Deoxyribonucleic acid

“ A feature common to nucleic acids of animal and vegetable origin is that, on hydrolysis with boiling mineral acid, they yield two purin derivatives, guanine and adenine, and a pyrimidin derivative, cytosine. From thence as regards their remaining constituent elements they display distinctions. Thus animal nucleic acids yield thymine, and contain a hexose group in their molecule. On the other hand, vegetable nucleic acids give forth uracil and possess a hexose group. ”

“ Because it has several important implications in biology and medicine, it is important to remember that DNA synthesis occurs only during the short, well-defined S period of the cell cycle. Other synthetic processes go on 40 throughout the cycle. We mentioned, for instance, that all cells can be labeled by a brief exposure to a radioactive amino acid, a precursor of proteins; this means that protein synthesis occurs throughout the entire cell cycle, including mitosis. When we use a radioactive RNA precursor, all cells except those in anaphase and metaphase are labeled ”

“ As may be imagined, the primary difficulty was to prepare nucleic acids of such purity as admitted of their elementary chemical analysis. The necessary researches were to a large extent confined to two types of nucleic acid, one derived from yeast, and the other from the thymus gland; in other words, to representatives of the only two nucleic acids in nature, one derived from the nuclei of animal cells, the other from the nuclei of vegetable cells. ”

“ When a cell divides, the readily stainable bodies or chromosomes, present in definite number within the nucleus, are divided, usually by a most intricate process, in such a manner that equal amounts are bequeathed by the mother-cell to each of the two daughter-cells. Spencer favoured the view that the chromatin, which "consists of an organic acid (nucleic acid) rich in phosphorus, combined with an albuminous substance, probably a combination of various proteids" may be peculiarly unstable and active. ”

“ For example, if the enzyme were furnished with a mixture of 5 parts of A and 1 part of C, it would make strands containing, on the average, 25 sequences of AAA, 5 of AAC, 5 of ACA, 5 of CAA, and 1 each of ACC, CAC, and CCA. The proportion of triplets within the strands of a polynucleotide is reflected in the proportion of amino acids in polypeptides that are obtained in the cell-free system. Most of the present knowledge of the amino acid code is based on this concept. ”

“ From later studies it seems probable that substances resembling the albumin of higher forms do not occur in bacteria, at least in appreciable quantities. Globulin has been reported by Hellmich in an undetermined bacterium, but is certainly not commonly found. The larger portion of the protein is of a comparatively simple type, in fact, consists of protamins most of which are in combination with nucleic acid as nucleoprotamins. ”

“ It is assumed that the biogen molecules already present in living substance take out of the proteids of food certain groups of atoms, and dispose them so as to produce cyanogen-like compounds. The addition of oxygen atoms then brings the biogen molecule to the maximum of its power of decomposition, so that—partly spontaneously, but more especially when impelled by a stimulus—it breaks down somewhat explosively, causing the formation of carbonic acid. ”

“ In the yeast cell the nucleus is represented by a homogeneous granule, probably of a nucleolar nature, surrounded and perhaps to some extent impregnated by chromatin and closely connected with a vacuole which often has chromatin at its periphery, and contains one or more volutin granules which appear to consist of nucleic acid in combination with an unknown base. Some observers consider that the yeast nucleus possesses a typical nuclear structure, and exhibits division by mitosis, but the evidence for this is not very satisfactory. ”

“ Artificial syntheses of amino-acids, by the action of ammonia upon glyoxylic acid and sorbic acid, both of which occur in plants and may be obtained by the oxidation of simple sugars, have been accomplished, and it seems probable that similar reactions in the plant protoplasm may give rise to the various amino-acids which unite together to form proteins. Nothing is known, however, of the process by which the more complicated closed-ring amino-acid compounds, such as proline, histidine, or tryptophane, are synthetized. ”

“ Should you be interested, we now have an article in press on the Journal of Cellular Physiology entitled: “Nucleic acid synthesis in the frog liver cell: A definitive study.” We have found substantial evidence which demonstrates that there is no interconversion of the two types of nucleic acid.
I cannot help but comment about your recent paper in Scientia—I do not believe that it is at all possible to devise computers which can handle the species of data which we obtain. Your data being less complex, of course, may fit. ”

“ Recently it has been possible to combine amino acids and other chemicals into simple forms that act much like viruses but are not quite the same. But there is one obstacle that we have not yet overcome. Whether we have recombined different parts of various viruses or whether we have made up amino acid combinations, it has not been possible to have this synthetic virus transmit all its characteristics from generation to generation. ”

“ The chromacea, as protophyta, are plasmodomous. They form new plasm by synthesis and reduction from simple inorganic compounds—water, carbonic acid, ammonia, nitric acid, etc. But the bacteria, as protozoa, are plasmophagous. They cannot, as a rule, form new plasm, but have to take it from other organisms (as parasites, saprophytes, etc.) ; they decompose it by analysis and oxydation. Hence the [201] colorless bacteria are without the important green, blue, or red coloring matter (phycocyan) which tints the plastids of the chromacea, and is the real instrument of the carbon-assimilation. ”

“ Four Metropolis-coupled Markov chain Monte Carlo (MCMC) analyses were run for 1 million generations, and sampled every 100 generations. The mixed model option was used for the amino acid sequence data sets. For the analysis of nucleotide sequence data sets, all 13 protein-coding genes, ribosomal RNAs, and tRNAs were considered as three different partitions in the allnuc data set. A fourth partition of nuclear genes was considered in the combined data sets. ”

“ A C.sinensis transcriptome database containing 127,094 unigenes has been obtained recently by high-throughput Illumina for large-scale ribonucleic acid (RNA) sequencing in the Key Laboratory of Tea Biochemistry and Biotechnology, and a large number of predicted structural and regulatory genes related to the metabolism of phenolic compounds have been screened out from this database [26] . A genome-wide bioinformatic analysis of transcription factors in the biosynthesis of phenolic compounds has been published [27] . ”

“ No further stage in hydrolysis of nucleic acid occurs in the intestine, but the nucleosides are again in turn split up after reaching the tissues, particularly in the spleen, liver, and thymus. This, [101] under the action of specific enzymes, nucleosidases, which succeed in breaking the nucleosides down into the so-called “building stones” of the nucleic acid molecule, phosphoric acid group, carbohydrate group, pyrimidine and purin bases, especially adenine and guanine. ”

“ During life, when nutritive material is abundant, through the reversible action of certain enzymes, synthetic compounds are formed from the building stones furnished by the blood. These synthetic isomers cannot be hydrolyzed by the enzymes by which they are formed and hence on account of the isomeric structure are immune against destruc­tion. It is not impossible that the increase of the concentra­tion of acid in the cells after death trans­forms the isomers into that form in which they can be digested by the enzymes contained in the cell. ”

“ He reminds us that the oxidation and deaminisation of the nuclein derivatives, nucleins, nucleotides and nucleosides, is never complete. For purin bases and pyrimidin bases run side by side in the blood-stream together with uric acid. Also, that the unstable but soluble biurate is constantly changing into a less soluble type, viz., from one isomer to another. Moreover, since the red blood corpuscles abound in potassium, urates of potassium must also occur, and to these may be added, too, ammonium and calcium compounds in small quantities. ”

“ Thus their suggestion [ [166] leads to a (weak) argument for eubacteria first and archaebacteria later! As isoprenoid biosynthesis is so complex and requires many lipid-embedded enzymes (i.e. relatively complex pre-existing membranes) it presents a greater chicken-and-egg problem than does the origin of acyl ester lipids. Fatty acid biosynthesis does not depend on membrane-embedded proteins, but on water soluble ones, so may have been easier to evolve by simply extending pre-existing prebiotic fatty acids. ”

“ By simple hydrolysis with dilute mineral acids they are broken down into proteid, phosphoric acid, and one or more bodies known as nuclein bases. Of these latter substances, there are four well-defined bodies, viz., adenin, hypoxanthin, guanin, and xanthin, which from their peculiar chemical constitution are known as “purin bases.” In the body, there is present in many cells a peculiar intracellular enzyme termed nuclease, which has the power of liberating these purin bases from their combination as a component part of tissue nucleoproteids, or of the contained nucleic acid. ”

“ We have mentioned previously that there are two main types of nucleic acids: DNA, the genetic material itself, and RNA, the molecule that translates the genetic message from DNA into terms the cell can use as “instructions” for making protein. Cells differ from each other on the basis of kinds of proteins they contain, and, since differences among cells determine differences among organisms, it follows that differences in the composition of DNA serve to explain the variety in living organisms populating the world. ”

“ If a gene is repressed, nothing happens; it remains inactive, presumably until something removes the repressing factor. But an active gene sets in motion a train of events that results in activation of one of the processes of life: The gene’s DNA directs the manufacture of RNA, which in turn brings about the synthesis of a specific protein to carry out a specific metabolic process. In other words, all the activities of the cell are dictated by active genes (the DNA molecules) through the mediation of RNA and are executed by proteins. ”

“ Ideas of how free sRNA might be taken up by target cells come from studies in C. elegans, which revealed key components for uptake of free extracellular dsRNA. These are the transmembrane protein channel, Systemic RNAi-Deficient (SID) -1 [40] , and the single-pass transmembrane receptor, SID-2 [37] . It is thought that free dsRNA is internalized from the intestinal lumen by a SID-2–receptor mediated endocytosis, after which dsRNA can escape from the endosome into the cytoplasm by SID-1 (Figure 2) [37] . Unlike SID-1, which is conserved in animals, SID-2 is poorly conserved [41] . ”

“ As they have ornithine not diaminopimelic acid in their murein cell wall polymer and are the only negibacteria lacking lipopolysaccharide or lipo-oligosaccharide in their outer membrane, I grouped them as phylum and infrakingdom Eobacteria [1] . Eo- ('dawn') emphasised that lipopolysaccharide (LPS) absence may be primitive and they could be the earliest cells. Although I still think that both phyla primitively lack LPS and diaminopimelic acid, I now consider Chlorobacteria as markedly more primitive than Hadobacteria and that Eobacteria are paraphyletic, not holophyletic [ [1] . ”

“ Thus loss played a much bigger role than innovation in the origin of archaebacteria. In terms of major innovations of protein structure, as well as in cell structure and cell biology, the dichotomy between prokaryotes and eukaryotes is immensely more important than that between eubacteria and archaebacteria. Ribosomal and DNA-handling proteins underwent episodic accelerated evolution during the neomuran revolution, as did rRNA [ [1] , giving the impression on sequence trees that archaebacteria are much more distant from eubacteria than the vast majority of proteins indicates to be the case. ”

“ Muscle tissue was homogenized in TriZol reagent (Life Technologies, Carlsbad, CA) , and the total RNA was precipitated with isopropanol and dissolved in ddH2O. The quality of RNA was assessed on a 2100 Bioanalyzer and with agarose gel electrophoresis. ”

“ After entering the target cell, it is likely that sRNAs will make use of the RNAi-machinery of that cell. For instance, when the fungus B. cinerea exploits sRNAs to silence defense genes in Arabidopsis and tomato, this process is dependent on plant AGO1 (Figure 2) [19] . This protein controls the cytosolic RNAi pathways, suggesting target mRNA cleavage or translational inhibition. However, as mentioned before, it has been shown that sRNAs can reduce gene expression in species that lack the canonical RNAi-mechanisms. ”

“ Introduction Homing endonuclease genes (HEGs) are superfluous, but invade populations because they cheat the rules of Mendelian inheritance and over-represent themselves in the next generation [1] – [3] . Each homing endonuclease (HE) , the protein product of an HEG, recognises and cuts a specific 15–30 bp DNA recognition sequence which is typically unique within a genome [4] , [5] . HEGs are located in the middle of their own recognition sequence and so their presence splits this site in two and protects against chromosome cleavage. ”