Mitochondrial DNA

“ The deep roots of M phylogeny clearly establish the antiquity of Indian lineages, especially M2, as compared to Ethiopian M1 lineage and hence, support an Asian origin of M majorhaplogroup.
Background
During the last few years a surge in information on mitochondrial DNA control region sequence has been observed along with information from coding region substitutions in diverse populations of the world to understand their genetic diversity, structuring and origins [1] - [2] . ”

“ Genomic DNA was extracted from the muscle tissue using a standard phenol-chloroform extraction protocol [22] . We amplified a fragment of the mitochondrial 16s rRNA gene from Xenophrys species using the primer pairs L3975 and H4551 [23] , and mitochondrial 12s rRNA gene using the primer pair Fphe40L and 12S600H [24] . PCR amplifications were performed in a reaction volume of 25 μl containing 100 ng of template DNA, 0.3 mM of each PCR primer and 10 μl Premix EX TaqTM (Takara, Dalian, China) . The PCR condition for 16s rRNA was, an initial denaturation step at 94°C for 1.5 min ”

“ While some authors have suggested a southwest Asian origin of M macrohaplogroup, followed by a back migration to Africa [ [5] , others support its African ancestry [ [11] . One major drawback in arriving to a conclusion is the limitation of control region sequences in providing reliable estimate of phylogeny owing to homoplasy and recurrent mutations [ [9] , [12] .
Complete mitochondrial genome sequencing has gained importance in resolving phylogenies and understanding human evolution. ”

“ 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. ”

“ The mitochondria have a central role in the reactions by which the energy of sugars is supplied for cellular activity. The importance of this vital activity is obvious. In this booklet, however, we are concerned with the processes, involving nucleic acids and proteins, that can be described as making up “the gene-action system”. The gene-action system is the series of biochemical events that regulate and direct all life processes by “transcription” of the genetic “information” contained in molecules of DNA.
10 RADIOACTIVE ISOTOPES: THE BIOLOGICAL DETECTIVES
Man ... ”

“ However, the mean number of coding region substitutions accumulated in M1a2 lineages (11 ± 0.0) is significantly higher (p < 0.001) than in the rest of M1 (5.6 ± 0.7) . Conversely, the mean number of regulatory region substitutions accumulated in M1a2 lineages (1.5 ± 0.7) is smaller than in the rest (2.8 ± 0.9) although not reaching statistical significance (p = 0.175) . If the mutation rate was constant along the whole mtDNA molecule, for each mutation in the regulatory region roughly fourteen mutations should accumulate in the coding region. ”

“ Phylogenetic performance of mitochondrial genes
ML phylogenies were reconstructed at the nucleotide level based on each of the mt protein-coding (including all codon positions) , each the two rRNA genes, and a combined data set including all mt tRNA genes. The number of congruent internal branches (i.e. nodes) between the individual phylogenies, and the whole-mt genome topology (Fig. 3) was used as a measure of the phylogenetic performance of mt genes (Table 3) . None of the individual gene analysis recovered the 12 nodes (A-L) of the reference topology (Table 3 and Fig. 3) . ”

“ The phylogenetic analysis presented herein had a total of 5,238 base pairs including: one mitochondrial gene (cytochrome oxidase I, 812 bps) , and five protein-coding genes (glycosyltransferase gene, 732 bps; myosin heavy chain 6 alpha gene, 737 bps; pleiomorphic adenoma protein-like 2-like gene, 659 bps; recombination activating gene 1, 1403 bps; zic family member protein, 890 bps) . For each maximum likelihood analysis, the dataset was partitioned by individual gene fragments. ”

“ 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 ”

“ The synthesis of proteins is under the control of deoxyribonucleic acid or ribonucleic acid, abbreviated by the symbols DNA and RNA. The genes in the nucleus are parts of a giant DNA molecule. RNA is a universal constituent of all living cells. Where protein synthesis is intense, the content in RNA is high. ”

“ When DNA is replicated, or copied, as the organism grows, the two nucleotide strands separate from each other by disjoining the rungs at the point where the bases meet, and each strand then makes a new and similarly complementary strand. The result is two double-stranded DNA molecules, each of which is identical to the parent molecule and contains the same genetic material. When the cell divides, each of the two daughter cells gets one of the new double strands; each new cell thus always has the same amount of DNA and the same genetic material as the parent cell. ”

“ The nucleus, which in many cells is the largest and most central body, is of special importance. It contains a number of threadlike bodies, or chromosomes, that are the carriers of the cell’s heredity-controlling system. These contain granules of a material called chromatin, which is rich in a nucleic acid, DNA (deoxyribonucleic acid) . The chromosomes usually are not readily seen in the nucleus except when the cell, along with its nucleus, is dividing. When the nucleus is not dividing, a spherical body, the nucleolus, can be seen. (In some nuclei there may be more than one.) ”

“ If so, then perhaps genome assembly methods are the best. What if instead, as in the sharpshooter example, we are trying to have each bin include every fragment that came from a particular species, knowledge which may be useful for predicting community metabolic potential? If the level of genetic polymorphism among individual cells from the same species is high, then genome assembly methods may not work well (the polymorphisms will break up assemblies) . A better approach might be to look for species-specific “word” frequencies in the DNA, such as ones created by patterns in codon usage. ”

“ It is difficult to chart the future course of modern molecular biology, but it is not difficult to predict that the next few years will bring to biology the same kind of sweeping advances that revolutionized physics a few decades ago. The DNA molecule has been called the atom of life. When we have harnessed it, the harnessing of the uranium atom will seem, in comparison, a result of scientific adolescence. When man has mastered the genetic code, he’ll hold a vast power in his hands—power over the nature of coming generations. ”

“ Mitochondrial protein sequences are used widely in phylogenetic studies and have been particularly popular in studying placental mammals. A desirable feature of these data is relatively long sequences, good taxon sampling and very little missing data. Following alignment, we retained 3660 amino acid sites present in all of 62 placental mammals plus seven outgroup taxa (Table S1 gives the accession numbers of protein sequences) . In contrast, large nuclear protein datasets of mammals with diverse taxon sampling [25] , [5] show a large proportion of missing data. ”

“ However, this is not the case for the trimmed datasets, where the changes in support with and without mitochondria vary between alignment method and inference model.
In contrast to the increase in support for the primary clade containing the mitochondria in the full trees, the monophyly of the Rhodospirillales and the Rhodospirillaceae loses support when the mitochondria are added, especially in the RYMK-recoded dataset. The internal topology of the Rhizobiales also changes. ”

“ 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. ”

“ For example, the primary clade composed of Rickettsiaceae, Anaplasmataceae, Midichloria mitochondrii and Pelagibacterales – in which mitochondrial sequences also cluster – and the clade with a basal Holosporaceae and various orders are supported much more strongly in the datasets with mitochondria, especially the Arb-Sina-aligned datasets. ”

“ ML phylogram inferred from a single concatenated data set of deduced amino acid sequences of all 13 mitochondrial protein-coding genes (13-protein data set) . Species whose complete mt genome was sequenced in this study are presented in bold. Lottia digitalis (Patellogastropoda) was used as outgroup. Numbers in the nodes correspond to ML bootstrap proportions (above branches) and BI posterior probabilities (below branches) . Only values above 70% are represented. The inset shows a ML topology based on fragments of mt and nuclear data (adapted from Fig. two of Colgan et al., 2007) . ”

“ In the present work, we have applied HMM in a novel way to suggest and possibly discover still unknown protein functions in several well-studied model organisms. Starting from sequence alignments for proteins involved in DNA damage repair, we created Hidden Markov Models and used these models to search for similar genes in the metagenomic samples from different environments. Combining the original HMM with the genes found in the metagenomes, we created a second, more trained HMM that we used to interrogate proteomes of higher order model organisms. ”

“ How can we explain that cells of the human pancreas secrete insulin, whereas other cells in man produce no insulin? Or how can we explain that certain cells make bone and others make fat? If indeed all cells in the same organism contain the same amount and kind of DNA (since all DNA in an organism derives from the duplication of the DNA of the fertilized egg cell and its descendants) , it would seem, at first glance, that DNA is not the molecule responsible for differences among the cells. ”

“ If cells are irradiated shortly after induction, the transcription of the DNA ceases and the enzyme produced by the messenger RNA is observed to reach a maximum. This enables the calculation of the half-life of unstable messenger RNA. The half-life for this decay is readily measurable, and values are given over a temperature range of 17° C (5.2 minimum) to 45° C (0.56 minimum) . These agree very well with half-lives measured by others by inducing for short times and measuring the course of enzyme formation. ”

“ However, the raw genomic material does not come from a single organism: it comes from a community of microbes, hence the name environmental shotgun sequencing or ESS. Depending on our ability to sample, this DNA may provide only a partial genomic picture of the organisms in the environment, since the genomic material from the more abundant species dominates the sample. To obtain a better picture of the species composing the community, 16S rDNA or 18S rDNA for prokaryotic and eukaryotic samples, respectively, are sequenced separately using universal primers, see Figure 1. ”

“ 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. ”

“ Neuronal RNA with changed cytosine-guanine ratios synthesized during a short period of induced protein synthesis could be blocked by actinomycin D. It was concluded, therefore, that the RNA was immediately DNA dependent and directly related to the genetic apparatus.
Rats which were normally right handed were forced to modify their handedness in order to obtain food. The RNA of nerve cells in that part of the cortex, whose destruction destroys the ability to transfer handedness, was analyzed. ”

“ It is also important to remember that a cell that has synthesized DNA is a cell that, with a few exceptions, will divide in the very near future. Thus, for an understanding of the mechanisms that control cellular proliferation, it is important to investigate the factors that control DNA synthesis. ”

“ Practically all the DNA of most cells is concentrated in the nucleus. RNA, on the other hand, is distributed throughout the cell. Some RNA is present in the nucleus, but most of it is associated with minute particles in the cytoplasm known as microsomes, some of which are especially rich in RNA and are accordingly named ribosomes. ”