Wnt/β‐catenin‐signaling and the formation of Müller glia‐derived progenitors in the chick retina

Müller glia can be stimulated to de‐differentiate, proliferate, and form Müller glia‐derived progenitor cells (MGPCs) that are capable of producing retinal neurons. The signaling pathways that influence the de‐differentiation of mature Müller glia and proliferation of MGPCs may include the Wnt‐pathway. The purpose of this study was to investigate how Wnt‐signaling influences the formation of MGPCs in the chick retina in vivo. In NMDA‐damaged retinas where MGPCs are known to form, we find dynamic changes in retinal levels of potential readouts of Wnt‐signaling, including dkk1, dkk3, axin2, c‐myc, tcf‐1, and cd44. We find accumulations of nuclear β‐catenin in MGPCs that peaks at 3 days and rapidly declines by 5 days after NMDA‐treatment. Inhibition of Wnt‐signaling with XAV939 in damaged retinas suppressed the formation of MGPCs, increased expression of ascl1a and decreased hes5, but had no effect upon the differentiation of progeny produced by MGPCs. Activation of Wnt‐signaling, with GSK3β‐inhibitors, in the absence of retinal damage, failed to stimulate the formation of MGPCs, whereas activation of Wnt‐signaling in damaged retinas stimulated the formation of MGPCs. In the absence of retinal damage, FGF2/MAPK‐signaling stimulated the formation of MGPCs by activating a signaling network that includes Wnt/β‐catenin. In FGF2‐treated retinas, inhibition of Wnt‐signaling reduced numbers of proliferating MGPCs, whereas activation of Wnt‐signaling failed to influence the formation of proliferating MGPCs. Our findings indicate that Wnt‐signaling is part of a network initiated by FGF2/MAPK or retinal damage, and activation of canonical Wnt‐signaling is required for the formation of proliferating MGPCs. © 2015 Wiley Periodicals, Inc. Develop Neurobiol 76: 983–1002, 2016     

Effect of various inhibitors on readhesion of trypsinized cells in culture

The reattachment of freshly trypsinized cells in the presence of various inhibitors and inhibition procedures was studied under the phase contrast microscope. These inhibitors were thymidine, actinomycin, emetine, salicylate, colchicine, neuraminidase, X-irradiation, serum deprivation and reduced temperature. Of these inhibitors, only reduced temperature and colchicine altered the normal process of adhesion and spreading of the cells.     

Effect of nitrogen source on cyanophycin synthesis in Synechocystis sp. strain PCC 6308

Experiments were carried out to examine the effects of nitrogen source on nitrogen incorporation into cyanophycin during nitrogen limitation and repletion, both with or without inhibition of protein synthesis, in cyanobacteria grown on either nitrate or ammonium. The use of nitrate and ammonium, 14N labeled in the growth medium and 15N labeled in the repletion medium, allows the determination of the source of nitrogen in cyanophycin using proton nuclear magnetic resonance spectroscopy. The data suggest that nitrogen from both the breakdown of cellular protein (14N) and directly from the medium (15N) is incorporated into cyanophycin. Nitrogen is incorporated into cyanophycin at different rates and to different extents, depending on the source of nitrogen (ammonium or nitrate) and whether the cells are first starved for nitrogen. These differences appear to be related to the activity of nitrate reductase in cells and to the possible expression of cyanophycin synthetase during nitrogen starvation.     

Protein decoy assembly using short fragments under geometric constraints

A small set of protein fragments can represent adequately all known local protein structure. This set of fragments, along with a construction scheme that assembles these fragments into structures, defines a discrete (relatively small) conformation space, which approximates protein structures accurately. We generate protein decoys by sampling geometrically valid structures from this conformation space, biased by the secondary structure prediction for the protein. Unlike other methods, secondary structure prediction is the only protein-specific information used for generating the decoys. Nevertheless, these decoys are qualitatively similar to those found by others. The method works well for all-alpha proteins, and shows promising results for alpha and beta proteins.     

Effects of light and chloramphenicol stress on incorporation of nitrogen into cyanophycin in Synechocystis sp. strain PCC 6308

(1)H NMR spectroscopy was used to compare the uptake of nitrogen into cyanobacterial cyanophycin from two sources: from the breakdown of intracellular proteins and amino acids, and directly from the external growth medium. Cells grown initially in medium containing (14)N-nitrate were transferred to (15)N-nitrate medium in the presence of chloramphenicol in both low (4 microE m(-2) s(-1)) and normal (100 microE m(-2) s(-1)) light, and in low light alone. Cyanophycin was separated from cells and analyzed by (1)H NMR spectroscopy. Cyanophycin is synthesized both from (14)N (degradation of cellular proteins) and from (15)N in the medium, the latter at a faster rate and to a greater extent under all conditions. SDS-PAGE showed that cyanophycin synthesis takes place by addition of monomers to already synthesized polymer.     

Evaluation of protein <Emphasis Type="BoldItalic">in vitro</Emphasis> digestibility of <Emphasis Type="BoldItalic">Palmaria palmata</Emphasis> and <Emphasis Type="BoldItalic">Gracilaria verrucosa</Emphasis>

Palmaria palmata and Gracilaria verrucosa are edible red seaweeds and potential protein sources for human or animal nutrition, so studies were conducted on their in vitro protein digestibility. After 30 min predigestion by pepsin followed by 6 h digestion into a cell dialysis containing porcine pancreatin, the in vitro protein digestibility of P. palmata and G. verrucosa, expressed in regard to casein digestibility, was 4.9% and 42.1%, respectively. The level of protein digestibility seems to be related to the amount of soluble fibre, which was 45.3% and 30.5%, respectively.     

A rapid and sensitive method for the analysis of cyanophycin

A method has been devised for the quantitative analysis of cyanophycin, based on (1)H nuclear magnetic resonance (NMR) spectroscopy, allowing determination of the nitrogen status of cyanobacteria. Cyanophycin is extracted with minimal washing from small volumes of cells and quantified by integration of the NMR peak attributed to the protons attached to the delta-carbon of arginine. Linear relationships were found between the amount of cyanophycin determined by this method and both known concentrations of cyanophycin solutions and the amount of cyanophycin determined using the standard chemical arginine assay.     

Small libraries of protein fragments model native protein structures accurately

Prediction of protein structure depends on the accuracy and complexity of the models used. Here, we represent the polypeptide chain by a sequence of rigid fragments that are concatenated without any degrees of freedom. Fragments chosen from a library of representative fragments are fit to the native structure using a greedy build-up method. This gives a one-dimensional representation of native protein three-dimensional structure whose quality depends on the nature of the library. We use a novel clustering method to construct libraries that differ in the fragment length (four to seven residues) and number of representative fragments they contain (25-300). Each library is characterized by the quality of fit (accuracy) and the number of allowed states per residue (complexity). We find that the accuracy depends on the complexity and varies from 2.9A for a 2.7-state model on the basis of fragments of length 7-0.76A for a 15-state model on the basis of fragments of length 5. Our goal is to find representations that are both accurate and economical (low complexity). The models defined here are substantially better in this regard: with ten states per residue we approximate native protein structure to 1A compared to over 20 states per residue needed previously.For the same complexity, we find that longer fragments provide better fits. Unfortunately, libraries of longer fragments must be much larger (for ten states per residue, a seven-residue library is 100 times larger than a five-residue library). As the number of known protein native structures increases, it will be possible to construct larger libraries to better exploit this correlation between neighboring residues. Our fragment libraries, which offer a wide range of optimal fragments suited to different accuracies of fit, may prove to be useful for generating better decoy sets for ab initio protein folding and for generating accurate loop conformations in homology modeling.     

Absence of DNA-associated RNA in the fully repressed nucleus of chicken erythrocyte

DNA from fully repressed chicken erythrocyte nuclei was examined for stably associated RNA which could possibly serve a role in genetic repression. Alkaline hydrolysates of DNA purified on cesium chloride gradients showed an absence of sufficient ribonucleotides, in stable association with DNA, on both thin layer chromatography and by in vitro tritium labeling to serve to localize or identify all the deoxynucleotide gene sequences in the fully repressed chicken erythrocyte nucleus.