A computer algorithm to determine the recognition site of restriction enzymes

A new algorithm is proposed to determine the type-II restrictionendonucleases' recognition site knowing the digested DNA sequenceand fragment lengths in an actual case. The algorithm is implementedfor the Commodore 64 microcomputer. Received on January 6, 1987; accepted on June 19, 1987     

How the Visual Cortex Handles Stimulus Noise: Insights from Amblyopia

Adding noise to a visual image makes object recognition more effortful and has a widespread effect on human electrophysiological responses. However, visual cortical processes directly involved in handling the stimulus noise have yet to be identified and dissociated from the modulation of the neural responses due to the deteriorated structural information and increased stimulus uncertainty in the case of noisy images. Here we show that the impairment of face gender categorization performance in the case of noisy images in amblyopic patients correlates with amblyopic deficits measured in the noise-induced modulation of the P1/P2 components of single-trial event-related potentials (ERP). On the other hand, the N170 ERP component is similarly affected by the presence of noise in the two eyes and its modulation does not predict the behavioral deficit. These results have revealed that the efficient processing of noisy images depends on the engagement of additional processing resources both at the early, feature-specific as well as later, object-level stages of visual cortical processing reflected in the P1 and P2 ERP components, respectively. Our findings also suggest that noise-induced modulation of the N170 component might reflect diminished face-selective neuronal responses to face images with deteriorated structural information.     

Characterization of [3H]Met-Enkephalin-Arg6-Phe7 Binding to Opioid Receptors in Frog Brain Membrane Preparations

Abstract: A tritiated heptapeptide, [³H]Tyr-Gly-Gly-Phe-Met-Arg-Phe ([³H]Met-enkephalin-Arg⁶-Phe⁷), with high specific radioactivity has been synthesized in order to characterize its opioid binding activity to frog brain membrane fractions. The apparent K _D value of the radioligand calculated from homologous displacement experiments was 3.4 n M , and the maximal number of specific binding sites was 630 fmol/mg of protein. The K _D determined from equilibrium saturation binding studies was found to be 3.6 n M . However, the Hill coefficient was far below unity ( n _H = 0.43), which suggests the presence of a second, lower affinity binding site. The presence of this binding component is strengthened by the displacement experiments performed with levorphanol and some other ligands. It is assumed that the lower affinity site has no opiate character. The rank order of potency of the applied ligands in competing reversibly with [³H]Met-enkephalin-Arg⁶-Phe⁷ binding reflects a κ₂- and/or δ-subtype specificity of the heptapeptide. Binding to a κ₁ and/or μ site of opioid receptors is excluded, but the existence of a novel endogenous opiate receptor subtype for Met-enkephalin-Arg⁶-Phe⁷ in frogs cannot be ruled out. The [³H]Met-enkephalin-Arg⁶-Phe⁷ binding was inhibited by both sodium ions and GppNHp, which suggests the opioid agonist character of the heptapeptide.     

Agrobacterium mediated genetic transformation and plant regeneration via organogenesis and somatic embryogenesis from cotyledon leaves in eggplant (Solanum melongena L. cv. ‘Kecskeméti lila’)

Summary Novel and efficient protocols for plant regeneration and genetic transformation from longitudinally-halved cotyledons ofin vitro raised seedlings in eggplant (Solanum melongena L.) are described. After co-cultivation withAgrobacterium vectors harboring neomycin phosphotransferase (nptll) as selectable marker, transgenic plantlets were regenerated on selective media containing 100 mg/l kanamycin. Transformants were recovered from embryogenic calli induced by 4 mg/l-naphthaleneacetic acid (NAA), and from organogenic calli induced by the addition of 2 mg/l zeatin plus 0.01 mg/l NAA. Nineteen independent transgenic lines were grown to maturity. The structural integrity, expression and sexual transmission of the introduced genes for neomycin phosphotransferase and ß-glucuronidase (gus) were investigated.     

Stir-up effect of wind on a more-or-less stratified shallow lake phytoplankton community,Lake Balaton,Hungary

Microstratification of phytoplankton in the large shallow Lake Balaton (Hungary) was studied during a 24 h period. Dissolved O₂ showed biological stratification; flagellates exhibited a definite circadian rhythm. In the middle of the investigation a heavy storm broke out which was followed by the disappearance of differences between different layers of water. Storm-induced destratification is described by cluster-analysis. Abundances of dominant species changed differently in connection with the storm. Numbers of Nitzschia sp. increased due to stirring up from the sediment surface. Numbers of single-celled or colony-forming species (Cyclotella comta, Crucigenia quadrata, Coelosphaerium kuetzingianum) practically did not change. Numbers of all the three dominant filamentous species (Aphanizomenon fos-aquae f. klebahnii, Lyngbya limnetica, Planctonema lauterbornii) significantly decreased, which might be attributed to an unknown loss process and was followed by a competitive displacement by algae of small cell size.     

Photosensitizers and antioxidants: a way to new drugs?

Photodynamic therapy (PDT) is a relatively new modality of treatment of diseases involving uncontrolled cell proliferation. It is based on the production of reactive species upon illumination of a photosensitizer in the presence of oxygen. Antioxidants are primarily reducing agents prone to scavenge reactive species in one way or another. Their presence in photodynamic reactions usually reduces the efficacy of PDT. Some antioxidants like ascorbic acid, alpha-tocopherol or butyl-4-hydroxyanisole, however, when added to cells at adequate concentrations may enhance the photodamaging activity of PDT. The presence of transition metals and precise timing of antioxidant administration may also be important factors in increasing the efficacy of PDT. Antioxidant carrier sensitizers have been designed, synthesised and tested for their antibacterial PDT activity. The promising results raise the question whether the introduction of antioxidant moieties into sensitizer molecules would lead to the synthesis of highly effective new drugs.     

Susceptibility of dopamine D5 receptor targeted mice to cysteamine

BACKGROUND: Recently we demonstrated that gastric mucosa of rats can synthesize, store and release dopamine. Out of five different subtypes, mRNA of D5 (=D1b) dopamine receptor is very abundant in the gastric epithelium. D1 receptor selective dopamine agonists have been shown to protect against experimental gastro-duodenal lesions. AIMS: To test the hypothesis that protective effects of dopamine involve D5 receptors, mucosal lesions were induced in D5 receptor deficient (KO) and wild-type (WT) mice using cysteamine. Morphology and gastric acid secretion of D5 KO mice were also studied. METHODS: Single doses of 600 mg/kg, 300 mg/kg cysteamine or vehicle were administered subcutaneously to fasted animals. After 24 h, number and severity of gastro-duodenal lesions were analyzed. Basal and histamine-induced maximal gastric acid output were measured by a stomach-sac wash-through method. RESULTS: All the KOs in the 600 mg/kg cysteamine group died within 4 h showing symptoms of toxicity while three out of four WTs survived (P<0.05). Mortality after 300 mg/kg cysteamine was significantly higher in KOs versus the WTs: 6/14 versus 2/11, P<0.05. Gastric lesion-index was also significantly higher in KOs (median, middle quartile): four (3-9) versus 0 (0-0), P<0.05. Duodenal lesions did not develop from this single dose of cysteamine in either genotype. Basal and histamine-induced maximal gastric acid output were comparable in the two genotypes. CONCLUSIONS: This study demonstrates that loss of D5 receptor causes mucosal vulnerability and increased toxicity of cysteamine in genetically manipulated mice. Thus, D5 receptor subtype is indeed likely to be involved in protective effects of dopamine in the stomach.     

Synchrotron-based infrared and X-ray imaging shows focalized accumulation of Cu and Zn co-localized with beta-amyloid deposits in Alzheimer's disease

Alzheimer's disease (AD) is characterized by the misfolding and plaque-like accumulation of a naturally occurring peptide in the brain called amyloid beta (Abeta). Recently, this process has been associated with the binding of metal ions such as iron (Fe), copper (Cu), and zinc (Zn). It is thought that metal dyshomeostasis is involved in protein misfolding and may lead to oxidative stress and neuronal damage. However, the exact role of the misfolded proteins and metal ions in the degenerative process of AD is not yet clear. In this study, we used synchrotron Fourier transform infrared micro-spectroscopy (FTIRM) to image the in situ secondary structure of the amyloid plaques in brain tissue of AD patients. These results were spatially correlated with metal ion accumulation in the same tissue sample using synchrotron X-ray fluorescence (SXRF) microprobe. For both techniques, a spatial resolution of 5-10 microm was achieved. FTIRM results showed that the amyloid plaques have elevated beta-sheet content, as demonstrated by a strong amide I absorbance at 1625cm(-1). Using SXRF microprobe, we find that AD tissue also contains "hot spots" of accumulated metal ions, specifically Cu and Zn, with a strong spatial correlation between these two ions. The "hot spots" of accumulated Zn and Cu were co-localized with beta-amyloid plaques. Thus for the first time, a strong spatial correlation has been observed between elevated beta-sheet content in Abeta plaques and accumulated Cu and Zn ions, emphasizing an association of metal ions with amyloid formation in AD.     

The influence of the thymine C5 methyl group on spontaneous base pair breathing in DNA

Sequences of four or more AT base pairs without a 5'-TA-3' step, so-called A-tracts, influence the global properties of DNA by causing curvature of the helix axis if phased with the helical repeat and also influence nucleosome packaging. Hence it is interesting to understand this phenomenon on the molecular level, and numerous studies have been devoted to investigations of dynamical and structural features of A-tract DNA. It was early observed that anomalously slow base pair-opening kinetics were a striking physical property unique to DNA A-tracts (Leroy, J. L., Charretier, E., Kochoyan, M., and Gueron, M. (1988) Biochemistry 27, 8894-8898). Furthermore, a strong correlation between DNA curvature and anomalously slow base pair-opening dynamics was found. In the present work it is shown, using imino proton exchange measurements by NMR spectroscopy that the main contribution to the dampening of the base pair-opening fluctuations in A-tracts comes from the C5 methylation of the thymine base. Because the methyl group has been shown to have a very limited effect on the DNA curvature as well as the structure of the DNA helix, the thymine C5 methyl group stabilizes the helix directly. Empirical potential energy calculations show that methylation of the tract improves the stacking energy of a base pair with its neighbors in the tract by 3-4 kcal/mol.