A new micro-test for the detection of incomplete coupling reactions in solid-phase peptide synthesis using 2,4,6-trinitrobenzenesulphonic acid.

A rapid micro-test using 2,4,6-trinitrobenzenesulphonic acid has been developed to detect incomplete coupling reactions in solid phase peptide synthesis. This new test will detect 3 nmol of free amino groups per milligram of resin.     

DNA of a circular minichromosome linearized by restriction enzymes or other reagents is resistant to further cleavage: an influence of chromatin topology on the accessibility of DNA

The accessibility of DNA in chromatin is an essential factor in regulating its activities. We studied the accessibility of the DNA in a ∼170 kb circular minichromosome to DNA-cleaving reagents using pulsed-field gel electrophoresis and fibre-fluorescence in situ hybridization on combed DNA molecules. Only one of several potential sites in the minichromosome DNA was accessible to restriction enzymes in permeabilized cells, and in growing cells only a single site at an essentially random position was cut by poisoned topoisomerase II, neocarzinostatin and γ-radiation, which have multiple potential cleavage sites; further sites were then inaccessible in the linearized minichromosomes. Sequential exposure to combinations of these reagents also resulted in cleavage at only a single site. Minichromosome DNA containing single-strand breaks created by a nicking endonuclease to relax any unconstrained superhelicity was also cut at only a single position by a restriction enzyme. Further sites became accessible after ≥95% of histones H2A, H2B and H1, and most non-histone proteins were extracted. These observations suggest that a global rearrangement of the three-dimensional packing and interactions of nucleosomes occurs when a circular minichromosome is linearized and results in its DNA becoming inaccessible to probes.     

Short-term response in leaf metabolism of perennial ryegrass (Lolium perenne) to alterations in nitrogen supply

Nitrogen is a macronutrient present in a wide range of cellular compounds including proteins, nucleic acids, amino acids and lipids. The levels of nitrogen often regulate many aspects of plant metabolism, growth and development. Extensive research has been conducted into the effects of N nutrition in model plants, however relatively little is known about the metabolic response of perennial ryegrass (Lolium perenne) grown under different N-supply conditions. This study aimed to identify key metabolic responses activated rapidly after challenging plants with different levels of N-supply. The metabolic response of the leaves of seven different L. perenne genotypes to three N treatments (low, medium and high levels of N) was characterized using a GC–MS approach. After 24 h it was observed that the levels of amino acids correlated with the levels of N-supply. Furthermore the results indicated that plants experiencing N-limitation accumulated very-long chain fatty acids and precursors of secondary aromatic metabolites while sugar levels were not significantly affected indicating a remobilization of carbon. Plants grown under high levels of N were found to have enhanced levels of inositol and threonic acid which could reflect an alteration of the redox potential under stress. Further analysis of Pearson’s correlation coefficient provided evidence that the chlorophyll metabolism may also be regulated in plants grown at high N concentrations.     

Anterograde Microtubule Transport Drives Microtubule Bending in LLC-PK1 Epithelial Cells

Microtubules (MTs) have been proposed to act mechanically as compressive struts that resist both actomyosin contractile forces and their own polymerization forces to mechanically stabilize cell shape. To identify the origin of MT bending, we directly observed MT bending and F-actin transport dynamics in the periphery of LLC-PK1 epithelial cells. We found that F-actin is nearly stationary in these cells even as MTs are deformed, demonstrating that MT bending is not driven by actomyosin contractility. Furthermore, the inhibition of myosin II activity through the use of blebbistatin results in microtubules that are still dynamically bending. In addition, as determined by fluorescent speckle microscopy, MT polymerization rarely results, if ever, in bending. We suppressed dynamic instability using nocodazole, and we observed no qualitative change in the MT bending dynamics. Bending most often results from anterograde transport of proximal portions of the MT toward a nearly stationary distal tip. Interestingly, we found that in an in vitro kinesin-MT gliding assay, MTs buckle in a similar manner. To make quantitative comparisons, we measured curvature distributions of observed MTs and found that the in vivo and in vitro curvature distributions agree quantitatively. In addition, the measured MT curvature distribution is not Gaussian, as expected for a thermally driven semiflexible polymer, indicating that thermal forces play a minor role in MT bending. We conclude that many of the known mechanisms of MT deformation, such as polymerization and acto-myosin contractility, play an inconsequential role in mediating MT bending in LLC-PK1 cells and that MT-based molecular motors likely generate most of the strain energy stored in the MT lattice. The results argue against models in which MTs play a major mechanical role in LLC-PK1 cells and instead favor a model in which mechanical forces control the spatial distribution of the MT array.     

SIMPLE34: an improved and enhanced implementation for VAX and Sun computers of the SIMPLE algorithm for analysis of clustered repetitive motifs in nucleotide sequences

SIMPLE34 is an improved and enhanced version of SIMPLE for Vaxand SunOS systems. It now provides a length-independent measureof the overall level of tri- and tetra nucleotide motif clusteringwithin nucleotide sequences and its significant deviation fromrandom expectation. It now also provides information on tri-and tetranucleotide motifs showing higher levels of clusteringthan would be expected in random sequences. Sequence simplicityof test sequences can be judged with respect to random sequencesgenerated on the basis of base composition, positional basecomposition or doublet frequency. These options can be usedto investigate factors resulting in sequence simplicity.     

(Curcumin+sildenafil) enhances the efficacy of 5FU and anti-PD1 therapies in vivo

We have extended our analyses of (curcumin+sildenafil) biology. The drug combination caused vascularization and degradation of mutant K-RAS that correlated with reduced phosphorylation of ERK1/2, AKT T308, mTORC1, mTORC2, ULK1 S757, STAT3, STAT5, and NFκB and increased phosphorylation of eIF2α, ATM, AMPKα, ULK1 S317; all concomitant with elevated ATG13 S318 phosphorylation and autophagosome formation. Prior studies with drug combinations utilizing sildenafil have delineated an ATM-AMPK-ULK1 S317 pathway and an AKT-mTOR-ULK1 S757 pathway as modules which control ATG S318 phosphorylation and autophagosome formation. The knockdown of PKG reduced cell killing as well as reducing drug-enhanced phosphorylation of ATM, AMPKα, and ATG13. In the absence of PKG, no significant increase in ULK1 S317 phosphorylation was observed. In a Beclin1-dependent fashion, the drug combination reduced the expression of multiple histone deacetylase (HDAC) proteins, including HDAC2 and HDAC3. Molecular knockdown of HDAC2, HDAC3, and especially (HDAC2+HDAC3) significantly reduced the expression of PD-L1 and elevated expression of Class I human major histocompatibility complex. In vivo, (curcumin+sildenafil) enhanced the efficacy of 5-flurouracil against CT26 colorectal tumors. Prior exposure of established CT26 tumors to (curcumin+sildenafil) significantly enhanced the efficacy of a subsequently administered anti-PD-1 antibody. Collectively our data argue that (curcumin+sildenafil) has the potential in several settings to be an efficacious neoadjuvant therapy for colon cancer.     

Selective labelling of apolipoproteins A-I and C-I at methionine residues by (3H) methyl exchange

Apolipoproteins C-I and A-I were radioactively labelled with tritium by (3H)-methyl exchange. The methionine residues were first methylated with (3H)-methyl iodide at pH 4 and the reaction products were purified by gel filtration and cation exchange chromatography. The products were then demethylated with 2-mercaptoethanol (6 M) at pH 8.6 to regenerate the apolipoproteins in an unmodified but tritiated form. The specific radioactivity for apolipoprotein C-I and A-I was 3.5 X 10(6) and 1.5 X 10(7) dpm/pmol respectively. The properties of (3H)-apolipoprotein C-I were examined by reversed phase HPLC and by incorporation into very low density lipoproteins (VLDL).