Contrasting Zooplankton Assemblages in Two Oxbow Lakes with Low Transparencies and Narrow Emergent Macrophyte Belts (Krapina River,Croatia)

The aim of this study was to examine the combined effect of water transparency and narrow macrophyte belts on zooplankton assemblages in two oxbow lakes (Krapina River, Croatia). Samples were collected in open water and among helophytes in the littoral zone from April until September 2008. Rotifers were the most abundant group of zooplankton in both lakes, and dominated in the Krapina oxbow lake 1 (KO1). Lake KO1 had significantly lower transparency, lower percentage macrophyte cover and higher chlorophyll a concentration than Krapina oxbow lake 2 (KO2). In lake KO1, variation in the horizontal distribution of cladocerans and rotifers in terms of their abundance seemed to be determined by competition between Bosmina longirostris and Keratella cochlearis, initiated by oscillation in transparency and detritus availability. In lake KO2, with higher transparency and higher percentage macrophyte cover, the abundance of small‐ and large‐bodied cladocerans increased in the littoral zone simultaneously with higher transparency, suggesting fish predation. Results of this study indicated that small differences in transparencies between the two lakes caused significant differences in horizontal distribution of the zooplankton assemblage. Even narrow helophyte belts offered a refuge to zooplankton, although lower transparencies reduced the effectiveness of macrophytes as a refuge from predators. (© 2011 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

SIMPLEX: Cloud-Enabled Pipeline for the Comprehensive Analysis of Exome Sequencing Data

In recent studies, exome sequencing has proven to be a successful screening tool for the identification of candidate genes causing rare genetic diseases. Although underlying targeted sequencing methods are well established, necessary data handling and focused, structured analysis still remain demanding tasks. Here, we present a cloud-enabled autonomous analysis pipeline, which comprises the complete exome analysis workflow. The pipeline combines several in-house developed and published applications to perform the following steps: (a) initial quality control, (b) intelligent data filtering and pre-processing, (c) sequence alignment to a reference genome, (d) SNP and DIP detection, (e) functional annotation of variants using different approaches, and (f) detailed report generation during various stages of the workflow. The pipeline connects the selected analysis steps, exposes all available parameters for customized usage, performs required data handling, and distributes computationally expensive tasks either on a dedicated high-performance computing infrastructure or on the Amazon cloud environment (EC2). The presented application has already been used in several research projects including studies to elucidate the role of rare genetic diseases. The pipeline is continuously tested and is publicly available under the GPL as a VirtualBox or Cloud image at http://simplex.i-med.ac.at; additional supplementary data is provided at http://www.icbi.at/exome.     

Effect of magnetic fields on antioxidative defense and fitness-related traits of Baculum extradentatum (insecta, phasmatodea)

This study aimed to determine the effect of magnetic fields on the antioxidative defense and fitness-related traits of Baculum extradentatum. Following exposure to magnetic fields, antioxidative defense (superoxide dismutase (SOD), catalase (CAT) activities, and total glutathione (GSH) content) and fitness-related traits (egg mortality, development dynamics, and mass of nymphs) were monitored in nymphs. The experimental groups were: control (kept out of influence of the magnets), a group exposed to a constant magnetic field (CMF) of 50 mT, and a group exposed to an alternating magnetic field (AMF) of 50 Hz, 6 mT. We found increased SOD and CAT activities in animals exposed to constant and AMFs, whereas GSH activity was not influenced by experimental magnetic fields. No differences were found in egg mortality between control and experimental groups. Significant differences in the time of development between the control and the CMF group were observed, as well as between the CMF and the AMF group. No differences were found in the mass of the nymphs between the three experimental groups. In conclusion, CMF and AMF have the possibility to modulate the antioxidative defense and some of the fitness-related traits in B. extradentatum.     

Bioinformatics for cancer immunology and immunotherapy

Recent mechanistic insights obtained from preclinical studies and the approval of the first immunotherapies has motivated increasing number of academic investigators and pharmaceutical/biotech companies to further elucidate the role of immunity in tumor pathogenesis and to reconsider the role of immunotherapy. Additionally, technological advances (e.g., next-generation sequencing) are providing unprecedented opportunities to draw a comprehensive picture of the tumor genomics landscape and ultimately enable individualized treatment. However, the increasing complexity of the generated data and the plethora of bioinformatics methods and tools pose considerable challenges to both tumor immunologists and clinical oncologists. In this review, we describe current concepts and future challenges for the management and analysis of data for cancer immunology and immunotherapy. We first highlight publicly available databases with specific focus on cancer immunology including databases for somatic mutations and epitope databases. We then give an overview of the bioinformatics methods for the analysis of next-generation sequencing data (whole-genome and exome sequencing), epitope prediction tools as well as methods for integrative data analysis and network modeling. Mathematical models are powerful tools that can predict and explain important patterns in the genetic and clinical progression of cancer. Therefore, a survey of mathematical models for tumor evolution and tumor–immune cell interaction is included. Finally, we discuss future challenges for individualized immunotherapy and suggest how a combined computational/experimental approaches can lead to new insights into the molecular mechanisms of cancer, improved diagnosis, and prognosis of the disease and pinpoint novel therapeutic targets.     

Heterozygous carriage of a dysfunctional Toll-like receptor 9 allele affects CpG oligonucleotide responses in B cells

Toll-like receptors (TLR) are employed by the innate immune system to detect microbial pathogens based on conserved microbial pathogen molecules. For example, TLR9 is a receptor for CpG-containing microbial DNA, and its activation results in the production of cytokines and type I interferons from human B cells and plasmacytoid dendritic cells, respectively. Both are required for mounting an efficient antibacterial or antiviral immune response. These effects are mimicked by synthetic CpG oligodeoxynucleotides (ODN). Although several hyporesponsive TLR9 variants have been reported, their functional relevance in human primary cells has not been addressed. Here we report a novel TLR9 allele, R892W, which is hyporesponsive to CpG ODN and acts as a dominant-negative in a cellular model system. The R892W variant is characterized by increased MyD88 binding and defective co-localization with CpG ODN. Whereas primary plasmacytoid dendritic cells isolated from a heterozygous R892W carrier responded normally to CpG by interferon-α production, carrier B cells showed impaired IL-6 and IL-10 production. This suggests that heterozygous carriage of a hyporesponsive TLR9 allele is not associated with complete loss of TLR9 function but that TLR9 signals elicited in different cell types are regulated differently in human primary cells.     

<Emphasis Type="Italic">In vitro</Emphasis> stem elongation of stemless carline thistle

In vitro culture of stemless carline thistle was established using immature zygotic embryos. A satisfactory bud multiplication was achieved on MS medium supplemented with BAP (1 mg L^–1) and IAA (0.2 mg L^–1). Maximum rooting of buds was induced upon short cultivation (4 or 8 days) on an auxin-supplemented medium. Highest number of roots was obtained with NAA in the medium while the longest roots developed on the IAA-supplemented medium. Plantlets that subsequently developed were in rosette form if grown in light (16/8 h light to darkness photoperiod) and with elongated stems if raised in darkness. Light grown plantlets treated with GA₃ showed dose dependent stem increase in length, reaching maximum at the concentration of 10^–4 M. This was correlated with the length and the average number of internodes. If cultivated in the presence of ancymidol, dark grown plantlets showed reduced stem length. However, the inhibitory effect of the growth retardant on stem elongation was completely overcome by the addition of GA₃.     

Diagnostic value of a peroral sucrose permeability test in children with recurrent upper abdominal pain

The access of ingested sucrose into blood and urine indicates the presence of mucosal lesions in the upper gastrointestinal tract. The study involved 42 children, aged 5-15, having recurrent upper abdominal pain and 43 peers with minor extra-abdominal complaints. Sucrose in urine was determined by thin layer chromatography. The test was positive in 27 out of 42 children having recurrent abdominal pain (64.3%) and in none of the control children (chi2 = 37.6, p < 0.0001). When correlated with endoscopic findings it was falsely negative in 12 out of 38 patients with endoscopically verified lesions of the stomach or duodenum and falsely positive in 1 out of 4 without lesions. Sensitivity of the test was 68.4%, specificity 97.9%, positive predictive value 96.3%. The test cannot be used as an alternative to endoscopy, but may serve for screening of candidates for it.     

Molecular and biochemical analyses of spontaneous and X-ray-induced mutants in human lymphoblastoid cells

We have isolated a series of 14 spontaneously arising and 28 X-ray-induced mutants at the hypoxanthine-guanine phosphoribosyltransferase (hgprt) locus in human lymphoblastoid cells. Among the spontaneous mutants, 5/14 (36%) had detectable alterations in their restriction fragment pattern after hybridization with a human cDNA probe for hgprt. Of the 10 remaining mutants, 4 had partial HGPRT enzyme activity, which suggested that they contained point mutations. Among the 28 mutants induced by 150 rad of X-rays, 15 (54%) had deletions of part or all of the hgprt gene. 5 of the remaining 13 (18% overall) had partial HGPRT enzyme activity, which suggested that they contained point mutations. These data imply that in this human cell system, X-rays induce both point mutants which have residual enzyme activity as well as mutations involving relatively large deletions of DNA.     

Tissue zinc dynamics during the immune reaction in mice

Owing to the importance of zinc for the functioning of the immune system, the role of endogenous Zn, located both in lymphoid and nonlymphoid organs, was investigated during the standard humoral and cellular types of immune response. For this purpose, the dynamics of hepatic, thymic, splenic, and renal Zn content was determined in mice sensitized with (a) sheep red blood cells and (b) semiallogeneic lymphocytes during the local host vs graft reaction (HVGR). The data obtained by ion-coupled plasma spectrometry revealed that the humoral type of immunity is characterized by a significant increase of Zn concentration in the liver and in the thymus. Simultaneously, linear regression analysis showed that the generation of plaque-forming cells in the individual mouse was highly positively correlated with Zn concentration in the liver (r = 0.897), and spleen (r = 0.833), and negatively with Zn concentration in the thymus (r = -0.624). Similar relationships between the intensity of local immune reaction and tissue Zn levels were found in local HVGR at the fifth day in the liver and spleen (r = 0.861 andr = 0.695, respectively), at the seventh day in the thymus (r = -0.797), and at the tenth day in the liver (r = -0.859). The data emphasize the necessity of Zn for the development of normal immune response and point to the existence of a Zndependent hepato-thymic axis during the humoral and cellular types of immune reactivity.