Structural parameters affecting the kinetics of RNA hairpin formation

There is little experimental knowledge on the sequence dependent rate of hairpin formation in RNA. We have therefore designed RNA sequences that can fold into either of two mutually exclusive hairpins and have determined the ratio of folding of the two conformations, using structure probing. This folding ratio reflects their respective folding rates. Changing one of the two loop sequences from a purine- to a pyrimidine-rich loop did increase its folding rate, which corresponds well with similar observations in DNA hairpins. However, neither changing one of the loops from a regular non-GNRA tetra-loop into a stable GNRA tetra-loop, nor increasing the loop size from 4 to 6 nt did affect the folding rate. The folding kinetics of these RNAs have also been simulated with the program ‘Kinfold’. These simulations were in agreement with the experimental results if the additional stabilization energies for stable tetra-loops were not taken into account. Despite the high stability of the stable tetra-loops, they apparently do not affect folding kinetics of these RNA hairpins. These results show that it is possible to experimentally determine relative folding rates of hairpins and to use these data to improve the computer-assisted simulation of the folding kinetics of stem–loop structures.     

Dynamics of root growth stimulation in Nicotiana tabacum in increasing light intensity

Light intensity is crucial for plant growth. In this study, the hypothesis was tested whether a sudden increase in light intensity leads to an immediate increase of root growth. Seedlings of Nicotiana tabacum grown in agar-filled Petri dishes were subjected to light intensities of 60 and 300 micromol m(-2) s(-1), respectively. Seedling biomass, sucrose, glucose and fructose concentration as well as primary root growth increased significantly with light intensity. The dynamics of the increase in root growth were analysed here in more detail. In transition experiments from low to high light intensities, root growth increased by a factor of four within 4 d, reaching the steady-state level measured in plants that were cultivated in high-light conditions. The distribution of relative elemental growth rates along the root growth zone retained a constant shape throughout this transition. During the first three hours after light increase, strong growth fluctuations were repeatedly observed with the velocity of the root tip cycling in a sinusoidal pattern between 120 and 180 microm h(-1). These dynamic patterns are discussed in the context of hydraulic and photosynthetic acclimation to the altered conditions. Experiments with externally applied sucrose and with transgenic plants having reduced capacities for sucrose synthesis indicated clearly that increasing light intensity rapidly enhanced root growth by elevating sucrose export from shoot to root.     

Biophysical characterisation of electrofused giant HEK293-cells as a novel electrophysiological expression system

Giant HEK293 cells of 30-65 microm in diameter were produced by three-dimensional multi-cell electrofusion in 75 mOsm sorbitol media. These strong hypotonic conditions facilitated fusion because of the spherical shape and smooth membrane surface of the swollen cells. A regulatory volume decrease (RVD), as observed at higher osmolalities, did not occur at 75 mOsm. In contrast to field-treated, but unfused cells, the increase in volume induced by hypotonic shock was only partly reversible in the case of fused giant cells after their transfer into isotonic medium. The large size of the electrofused cells allowed the study of their electrophysiological properties by application of both whole-cell and giant excised patch-clamp techniques. Recordings on giant cells yielded a value of 1.1+/-0.1 microF/cm2 for the area-specific membrane capacitance. This value was consistent with that of the parental cells. The area-specific conductivity of giant cells (diameter > 50 microm) was found to be between 12.8 and 16.1 microS/cm2, which is in the range of that of the parental cells. Measurements with patch-pipettes containing fluorescein showed uniform dye uptake in the whole-cell configuration, but not in the cell-attached configuration. The diffusion-controlled uniform uptake of the dye into the cell interior excludes internal compartmentalisation. The finding of a homogeneous fusion was also supported by expression of the yellow fluorescent protein YFP (as part of the fusion-protein ChR2-YFP) in giant cells since no plasma-membrane bound YFP-mediated fluorescence was detected in the interior of the electrofused cells. Functional expression and the electrophysiological characterisation of the light-activated cation channel Channelrhodopsin 2 (ChR2) yielded similar results as for parental cells. Most importantly, the giant cells exhibited a comparable expression density of the channel protein in the plasma membrane as observed in parental cells. This demonstrates that electrofused cells can be used as a heterologous expression system.     

Neuronal Ca2+ signaling via caldendrin and calneurons

The calcium sensor protein caldendrin is abundantly expressed in neurons and is thought to play an important role in different aspects of synapto-dendritic Ca2+ signaling. Caldendrin is highly abundant in the postsynaptic density of a subset of excitatory synapses in brain and its distinct localization raises several decisive questions about its function. Previous work suggests that caldendrin is tightly associated with Ca2+ - and Ca2+ release channels and might be involved in different aspects of the organization of the postsynaptic scaffold as well as with synapse-to-nucleus communication. In this report we introduce two new EF-hand calcium sensor proteins termed calneurons that apart from calmodulin represent the closest homologues of caldendrin in brain. Calneurons have a different EF-hand organization than other calcium sensor proteins, are prominently expressed in neurons and will presumably bind Ca2+ with higher affinity than caldendrin. Despite some significant structural differences it is conceivable that they are involved in similar Ca2+ regulated processes like caldendrin and neuronal calcium sensor proteins.     

Implications of the genetic epidemiology of globin haplotypes linked to the sickle cell gene in southern Iran

To determine the origin of sickle cell mutation in different ethnic groups living in southern Iran, we studied the haplotype background of the betaS and betaA genes in subjects from the provinces of Fars, Khuzestan, Bushehr, Hormozgan, and Kerman and from the islands of Khark and Qeshm. beta-globin gene cluster haplotypes were determined using the PCR-RFLP technique. Detection of -alpha 3.7 deletion and beta-thalassemia mutations were defined by PCR and reverse dot blot techniques, respectively. The framework of the beta-globin gene was determined using denaturing gradient gel electrophoresis. We found that the betaS mutation in southern Iran is associated with multiple mutational events. Most of the patients were from two ethnic groups: Farsi speakers (presumably Persian in origin) from Fars province and patients of Arab origin from Khuzestan province. In both ethnic groups the Arab-Indian haplotype was the most prevalent. The frequencies of the Arab-Indian and African haplotypes in sickle cell anemia patients from the provinces of Fars and Khuzestan were similar. Among betaA chromosomes the Bantu A2 haplotype was the most prevalent. The decrease in alpha-globin production in SS patients and AS individuals appeared to be related to the reduction in mean cell volume and mean cell hemoglobin. The Arab-Indian haplotype gene flow into this region of Iran can be traced to the Sassanian Empire. It is likely that the influx of betaS genes linked to the Benin and Bantu haplotypes, of African origin, must have occurred during the Arab slave trade.     

Increased hepatic fibrosis and JNK2-dependent liver injury in mice exhibiting hepatocyte-specific deletion of cFLIP

Chronic liver disease promotes hepatocellular injury involving apoptosis and triggers compensatory regeneration that leads to the activation of quiescent stellate cells in the liver. The deposition of extracellular matrix from activated myofibroblasts promotes hepatic fibrosis and the progression to cirrhosis with deleterious effects on liver physiology. The role of apoptosis signaling pathways in the development of fibrosis remains undefined. The aim of the current study was to determine the involvement of the caspase-8 homologue cellular FLICE-inhibitory protein (cFLIP) during the initiation and progression of fibrosis. Liver injury and fibrosis from carbon tetrachloride (CCl(4)) and thioacetamide (TAA) were examined in mice exhibiting a hepatocyte-specific deletion of cFLIP (flip(-/-)). Acute liver injury from CCl(4) and TAA were enhanced in flip(-/-) mice. This was accompanied by increased activation of caspase-3 and -9, pronounced phosphorylation of JNK, and decreased phosphorylation of Erk. Deletion of the cJun NH(2)-terminal kinase 2 (JNK2) in flip(-/-) mice protected from injury. Hepatic fibrosis was increased at baseline in 12-wk-old flip(-/-) mice, and progression of fibrosis from TAA was accelerated compared with the wild type. In conclusion, deletion of cFLIP in hepatocytes leads to increased fibrosis and accelerated fibrosis progression. This is accompanied by increased injury involving the activation of caspases and JNK2. Thus predisposition to liver injury involving increased hepatocellular apoptosis is a critical mediator of accelerated fibrogenesis, and prevention of liver injury will be a most important measure for patients with chronic liver disease.     

Molecular markers in management of ex situ PGR – A case study

Worldwide germplasm collections contain about 7.4 million accessions of plant genetic resources for food and agriculture. One of the 10 largest ex situ genebanks of our globe is located at the Leibniz Institute of Plant Genetics and Crop Plant Research in Gatersleben, Germany. Molecular tools have been used for various gene bank management practices including characterization and utilization of the germplasm. The results on genetic integrity of long-term-stored gene bank accessions of wheat (self-pollinating) and rye (open-pollinating) cereal crops revealed a high degree of identity for wheat. In contrast, the out-pollinating accessions of rye exhibited shifts in allele frequencies. The genetic diversity of wheat and barley germplasm collected at intervals of 40 to 50?years in comparable geographical regions showed qualitative rather than a quantitative change in diversity. The inter- and intraspecific variation of seed longevity was analysed and differences were detected. Genetic studies in barley, wheat and oilseed rape revealed numerous QTL, indicating the complex and quantitative nature of seed longevity. Some of the loci identified were in genomic regions that co-localize with genes determining agronomic traits such as spike architecture or biotic and abiotic stress response. Finally, a genome-wide association mapping analysis of a core collection of wheat for flowering time was performed using diversity array technology (DArT) markers. Maker trait associations were detected in genomic regions where major genes or QTL have been described earlier. In addition, new loci were also detected, providing opportunities to monitor genetic variation for crop improvement.     

Protein-protein-interaction Network Organization of the Hypusine Modification System

Hypusine modification of eukaryotic initiation factor 5A (eIF-5A) represents a unique and highly specific post-translational modification with regulatory functions in cancer, diabetes, and infectious diseases. However, the specific cellular pathways that are influenced by the hypusine modification remain largely unknown. To globally characterize eIF-5A and hypusine-dependent pathways, we used an approach that combines large-scale bioreactor cell culture with tandem affinity purification and mass spectrometry: “bioreactor-TAP-MS/MS.” By applying this approach systematically to all four components of the hypusine modification system (eIF-5A1, eIF-5A2, DHS, and DOHH), we identified 248 interacting proteins as components of the cellular hypusine network, with diverse functions including regulation of translation, mRNA processing, DNA replication, and cell cycle regulation. Network analysis of this data set enabled us to provide a comprehensive overview of the protein-protein interaction landscape of the hypusine modification system. In addition, we validated the interaction of eIF-5A with some of the newly identified associated proteins in more detail. Our analysis has revealed numerous novel interactions, and thus provides a valuable resource for understanding how this crucial homeostatic signaling pathway affects different cellular functions.Cellular homeostasis is controlled by signaling networks that communicate through post-translational modifications (PTM)¹ of proteins, including phosphorylation, acetylation and methylation (1–3). These modifications are typically attached to various types of proteins by multiple independent enzymes, and thereby simultaneously regulate a wide range of protein functions. Consequently, most signaling pathways are highly redundant, enabling maintenance of cellular integrity even if the modification of a single signaling molecule is disrupted (4). A striking exception is hypusine. This essential PTM is limited to a single protein: the eukaryotic initiation factor 5A (eIF-5A) (5). Disruption of this PTM leads to growth arrest in proliferating eukaryotic cells and is fatal for the developing mammalian embryo (6, 7). During hypusine biosynthesis, the lysine residue at position 50 (Lys₅₀) in eIF-5A is converted into the unusual amino acid hypusine (N^ε-(4-amino-2-hydroxybutyl)lysine; depicted in Fig. 1A) (5). This process activates eIF-5A and is mediated by two enzymatic reactions: first, deoxyhypusine synthase (DHS) catalyzes the transfer of the 4-aminobutyl moiety of spermidine to the ε-amino group of Lys₅₀ to form an intermediate residue, deoxyhypusine (Dhp₅₀) (8). Subsequently, deoxyhypusine hydroxylase (DOHH) mediates the formation of hypusine (Hyp₅₀) by addition of a hydroxyl group to the deoxyhypusine residue (9). eIF-5A, DHS and DOHH are all essential for proliferation of higher eukaryotic cells (10, 11), and eIF-5A is strictly conserved throughout eukaryotic evolution (12).Open in a separate windowFig. 1.The hypusine modification and TAP fusion proteins employed in this study. A, The hypusine modification pathway and major proposed eIF-5A functions. B, Structure of the plasmid inserts coding for SG-tagged bait proteins. The amino acid positions of eIF-5A mutants are indicated in italic. SBP, streptavidin binding peptide. C, Metabolic incorporation of ³H-labeled spermidine into eIF-5A. Arrowheads indicate bands of SG-tagged and endogenous eIF-5A proteins. D, Anti-Myc-tag Western blot of cell lysates from retrovirally transduced Ba/F3 p210 cell lines for the quantification of constitutively expressed SG-tagged bait proteins. E, Representative TAP outputs for MS/MS analysis, after 1D PAGE separation and Coomassie staining. Separation distance varies from ∼2 to 4 cm.The eIF-5A protein has been proposed to promote various different cellular processes that potentially regulate proliferation, including translation initiation (13) and elongation (14) as well as nucleocytoplasmic transport of RNA or other cargoes (15, 16). Using inhibitors of DHS and DOHH or eIF-5A mutants deficient for hypusine modification, it has also been shown that this modification is a prerequisite of at least a subset of known eIF-5A functions (10, 11, 17, 18). The eIF-5A protein has also been implicated in numerous pathologic conditions including various types of cancer (19–23), β-cell inflammation (and therefore diabetes) (24) and HIV-1 infection (25). Human and rodent cells carry two highly homologous eIF-5A genes coding for distinct isoforms. Although eIF-5A1 is expressed at high levels throughout all tissues, eIF-5A2 is detectable only in a few embryonic tissues as well as adult testis, central nervous system (26), and cancer tissue (21, 22, 27–29).Although there have been ample reports suggesting eIF-5A is involved in translational control, the molecular mechanisms through which it ultimately influences cellular physiology and leads to disease remain unclear. Moreover, it remains equally possible that at least some of eIF-5A''s effects on cellular functions might not involve direct effects on translation. Also, there is no information available on whether the two isoforms of mammalian eIF-5A are functionally congruent.To address these fundamental questions systematically and comprehensively, we employed a bioreactor-based tandem affinity purification (TAP) approach followed by MS identification of purified protein complexes (“bioreactor-TAP-MS/MS”). To obtain a complete interaction map of the proteins involved in hypusine modification, we used this approach to identify interaction partners of both isoforms of eIF-5A, as well as the hypusine modification enzymes DHS and DOHH. In total, we identified 248 proteins that either directly interact with these bait proteins or are components of higher complexes containing the aforementioned proteins. Furthermore, we validated a subset of putative interaction partners of both eIF-5A isoforms, using Western blots of reciprocal TAP experiments, as well as a live-cell protein-fragment complementation assay (PCA). Our analysis provides a molecular framework for a detailed understanding on how this signal transduction pathway affects different crucial cellular functions.     

Altered velocity processing in schizophrenia during pursuit eye tracking

Smooth pursuit eye movements (SPEM) are needed to keep the retinal image of slowly moving objects within the fovea. Depending on the task, about 50%-80% of patients with schizophrenia have difficulties in maintaining SPEM. We designed a study that comprised different target velocities as well as testing for internal (extraretinal) guidance of SPEM in the absence of a visual target. We applied event-related fMRI by presenting four velocities (5, 10, 15, 20°/s) both with and without intervals of target blanking. 17 patients and 16 healthy participants were included. Eye movements were registered during scanning sessions. Statistical analysis included mixed ANOVAs and regression analyses of the target velocity on the Blood Oxygen Level Dependency (BOLD) signal. The main effect group and the interaction of velocity×group revealed reduced activation in V5 and putamen but increased activation of cerebellar regions in patients. Regression analysis showed that activation in supplementary eye field, putamen, and cerebellum was not correlated to target velocity in patients in contrast to controls. Furthermore, activation in V5 and in intraparietal sulcus (putative LIP) bilaterally was less strongly correlated to target velocity in patients than controls. Altered correlation of target velocity and neural activation in the cortical network supporting SPEM (V5, SEF, LIP, putamen) implies impaired transformation of the visual motion signal into an adequate motor command in patients. Cerebellar regions seem to be involved in compensatory mechanisms although cerebellar activity in patients was not related to target velocity.