Challenges in RNA virus bioinformatics.

Motivation: Computer-assisted studies of structure, function and evolution of viruses remains a neglected area of research. The attention of bioinformaticians to this interesting and challenging field is far from commensurate with its medical and biotechnological importance. It is telling that out of >200 talks held at ISMB 2013, the largest international bioinformatics conference, only one presentation explicitly dealt with viruses.

Combined chemical and toxicological long-term monitoring for AhR agonists with SPMD-based virtual organisms in drinking water Danjiangkou Reservoir, China.

SPMD-based virtual organisms (VOs) were employed for time-integrating, long-term sampling combined biological and chemical analyses for exposure assessment of hydrophobic organic pollutants (HOPs) in a drinking water reservoir, China. The SPMDs were deployed at four and five sites in the Danjiangkou (DJK) reservoir over two periods of 26 and 31 d to sequester the hydrophobic contaminants in water. The chosen bioassay response for the extracts of the SPMDs, the induction of 7-ethoxyresorufin-o-deethylase (EROD) was assayed using a rat hepatoma cell line (H4IIE).

Leveraging cross-species transcription factor binding site patterns: from diabetes risk loci to disease mechanisms.

Genome-wide association studies have revealed numerous risk loci associated with diverse diseases. However, identification of disease-causing variants within association loci remains a major challenge. Divergence in gene expression due to cis-regulatory variants in noncoding regions is central to disease susceptibility.

Early dynamic fate changes in haemogenic endothelium characterized at the single-cell level.

Haematopoietic stem cells (HSCs) are the founding cells of the adult haematopoietic system, born during ontogeny from a specialized subset of endothelium, the haemogenic endothelium (HE) via an endothelial-to-haematopoietic transition (EHT). Although recently imaged in real time, the underlying mechanism of EHT is still poorly understood. We have generated a Runx1 +23 enhancer-reporter transgenic mouse (23GFP) for the prospective isolation of HE throughout embryonic development.

CD4(+)and CD8(+)T-cell reactions against leukemia-associated- or minor-histocompatibility-antigens in AML-patients after allogeneic SCT.

T-cells play an important role in the remission-maintenance in AML-patients (pts) after SCT, however the role of LAA- (WT1, PR1, PRAME) or minor-histocompatibility (mHag, HA1) antigen-specific CD4(+) and CD8(+)T-cells is not defined. A LAA/HA1-peptide/protein stimulation, cloning and monitoring strategy for specific CD8(+)/CD4(+)T-cells in AML-pts after SCT is given. Our results show that (1) LAA-peptide-specific CD8+T-cells are detectable in every AML-pt after SCT.

Comparative evaluation of ELISA kit and HPLC DAD for the determination of chlorpyrifos ethyl residues in water and sediments.

Enzyme linked immunosorbent assay (ELISA) kit is a versatile, cheap and relatively available tool that can be used in remote areas. In this study, performance of ELISA kit was evaluated in terms of accuracy, recovery, precision, sensitivity, cross reactivity and matrix interference for pesticide residue determination in water and sediment samples. This method was compared with high performance liquid chromatography (HPLC) which is not a commonly available analytical technique for chlorpyrifos ethyl residue analysis in developing countries.

Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution.

Recent reports indicate that mutations in viral genomes tend to preserve RNA secondary structure, and those mutations that disrupt secondary structural elements may reduce gene expression levels, thereby serving as a functional knockout. In this article, we explore the conservation of secondary structures of mRNA coding regions, a previously unknown factor in bacterial evolution, by comparing the structural consequences of mutations in essential and nonessential Escherichia coli genes accumulated over 40 000 generations in the course of the 'long-term evolution experiment'. We monitored the extent to which mutations influence minimum free energy (MFE) values, assuming that a substantial change in MFE is indicative of structural perturbation.

Manganese speciation in paired serum and CSF samples using SEC-DRC-ICP-MS and CE-ICP-DRC-MS.

Occupational manganese (Mn) overexposure leads to accumulation in the brain and has been shown to cause progressive, permanent, neuro-degenerative damage with syndromes similar to idiopathic Parkinsonism. Mn is transported by an active mechanism across neural barriers (NB) finally into the brain; but to date, modes of Mn neurotoxic action are poorly understood. This paper investigates the relevant Mn-carrier species which are responsible for widely uncontrolled transport across NB.

MIPS PlantsDB: a database framework for comparative plant genome research.

The rapidly increasing amount of plant genome (sequence) data enables powerful comparative analyses and integrative approaches and also requires structured and comprehensive information resources. Databases are needed for both model and crop plant organisms and both intuitive search/browse views and comparative genomics tools should communicate the data to researchers and help them interpret it. MIPS PlantsDB (http://mips.

The adaptor protein FADD and the initiator caspase-8 mediate activation of NF-κB by TRAIL.

Besides inducing apoptosis, tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) activates NF-κB. The apoptosis signaling pathway of TRAIL is well characterized involving TRAIL receptors, Fas-associated protein with death domain (FADD) and caspase-8. In contrast, the molecular mechanism of TRAIL signaling to NF-κB remains controversial.

Molecular live cell bioimaging in stem cell research.

Functional heterogeneity within stem and progenitor cells has been shown to influence cell fate decisions. Similarly, intracellular signaling activated by external stimuli is highly heterogeneous and its spatiotemporal activity is linked to future cell behavior. To quantify these heterogeneous states and link them to future cell fates, it is important to observe cell populations continuously with single cell resolution.

NOXA as critical mediator for drug combinations in polychemotherapy.

During polychemotherapy, cytotoxic drugs are given in combinations to enhance their anti-tumor effectiveness. For most drug combinations, underlying signaling mechanisms responsible for positive drug-drug interactions remain elusive. Here, we prove a decisive role for the Bcl-2 family member NOXA to mediate cell death by certain drug combinations, even if drugs were combined which acted independently from NOXA, when given alone.

Advances in tracking hematopoiesis at the single-cell level.

Purpose Of Review: Studying heterogeneous populations, such as hematopoietic stem cells (HSCs), requires continuous long-term observation of living cells at the single-cell level. The purpose of this review is to discuss recent advances in technologies required for continuous single-cell analysis and the contribution of this approach to find answers in hematopoiesis research.

Recent Findings: Continuous long-term imaging at the single-cell level still requires custom-made hardware, software and manual in-depth analysis of large amounts of data.

Efficient RNA interference in patients' acute lymphoblastic leukemia cells amplified as xenografts in mice.

Background: Signaling studies in cell lines are hampered by non-physiological alterations obtained in vitro. Physiologic primary tumor cells from patients with leukemia require passaging through immune-compromised mice for amplification. The aim was to enable molecular work in patients' ALL cells by establishing siRNA transfection into cells amplified in mice.

Important role of caspase-8 for chemosensitivity of ALL cells.

Purpose: Sensitivity of tumor cells toward chemotherapy mainly determines the prognosis of patients suffering from acute lymphoblastic leukemia (ALL); nevertheless, underlying mechanisms regulating chemosensitivity remain poorly understood. Here, we aimed at characterizing the role of caspase-8 for chemosensitivity of B- and T-ALL cells.

Experimental Design: Primary tumor cells from children with ALL were evaluated for expression levels of the caspase-8 protein, were amplified in nonobese diabetic/severe combined immunodeficient mice, transfected with siRNA, and evaluated for their chemosensitivity in vitro.

MicroRNA-mediated processes are essential for the cellular radiation response.

A detailed understanding of the mechanisms that determine the variable cellular sensitivity to radiation is needed for improved radiation therapy as well as for the identification of individuals with innate radiation hypersensitivity. MicroRNAs (miRNAs) are a class of small non-coding RNAs that post-transcriptionally regulate protein expression. Alterations in miRNA expression patterns in response to ionizing radiation have been shown, but there are almost no data describing the functional impact of these miRNA changes.

Complex principal component and correlation structure of 16 yeast genomic variables.

A quickly growing number of characteristics reflecting various aspects of gene function and evolution can be either measured experimentally or computed from DNA and protein sequences. The study of pairwise correlations between such quantitative genomic variables as well as collective analysis of their interrelations by multidimensional methods have delivered crucial insights into the processes of molecular evolution. Here, we present a principal component analysis (PCA) of 16 genomic variables from Saccharomyces cerevisiae, the largest data set analyzed so far.

Caught you: threats to confidentiality due to the public release of large-scale genetic data sets.

Background: Large-scale genetic data sets are frequently shared with other research groups and even released on the Internet to allow for secondary analysis. Study participants are usually not informed about such data sharing because data sets are assumed to be anonymous after stripping off personal identifiers.

Discussion: The assumption of anonymity of genetic data sets, however, is tenuous because genetic data are intrinsically self-identifying.

Comparative surface plasmon resonance and enzyme-linked immunosorbent assay characterisation of a monoclonal antibody with N-acyl homoserine lactones.

This study shows the detection of (N-acyl) homoserine lactones (AHLs or HSL) with monoclonal antibodies via a surface plasmon resonance (SPR)-based immunosensor in comparison to conventional microtiter plate-based enzyme-linked immunosorbent assay (ELISA). An HSL derivative, named HSL2 (Table 1), was attached to bovine serum albumin (BSA) and the conjugate (HSL2-BSA-r2) was either covalently immobilised on the SPR sensor chip surface via free amino groups or via adsorption on the ELISA polystyrene plate surface. With a newly developed rat monoclonal antibody (mAb HSL1/2 2C10), AHLs were detected sensitively in a competitive format with SPR and ELISA.

Conditional RNAi in mice.

RNA interference (RNAi)-mediated gene knockdown has developed into a routine method to assess gene function in cultured mammalian cells in a fast and easy manner. For the use of RNAi in mice, short hairpin (sh) RNAs expressed stably from the genome are a fast alternative to conventional knockout approaches. We developed a strategy for complete or conditional gene knockdown in mice, where the Cre/loxP system is used to activate RNAi in a time and tissue dependent manner.

Eye development.

The vertebrate eye comprises tissues from different embryonic origins: the lens and the cornea are derived from the surface ectoderm, but the retina and the epithelial layers of the iris and ciliary body are from the anterior neural plate. The timely action of transcription factors and inductive signals ensure the correct development of the different eye components. Establishing the genetic basis of eye defects in zebrafishes, mouse, and human has been an important tool for the detailed analysis of this complex process.

Economic perspectives on pediatric obesity: impact on health care expenditures and cost-effectiveness of preventive interventions.

This chapter surveys two segments of the economic literature on pediatric obesity: first, research regarding the impact of childhood obesity on health care expenditure, and second, research evaluating the cost-effectiveness of programs to prevent pediatric obesity. Evidence in support of the hypothesis that obese children and adolescents have higher health care costs than their otherwise similar healthy-weight peers has been found for female adolescents. Studies trying to calculate the complete lifetime health care costs attributable to childhood obesity are missing.

Excess direct medical costs of severe obesity by socioeconomic status in German adults.

Objective: Excess direct medical costs of severe obesity are by far higher than of moderate obesity. At the same time, severely obese adults with low socioeconomic status (SES) may be expected to have higher excess costs than those with higher SES, e.g.

Analysis of DDT isomers with enzyme-linked immunosorbent assay and optical immunosensor based on rat monoclonal antibodies as biological recognition elements.

New rat monoclonal antibodies (mAbs) for DDT [1,1,1 -trichloro-2,2-bis (4-chlorophenyl) ethane], namely DDT 7C12, DDT 1C1, and DDT 1B2, were developed, characterized, and applied in ELISA both in coating antigen and in enzyme-tracer format. The latter used horseradish peroxidase (HRP) or glucose oxidase as enzymes. The lowest concentration of p,p'-DDT was determined with mAb DDT 7C12 and DDT-hapten HRP, with a test midpoint (IC50) of 0.

PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes.

In recent years, microRNAs have been shown to play important roles in physiological as well as malignant processes. The PhenomiR database http://mips.helmholtz-muenchen.