6-Phosphofructo-2-kinase and D-fructose-2,6-bisphosphatase activities in mung bean seedlings

6-Phosphofructo-2-kinase (ATP: D-fructose-6-phosphate-2-phosphotransferase) and D-fructose-2,6-bisphosphatase activities have been found in extracts prepared from etiolated mung bean seedlings. The activity of 6-phosphofructo-2-kinase exhibits a sigmoidal shape in response to changes in concentrations of both substrates, D-fructose 6-phosphate and ATP (S_0.5 values of 1.8 and 1.2 mM, respectively). Inorganic orthophosphate (P_i) has a strong stimulating effect on the 2-kinase activity (A_0.5 at about 2 mM), moderately increasing the V_max and modifying the response into hyperbolic curves with K_m values of 0.4 and 0.2 mM for fructose 6-phosphate and ATP, respectively. 3-Phosphoglycerate (I_0.5 about 0.15 mM) partially inhibited the kinase activity by counteracting the P_i activation. In contrast, the activity of D-fructose-2,6-bisphosphatase (K_m 0.38 mM) is strongly inhibited by P_i (I_0.5 0.8 mM) lowering its affinity to fructose-2,6-P₂ (K_m 1.4 mM). 3-Phosphoglycerate activites the enzyme (A_0.5 at about 0.3 mM) without causing a significant change in its K_m for fructose-2,6-P₂. The activities of both of these enzymes in relationship to the metabolic role of D-fructose 2,6-bisphosphate in the germinating seed is discussed.     

Promotion and inhibition of vesicle fusion by polylysine

Polylysine induced rapid aggregation of large unilamellar vesicles composed of phosphatidylcholine-cardiolipin (1:1 molar ratio) but not their fusion. Application of the terbium-dipicolinic acid fusion assay showed that addition of polylysine at nanomolar concentrations enabled a significant lowering of the Ca2+ threshold concentration for vesicle fusion from 9 to 1 mM. Analysis of the kinetics of fusion with a mass-action kinetic model showed that polylysine enhanced significantly the rate of aggregation but affected only slightly the rate of fusion per se. Maximal enhancement of overall fusion rates occurred at a charge ratio (polylysine/cardiolipin) of about 0.5. At larger polylysine concentrations, e.g., at charge ratios greater than 3, polylysine inhibited vesicle fusion.     

Systematic Identification of Rhythmic Genes Reveals camk1gb as a New Element in the Circadian Clockwork

A wide variety of biochemical, physiological, and molecular processes are known to have daily rhythms driven by an endogenous circadian clock. While extensive research has greatly improved our understanding of the molecular mechanisms that constitute the circadian clock, the links between this clock and dependent processes have remained elusive. To address this gap in our knowledge, we have used RNA sequencing (RNA–seq) and DNA microarrays to systematically identify clock-controlled genes in the zebrafish pineal gland. In addition to a comprehensive view of the expression pattern of known clock components within this master clock tissue, this approach has revealed novel potential elements of the circadian timing system. We have implicated one rhythmically expressed gene, camk1gb, in connecting the clock with downstream physiology of the pineal gland. Remarkably, knockdown of camk1gb disrupts locomotor activity in the whole larva, even though it is predominantly expressed within the pineal gland. Therefore, it appears that camk1gb plays a role in linking the pineal master clock with the periphery.     

Coordinated gene networks regulating Arabidopsis plant metabolism in response to various stresses and nutritional cues

The expression pattern of any pair of genes may be negatively correlated, positively correlated, or not correlated at all in response to different stresses and even different progression stages of the stress. This makes it difficult to identify such relationships by classical statistical tools such as the Pearson correlation coefficient. Hence, dedicated bioinformatics approaches that are able to identify groups of cues in which there is a positive or negative expression correlation between pairs or groups of genes are called for. We herein introduce and discuss a bioinformatics approach, termed Gene Coordination, that is devoted to the identification of specific or multiple cues in which there is a positive or negative coordination between pairs of genes and can further incorporate additional coordinated genes to form large coordinated gene networks. We demonstrate the utility of this approach by providing a case study in which we were able to discover distinct expression behavior of the energy-associated gene network in response to distinct biotic and abiotic stresses. This bioinformatics approach is suitable to a broad range of studies that compare treatments versus controls, such as effects of various cues, or expression changes between a mutant and the control wild-type genotype.     

Structure of the bundle-forming pilus from enteropathogenic Escherichia coli

Bundle-forming pili (BFP) are essential for the full virulence of enteropathogenic Escherichia coli (EPEC) because they are required for localized adherence to epithelial cells and auto-aggregation. We report the high resolution structure of bundlin, the monomer of BFP, solved by NMR. The structure reveals a new variation in the topology of type IVb pilins with significant differences in the composition and relative orientation of elements of secondary structure. In addition, the structural parameters of native BFP filaments were determined by electron microscopy after negative staining. The solution structure of bundlin was assembled according to these helical parameters to provide a plausible atomic resolution model for the BFP filament. We show that EPEC and Vibriocholerae type IVb pili display distinct differences in their monomer subunits consistent with data showing that bundlin and TcpA cannot complement each other, but assemble into filaments with similar helical organization.     

Protective effect of vitamin E, beta-carotene and N-acetylcysteine from the brain oxidative stress induced in rats by lipopolysaccharide

The major goal of this study was to examine the ability of several antioxidants namely, vitamin E, beta-carotene and N-acetylcysteine, to protect the brain from oxidative stress induced by lipopolysaccharide (LPS, endotoxin). LPS, a component of the bacterial wall of gram-negative bacteria, has been recognized as one of the most potent bacterial products in the induction of host inflammatory responses and tissue injury and was used in this study to mimic infections. LPS injection resulted in a significant increase in the stress indices, plasma corticosterone and glucose concentration, a significant alteration of the brain oxidative status observed as elevation of the level of malondialdehyde (MDA, index of lipid peroxidation) and reduction of reduced glutathione (GSH), and a disturbance in the brain energy metabolism presented as a reduction in the ATP/ADP ratio and an increase in the mitochondrial/cytosolic hexokinase ratio. However, the activities of brain superoxide dismutase and Na+, K+-ATPase and contents of cholesterol and phospholipids were not altered. Administration of the aforementioned antioxidants prior to LPS injection ameliorated the oxidative stress by reducing levels of MDA, restoring GSH content and normalizing the mitochondrial/cytosolic hexokinase ratio in the brain in addition to lowering levels of plasma corticosterone and glucose. In conclusion, this study showed the increased free radical generation during infections and LPS-induced stress. It also suggests that brain oxidative status and energy is disturbed.     

The effect of light availability on the photosynthetic activity and productivity of outdoor cultures of Arthrospira platensis (Spirulina)

The basic requirement for establishing economically viable large-scale production of algal biomass, be it for food, feed, high-value product, or energy, is the ability to produce the biomass at a low price. To achieve this goal, an efficient production protocol is needed that ensures that the potential productivity is obtained at any given time. When productivity is defined by the ability to utilize the available solar radiation that drives photosynthesis, the production protocol must be optimized to meet this requirement. In the current study, we demonstrate that by modifying the light available to Arthrospira platensis cells cultured outdoors by a variety of options like modifying the standing biomass concentration, changing the mixing rate, or shading can change the potential photosynthetic activity and apparent activity. By optimizing the light available to algae cells under outdoor conditions, productivity can be increased by approximately 50 %, from 15.6 g m^?2 day^?1 in a culture that suffers from overexposure to light to 22.4 g m^?2 day^?1 in a culture in which light downregulation is minimized. Therefore, by using a variety of methodologies to estimate photosynthetic activity, we demonstrate that overexposing the cells to light may result in downregulation of the photosynthetic activity leading to photoinhibition and lower biomass productivity.     

Compound heterozygosity in nonphenylketonuria hyperphenylalanemia: the contribution of mutations for classical phenylketonuria

Hyperphenylalaninemia (HPA) results from defective hydroxylation of phenylalanine in the liver, in most cases because of defective phenylalanine hydroxylase. HPA is highly variable, ranging from moderate elevation of plasma phenylalanine with no clinical consequences to a severe disease, classical phenylketonuria (PKU). Non-PKU HPA was found in excess of PKU in Israel, while the opposite is true in Europe. To study the genetic basis of non-PKU HPA, we performed haplotype analysis at the phenylalanine hydroxylase locus in 27 families with non-PKU HPA. All individuals with this condition were compound heterozygotes. In six of these families, in which both PKU and non-PKU HPA were segregating, haplotype analysis showed that non-PKU HPA resulted from compound heterozygosity for a PKU mutation and a second mutation, with milder effect, which is probably expressed only when it interacts with the severe mutation. The involvement of PKU mutations in non-PKU HPA was further demonstrated in Jewish Yemenite families with non-PKU HPA, in which the individuals with this condition were carriers of the single PKU allele which exists in this community. In addition, two previously known PKU point mutations (R261Q and R408W) were found in individuals with non-PKU HPA. These mutations are associated, in our population, with the same haplotypes as those with which it is associated in Europe. Based on the above-mentioned genetic model for non-PKU HPA, successful prenatal diagnosis of this condition was performed in one family.(ABSTRACT TRUNCATED AT 250 WORDS)     

Gene proximity analysis across whole genomes via PQ trees.

Permutations on strings representing gene clusters on genomes have been studied earlier by Uno and Yagiura (2000), Heber and Stoye (2001), Bergeron et al. (2002), Eres et al. (2003), and Schmidt and Stoye (2004) and the idea of a maximal permutation pattern was introduced by Eres et al. (2003). In this paper, we present a new tool for representation and detection of gene clusters in multiple genomes, using PQ trees (Booth and Leuker, 1976): this describes the inner structure and the relations between clusters succinctly, aids in filtering meaningful from apparently meaningless clusters, and also gives a natural and meaningful way of visualizing complex clusters. We identify a minimal consensus PQ tree and prove that it is equivalent to a maximal pi pattern (Eres et al., 2003) and each subgraph of the PQ tree corresponds to a nonmaximal permutation pattern. We present a general scheme to handle multiplicity in permutations and also give a linear time algorithm to construct the minimal consensus PQ tree. Further, we demonstrate the results on whole genome datasets. In our analysis of the whole genomes of human and rat, we found about 1.5 million common gene clusters but only about 500 minimal consensus PQ trees, with E. Coli K-12 and B. Subtilis genomes, we found only about 450 minimal consensus PQ trees out of about 15,000 gene clusters, and when comparing eight different Chloroplast genomes, we found only 77 minimal consensus PQ trees out of about 6,700 gene clusters. Further, we show specific instances of functionally related genes in two of the cases.     

Astaxanthin Accumulation in the Green Alga Haematococcus pluvialis1

Cells of the green microalga Haematococcus pluvialis were inducedto accumulate the ketocarotenoid pigment, astaxanthin. Thisinduction was achieved by the application of the following environmentalconditions: light intensity (170 µmol m~^–2s^–1),phosphate starvation and salt stress (NaCl 0.8%). These conditionsretarded cell growth as reflected by a decrease in cell divisionrate, but led to an increase in astaxanthin content per cell.Accumulation of astaxanthin required nitrogen and was associatedwith a change in the cell stage from biflagellate vegetativegreen cells to non-motile and large resting cells. It is suggestedthat environmental or nutritional stresses, which interferewith cell division, trigger the accumulation of astaxanthin.Indeed, when a specific inhibitor of cell division was applied,a massive accumulation of astaxanthin occurred. ¹ Contribution No. 55 of The Microalgal Biotechnology Laboratory (Received April 22, 1991; Accepted August 6, 1991)