Experimental validation of the ANTS2 code for modelling optical photon transport in monolithic LYSO crystals

In this work the scintillation energy spectra originating from the background radioactivity from polished monolithic lutetium yttrium oxyorthosilicate coupled to position-sensitive silicon photomultipliers (SiPM) was studied using the open source Monte Carlo simulation package ANTS2. Two crystal sizes, fully and partially covering the photosensor area, three surface crystal wrappings (black, specular or diffuse) and the full signal formation process in the photosensor were considered. The simulation results were validated with experimental data acquired under the same geometric and detector operating conditions. In all cases ANTS2 simulated spectra have very good agreement with experimental results, reproducing the expected shape, with correct onset and end at 88 and 1190 keV, respectively, as well as sharp edges at the reference energies of 88, 88 + 202, 88 + 307 and 88 + 202 + 307 keV. The normalized root-mean square error between simulated and measured spectra varied between 4.3% and 10.4%.     

Dependence of batrachotoxin block of axoplasmic transport on sodium

Batrachotoxin (BTX) in the low concentration range of 19-190 nM blocks axoplasmic transport in the desheathed cat peroneal nerve in vitro. When the level of Na+ in the incubation medium was reduced to 10 mM, the blocking effect of BTX was much diminished, and in an Na+-free medium BTX had no effect on transport at all. The blocking action of BTX with Na+ present was inhibited by increasing the concentration of Ca2+ in the experimental medium. Relatively small increases were effective with a maximum protection seen when the Ca2+ concentrations were 7-10 mM. The results support the view that an increase in axonal Na+ is inhibitory to the transport mechanism. The results are discussed on the basis of the recently developed transport filament model of axoplasmic transport which takes into account an obligatory role for Ca2+ in transport and its axonal regulation. The possible relation of intraaxonal Na+ concentration to the Ca2+ level is also discussed.     

Molecular basis for the genetic code

Summary It was found by using the CPK molecular model that holes on the complexes of four nucleotides (C4N) on the tRNAs, namely complexes of the anticodon bases with the discriminator base at 4th position of 3 end, had lock and key relations to the corresponding protein amino acids. Various general features of the universal and mitochondrial genetic codes were easily explained in terms of the C4N model. The recognition mechanism of the tRNA by the aminoacyl-tRNA-synthetase is closely correlated with the formation of the C4N on the Rossmann fold on the synthetase. The meaning of the hypermodification of the tRNA base next to the third anticodon base and other phenomena were also discussed.     

Amino-terminal deletion mutants of the Rous sarcoma virus glycoprotein do not block signal peptide cleavage but can block intracellular transport

Protein sequence requirements for cleavage of the signal peptide from the Rous sarcoma virus glycoprotein have been investigated through the use of deletion mutagenesis. The phenotypes of these mutants have been characterized by expression of the cloned, mutated env genes in CV-1 cells using a late replacement SV40 vector. The deletion mutations were generated by Ba131 digestion at the XhoI site located near the 5' end of the coding sequence for the structural protein gp85, which is found at the amino terminus of the precursor glycoprotein, Pr95. The results of experiments with three mutants (X1, X2, and X3) are presented. Mutant X1 has a 14 amino acid deletion encompassing amino acids 4-17 of gp85, which results in the loss of one potential glycosylation site. In mutants X2 and X3 the amino terminal nine and six amino acids, respectively, of gp85 are deleted. During the biosynthesis of all three mutant polypeptides, the signal peptide is efficiently and accurately cleaved from the nascent protein, even though in mutants X2 and X3 the cleavage site itself has been altered. In these mutants the alanine/aspartic acid cleavage site has been mutated to alanine/asparagine and alanine/glutamine, respectively. These results are consistent with the concept that sequences C-terminal to the signal peptidase site are unimportant in defining the site of cleavage in eucaryotes. Mutants X2 and X3 behave like wild-type with respect to protein glycosylation, palmitic acid addition, cleavage to gp85 and gp37, and expression on the cell surface. Mutant X1, on the other hand, is defective in intracellular transport. Although it is translocated across the rough endoplasmic reticulum and core-glycosylated, its transport appears to be blocked at an early Golgi compartment. No terminal glycosylation of the protein, cleavage of the precursor protein to the mature products, or expression on the cell surface is observed. The deletion in X1 thus appears to destroy signals required for export to the cell surface.     

Protamines, histones and the genetic code. New evidence for code evaluations.

A new approach is presented to give evidence for the theories of Jukes and Crick (1-3) that at a more primitive stage the genetic code consisted of doublets separated by "comma-bases" rather than true triplets and that G and C or A and U are the exclusive bases used by the primordial code. This approach makes use of the conservation of the histone IV sequence over extremely long periods of time by comparing the amino acid composition of the average vertebrate protein with the one of histone IV, a reconstructed ancestral polypeptide and various nuclear proteins, homologous or otherwise related to it. All protamines studied and the majority of histones show deviations from the average vertebrate protein which are statistically highly significant if the amino acids sufficiently coded for by the first two bases are compared. A similar result is obtained for those amino acids which are sufficiently coded for by the first two bases of the codon and have codons composed of G and C only.     

Characterization of a cobalt-resistant mutant of Neurospora crassa with transport block

A cobalt-resistant strain of Neurospora crassa (cor) was obtained by repeated subculturing of the wild type on cobalt-containing agar medium. N. crassa cor is twentyfold more resistant to cobalt ions compared with the wild type. Resistance was stable on repeated subculturing of cor on cobalt-free media. N. crassa cor is also cross-resistant to nickel (fourfold), but not to zinc or copper. Higher concentrations of iron and magnesium ions are required to reverse growth inhibition due to cobalt toxicity in N. crassa cor, compared with the wild type. Germinating conidia and mycelia of the cor strain accumulated lower levels of cobalt ions compared with the parent N. crassa. The partial transport block for cobalt uptake is shown to be primarily due to decreased surface binding of cobalt to mycelia and cell walls. Efflux of mycelial cobalt was also observed in wild type and cobalt-resistant N. crassa. The characteristics of cor in comparison with wild type N. crassa are discussed in relation to the mechanisms of cobalt resistance.     

A search for symmetries in the genetic code

A search for symmetrics based on the classification theorem of Cartan for the compact simple Lie algebras is performed to verify to what extent the genetic code is a manifestation of some underlying symmetry. An exact continuous symmetry group can not be found to reproduce the present, universal code. However a unique approximate symmetry group is compatible with codon assignment for the fundamental amino acids and the termination codon. In order to obtain the actual genetic code, the symmetry must be slightly broken.     

Flexizymes for genetic code reprogramming

Genetic code reprogramming is a method for the reassignment of arbitrary codons from proteinogenic amino acids to nonproteinogenic ones; thus, specific sequences of nonstandard peptides can be ribosomally expressed according to their mRNA templates. Here we describe a protocol that facilitates genetic code reprogramming using flexizymes integrated with a custom-made in vitro translation apparatus, referred to as the flexible in vitro translation (FIT) system. Flexizymes are flexible tRNA acylation ribozymes that enable the preparation of a diverse array of nonproteinogenic acyl-tRNAs. These acyl-tRNAs read vacant codons created in the FIT system, yielding the desired nonstandard peptides with diverse exotic structures, such as N-methyl amino acids, D-amino acids and physiologically stable macrocyclic scaffolds. The facility of the protocol allows a wide variety of applications in the synthesis of new classes of nonstandard peptides with biological functions. Preparation of flexizymes and tRNA used for genetic code reprogramming, optimization of flexizyme reaction conditions and expression of nonstandard peptides using the FIT system can be completed by one person in approximately 1 week. However, once the flexizymes and tRNAs are in hand and reaction conditions are fixed, synthesis of acyl-tRNAs and peptide expression is generally completed in 1 d, and alteration of a peptide sequence can be achieved by simply changing the corresponding mRNA template.     

A unifying concept for the amino acid code

The structure of the genetic code is related to a Gray code, which is a plausible theoretical model for an amino acid code. The proposed model implies that the most important factor in shaping the code was the effects of mistakes in translation, not effects of mutations. Another possible implication is that the preservation of stiffness and flexibility at appropriate places in a protein chain is as important in protein structure as the appropriate placement of hydrophilic (external) and hydrophobic (internal) residues. Other results are a simple conceptualization of the relationships among the 20 amino acids and their relations to their codons. The detailed relationships are summarized in the following ‘similarity alphabet’: ala, thr, gly, pro, ser; asp, asn, glu, gln, lys; his, arg, trp, tyr, phe; leu, met, ile, val, cys; (ATGPS DNEQK HRWYF LMIVC in the one-letter code). This alphabet falls into four groups of amino acids: small, external, large, internal. The approximate relation of the groups to their codons is expressed as: the first base of a codon controls size—a purine means a small amino acid, a pyrimidine means large; the middle base controls cloisterednes—purine means external, pyrimidine means internal. These relationships express the minimum change principle upon which the code appears to be founded.     

Unraveling the epigenetic code of cancer for therapy

Alterations in the genome and the epigenome are common in most cancers. Changes in epigenetic signatures, including aberrant DNA methylation and histone deacetylation, are among the most prevalent modifications in cancer and lead to dramatic changes in gene expression patterns. Because DNA methylation and histone deacetylation are reversible processes, they have become attractive as targets for cancer epigenetic therapy, both as single agents and as 'enhancing' agents for other treatment strategies. In this review we discuss our current view of the mammalian epigenome, this view has changed over the years because of the availability of novel technologies. We further demonstrate how the profound understanding of epigenetic alterations in cancer will help develop novel strategies for epigenetic therapies.     

Anoxic block and recovery of axoplasmic transport and electrical excitability of nerve

Axoplasmic transport of cat sciatic nerves was studied in vitro in a chamber in which maximal α action potentials could also be elicited. After initiation of N₂ anoxia, electrical responses fell to zero at an average time of 22 min. A shorter time to zero of 11 min was seen during a second period of anoxia. A good recovery of both action potential responses and axoplasmic transport occurs after a period of anoxia lasting 1–1.5 hr. An apparent failure of recovery of axoplasmic transport was seen after 2 hr of anoxia with a good recovery of electrical responses. Axoplasmic transport tended to return toward normal when more time was allowed for recovery after anoxia. An adequate supply of ～P was shown to be present by measurement of ATP and creatine phosphate levels. The delay in recovery of transport thus signifies a failure of utilization of ～P by the transport mechanism. Longer periods of anoxia and recovery were limited in vitro and for this reason, ischemic anoxia was produced in vivo. Blood pressure cuffs were placed on the upper thigh of cats and maintained for times of 1–8 hr at pressures of 300–310 mm Hg. Then, recovery times up to 7 days were allowed. It was shown that axoplasmic transport could gradually recovery after an anoxia lasting up to 6–7 hr if sufficient recovery times were allowed. A possible explanation for the delay in the recovery of axoplasmic transport and the disassociation in the earlier recovery of electrical responses as against the recovery of transport was discussed.