = 0.01), characterized by statistically significant decreased iron levels, decreased transferrin saturation, and increased ferritin. Hepcidin levels tended to increase and transferrin levels tended to decrease. Conclusions: Using pathogens commonly involved in pulmonary sepsis, AI could not be induced in rats. Conversely, in pigs, P. aeruginosa induced pulmonary sepsis with concomitant AI. This AI model can be applied to study the pathophysiology of AI in the critically ill and to investigate the effectivity and toxicity of new therapies that aim to increase iron availability. Keywords: Anemia of inflammation; Animal model; ICU; Infection; Iron

Guideline adherence and patient satisfaction in the treatment of inflammatory bowel disorders – an evaluation study

Background: Crohn's disease (CD) and ulcerative colitis (UC) are the most frequent inflammatory bowel disorders (IBD). IBD cause a significant burden to society due to extensive health care utilization from the first clinical symptoms until diagnosis and thereafter due to direct and indirect costs. Besides the socio-economic impact of CD and UC, gastrointestinal and extraintestinal symptoms affect quality of life, but there is remarkably little data about the quality of treatment as assessed by patient satisfaction, quality of life and adherence to guidelines. Thus the aim of this study was to identify variables that influence quality of treatment and quality of life as well as patient satisfaction. Methods: The Essener Zirkel Study was a cross sectional study of 86 IBD-patients with a confirmed diagnosis of CD or UC. They were recruited at primary, secondary and tertiary care settings. Quality of treatment, quality of life and patient satisfaction were evaluated. Consulting behaviour and number of examinations, duration of disease and variables regarding adherence to guidelines were evaluated, too. Results: 59 (69%) patients had CD and 27 had UC (31%). 19% spent more than four years until the suspected diagnosis of IBD was confirmed and visited more than five physicians. All patients showed a significantly reduced quality of life compared to the 1998 German normative population. In spite of being under medical treatment, nearly half of the patients suffered from strong quality of life restricting symptoms. Over all, 35% described their treatment as moderate or bad. Patients who consulted psychotherapists and non-medical practitioners suffered significantly less from depression. Conclusion: Besides structural deficiencies due to the health care policy, we revealed the adherence to guidelines to be a problem area. Our findings support the assumption, that providing better health care and especially maintaining constant patient-physician communication improves patient satisfaction.Claudia Pieper, Sebastian Haag, Stefan Gesenhues, Gerald Holtmann, Guido Gerken and Karl-Heinz Jöcke

From bits to bites: Advancement of the Germinate platform to support prebreeding informatics for crop wild relatives

Management and distribution of experimental data from prebreeding projects is important to ensure uptake of germplasm into breeding and research programs. Being able to access and share this data in standard formats is essential. The adoption of a common informatics platform for crops that may have limited resources brings economies of scale, allowing common informatics components to be used across multiple species. The close integration of such a platform with commonly used breeding software, visualization, and analysis tools reduces the barrier for entry to researchers and provides a common framework to facilitate collaborations and data sharing. This work presents significant updates to the Germinate platform and highlights its value in distributing prebreeding data for 14 crops as part of the project ‘Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives’ (hereafter Crop Trust Crop Wild Relatives project) led by the Crop Trust (https://www.cwrdiversity.org). The addition of data on these species compliments data already publicly available in Germinate. We present a suite of updated Germinate features using examples from these crop species and their wild relatives. The use of Germinate within the Crop TrustCropWildRelatives project demonstrates the usefulness of the system and the benefits a shared informatics platform provides. These data resources provide a foundation on which breeding and research communities can develop additional online resources for their crops, harness new data as it becomes available, and benefit collectively from future developments of the Germinate platform

In Silico and Biochemical Analysis of Physcomitrella patens Photosynthetic Antenna: Identification of Subunits which Evolved upon Land Adaptation

Background. In eukaryotes the photosynthetic antenna system is composed of subunits encoded by the light harvesting complex (Lhc) multigene family. These proteins play a key role in photosynthesis and are involved in both light harvesting and photoprotection. The moss Physcomitrella patens is a member of a lineage that diverged from seed plants early after land colonization and therefore by studying this organism, we may gain insight into adaptations to the aerial environment. Principal Findings. In this study, we characterized the antenna protein multigene family in Physcomitrella patens, by sequence analysis as well as biochemical and functional investigations. Sequence identification and analysis showed that some antenna polypeptides, such as Lhcb3 and Lhcb6, are present only in land organisms, suggesting they play a role in adaptation to the sub-aerial environment. Our functional analysis which showed that photo-protective mechanisms in Physcomitrella patens are very similar to those in seed plants fits with this hypothesis. In particular, Physcomitrella patens also activates Non Photochemical Quenching upon illumination, consistent with the detection of an ortholog of the PsbS protein. As a further adaptation to terrestrial conditions, the content of Photosystem I low energy absorbing chlorophylls also increased, as demonstrated by differences in Lhca3 and Lhca4 polypeptide sequences, in vitro reconstitution experiments and low temperature fluorescence spectra. Conclusions. This study highlights the role of Lhc family members in environmental adaptation and allowed proteins associated with mechanisms of stress resistance to be identified within this large family