Specific DNA recognition by the Antp homeodomain: MD simulations of specific and nonspecific complexes

Four molecular dynamics simulation trajectories of complexes between the wild-type or a mutant Antennapedia homeodomain and 2 DNA sequences were generated in order to probe the mechanisms governing the specificity of DNA recognition. The starting point was published affinity measurements showing that a single protein mutation combined with a replacement of 2 base pairs yields a new high-affinity complex, whereas the other combinations, with changes on only 1 macromolecule, exhibited lower affinity. The simulations of the 4 complexes yielded fluctuating networks of interaction. On average, these networks differ significantly, explaining the switch of affinity caused by the alterations in the macromolecules. The network of mostly hydrogen-bonding interactions involving several water molecules, which was suggested both by X-ray and NMR structures of the wild-type homeodomain and its DNA operator sequence, could be reproduced in the trajectory. More interestingly, the high-affinity complex with alterations in both the protein and the DNA yielded again a dynamic but very tight network of intermolecular interactions, however, attributing a significantly stronger role to direct hydrophobic interactions at the expense of water bridges. The other 2 homeodomain-DNA complexes, with only 1 molecule altered, show on average over the trajectories a clearly reduced number of protein-DNA interactions. The observations from these simulations suggest specific experiments and thus close the circle formed by biochemical, structural, and computational studies. The shift from a water-dominated to a more "dry" interface may prove important in the design of proteins binding DNA in a specific manner.     

Comparison of the chiral separation of amino-acid derivatives by a teicoplanin and RN-beta-CD CSPs using waterless mobile phases: Factors that enhance resolution

A variety of compounds containing amines (i.e., amino acids, amino alcohols, etc.) were chemically derivatized with a variety of electrophilic tagging reagents to elucidate the chiral recognition sites on a teicoplanin-bonded chiral stationary phase (CSP) and on R-naphthylethylcarbamate-beta-cyclodextrin (RN-beta-CD)-bonded CSP. Solutes were separated under optimum chromatographic conditions on teicoplanin and RN-beta-CD CSPs for comparison using an acetonitrile-based mobile phase. It was noted that the size of the analyte or tagging reagent exerted a greater influence on compounds separated on teicoplanin than on RN-beta-CD when using the polar organic mode. This suggests that chiral recognition on teicoplanin CSP is more sensitive to size and indicates that the hydrophobic pocket of teicoplanin plays a significant role in chiral recognition in this mode. However, the type of functional groups had a greater impact than the size of analyte on separations obtained from RN-beta-CD phase in the polar-organic mode. Specifically, the pi-pi interaction was enhanced by derivatizing the aromatic ring of the tagging reagent with electron-withdrawing groups and thus altered the resolution substantially. For both phases, chiral recognition is most pronounced when the stereogenic center of the analyte is near the tagging moiety and surrounded by functional groups (e.g., carboxylic, etc.) which are favorable for hydrogen bonding.     

Immunocytochemical study by two photon fluorescence microscopy of the distribution of GABA<Subscript>A</Subscript> receptor subunits in rat cerebellar granule cells in culture

Summary. An immunocytochemical investigation of the expression of ₁, ₆, _2/3, ₂ and subunits was performed on rat cerebellum granule cells in culture by the two photon microscopy technique.The first four subunits appear to be expressed abundantly in these cells, whereas the one seems to be expressed at a lower level. Another major difference in the distribution of these subunits is that whereas ₆, _2/3 and ₂ appear only on plasma membranes ₁ and are present mainly in the cell bodies cytoplasm. Still another difference was found in that the presence of ₂ on neurites is polarized, preferentially labelling neurites with the appearance of dendrites. The subunits ₆ and _2/3 appear to label all types of neurites, with _2/3 being by far the most heavily expressed subunit type. A final distinct characteristic is that ₆ and, even more, ₂ appear to accumulate in the cytoplasmic domains immediately below the cone of emergence of neurites. This suggests a conspicuous transport of such subunits from the site of synthesis in the cell body to the site of final expression in the neurites (dendrites and axon terminals).     

Sap flow measurements with some thermodynamic methods,flow integration within trees and scaling up from sample trees to entire forest stands

Sap flow measurement techniques and evaluation of data are reviewed. Particular attention is paid to the trunk segment heat balance (THB) and heat field deformation (HFD) methods based on 30 years experience. Further elaboration of sap flow data is discussed in terms of integrating flow for whole stems from individual measuring points, considering variation of radial patterns in sapwood and variation around stems. Scaling up of data from sets of sample trees to entire forest stands based on widely available biometric data (partially on remote sensing images) is described and evaluated with a discussion of the magnitude of errors, the routine procedure applicable in any forest stand and practical examples.     

Cloning and developmental expression of MARK/Par-1/MELK-related protein kinase xMAK-V in<Emphasis Type="Italic"> Xenopus laevis</Emphasis>

MAK-V/Hunk is a recently identified MARK/Par-1-related mammalian protein kinase. Although the precise function of this protein kinase is yet to be established, available data suggest its involvement in animals development and in the physiology of the nervous system. Here we report characterization of a cDNA encoding Xenopus laevis orthologue of MAK-V/Hunk protein kinase, xMAK-V. The in silico analysis also revealed MAK-V/Hunk orthologues in the fish Fugu rubripes and primitive chordate Ciona intestinalis but not in invertebrate species such as Drosophila melanogaster and Caenorhabditis elegans, suggesting that MAK-V/Hunk is a chordate-specific protein kinase. The expression of xmak-v in X. laevis embryos was analyzed using whole-mount in situ hybridization. Expression of xmak-v has been detected in all developmental stages studied including maternal expression in unfertilized eggs. The xmak-v mRNA has a predominant occurrence on the animal hemisphere of the egg, and this pattern of expression is sustained throughout cleavage and blastula stages. At the gastrula stage xmak-v expression is restricted to the ectoderm. In the later stage embryos xmak-v is expressed over the entire embryonic surface including the open neural plate at stage 15 and also in neural tube at stage 22. At tadpole stage xmak-v expression is strong in embryonic epidermis, nervous system and sensory organs, and is also obvious in perisomitic mesoderm and brachial arches.Edited by N. Satoh     

The microbiology of a pharmaceutical effluent and its public health implications

The effluent of a pharmaceutical company was examined microbiologically. Its bacterial count was 2.15 × 10⁵ c.f.u./ml and there was evidence of faecal contamination with MPN of > 1800. The organisms encountered included Staphylococcus aureus, Escherichia coli, Proteus vulgaris, Serratia marcescens and Pseudomonas aeruginosa. The resistances of the 25 bacterial strains isolated from the effluent to the commonly used antibiotics were studied. About 80% of the isolates were resistant to Amoxycillin, 76% to Nitrofurantoin, 64% to Cotrimoxazole and Augmentin, 60% were resistant to Nalidixic acid, 52% were resistant to Tetracycline and Ofloxacin, while resistance of 12% was obtained for Gentamicin. Among the eight antibiotics tested, seven patterns of drug resistance were obtained and all of them were multiple-drug resistance with the number of antibiotics ranging from 2–8. All the strains of E. coli and S. aureus had high MIC values for Cloxacillin and Amoxycillin. In all, 13 strains of the bacterial isolates had evidence for the production of -lactamases. The potential of the effluent in spreading drug resistance and the public health implications are discussed.     

Object classification by echolocation in nectar feeding bats: size-independent generalization of shape

The nectar-feeding bat Glossophaga can be trained to discriminate two hollow forms, a hollow hemisphere and a paraboloid with the same diameter and depth, in total darkness. During training a saturation level of about 85-90% correct choices or more can be reached within 50-100 visits. To investigate generalization abilities, the bats were tested with pairs of the same shape but of different size. Although no reward was offered, they preferred the hollow sphere (30 mm and 50 mm diameter, but not 18 mm) over the corresponding paraboloids. Thus, the bats were able to generalize some features of the rewarded form and detect them in forms of the same shape but different size. This transposition is remarkable, since the bats could not use absolute spectral characters, but had to pay attention to size-independent features common to hollow hemispheres. Possible cues are the variation of echoes in dependence of different angles of calling direction (constant in spheres, changing with position in paraboloids) and/or the "timbre" of the echoes, i.e. their spectral pattern independent of their absolute pitch     

Neuronal adaptation improves the recognition of temporal patterns in a grasshopper

The recognition of the temporal structure of sound patterns by grasshopper males was investigated in behavioural experiments. Males were tested with short (165–335 ms) song models in which the characteristic subunit pattern of syllables and pauses was modified either at the beginning or at the end of the stimuli. The highly specific responses of the animals indicate that neuronal adaptation has a substantial influence on the detection of the pauses which are essential cues for the subunit structure: pauses were less likely detected shortly after the beginning of a song model than at later positions. Even adaptation in auditory neurons that was induced by unspecific stimulation (with unmodulated noise) facilitated the processing of sound envelopes. The effects of stimulus prolongation and introduction of pauses appeared to combine linearly, similar to the effects of introducing two pauses instead of a single one. In the responses to some song models large interindividual differences were observed. Comparison across stimuli and repeated testing of a smaller number of individuals indicated a considerable consistency of behavioural preferences. However, the data yielded no clear evidence for the existence of individually distinct processing types among males, that conceivably would focus on different features of the stimuli.     

In vitro Activation of Protein Kinase C by β-N-oxalyl-l-α, β-diaminopropionic acid,the Lathyrus sativus Neurotoxin

-N-oxalyl-l-,-diaminopropionic acid (l-ODAP) toxicity has been associated with lathyrism; a spastic paraparesis caused by excessive dietary intake of the pulse Lathyrus sativus. We investigated the effect of Lathyrus neurotoxin l-ODAP on protein kinase C (PKC) activity under in vitro conditions. l-ODAP activated phosphorylation activity of purified chick brain PKC. Both lysine-rich (histone III-S) and arginine-rich (protamine sulfate) substrate phosphorylation was enhanced in the presence of l-ODAP. The activation is concentration dependent, and maximal activation is observed at 100 M concentration. Protamine sulfate phosphorylation was enhanced by 47%, whereas histone III-S phosphorylation was enhanced by 50% over PS/PDBu/Ca²⁺ dependent activity. The nontoxic d-isomer (d-ODAP) did not affect both histone III-S and protamine sulfate phosphorylation activity. These results indicate that l-ODAP taken up by neuronal cells could also contribute to PKC activation and so be associated with toxicity.     

Signaling from Nucleotide Receptors to Protein Kinase Cascades in Astrocytes

In the CNS, extracellular ATP can function as an excitatory neurotransmitter as well as a trophic factor. These short-term and long-term actions are mediated by nucleotide receptors. Extracellular ATP can also act as a co-mitogen in conjunction with polypeptide growth factors such as basic fibroblast growth factor (FGF2). Cellular proliferation, differentiation and survival are regulated by signaling cascades composed of protein kinases, including extracellular signal regulated protein kinase (ERK) and protein kinase B (also called Akt). Here we summarize recent studies on nucleotide receptor signaling to ERK and Akt in astrocytes and the role of protein kinase cascades in mediating the trophic actions of extracellular ATP, alone or together with FGF2. Because extracellular ATP and FGF2 contribute to the hyperplastic and hypertrophic response of astrocytes to CNS injuries, an understanding of their protein kinase signaling mechanisms may lead to novel therapeutic approaches for neurological conditions that involve gliosis and the generation of reactive astrocytes, such as trauma, stroke, seizure and neurodegenerative and demyelinating disorders.Special issue dedicated to Lawrence F. Eng.