Cancer Biology and Genetics for Non-Biologists
Trevor F. Cox in Medical Statistics for Cancer Studies, 2022
All living things are made up of cells, from the simple unicellular amoeba to the complex human composed of about 37 trillion () cells. Cells that contain a nucleus are called eukaryotic cells; cells without a nucleus are called prokaryotic cells. Bacteria are examples of prokaryotic cells. Humans are eukaryotes consisting of eukaryotic cells, such as bone, nerve and stem cells. In fact, there are about 200 types of cells in our bodies. Figure 2.1 shows a typical eukaryotic cell, illustrating its structure. Cells come in different shapes and sizes; neurons in the brain and nervous system are long and thin, blood cells are roughly spherical, some bone cells are cuboidal and columnar while others have many branches. The size of a red blood cell is , the size of a skin cell is , an ovum , whilst the length of some nerve cells can be over .
Bacteria
Julius P. Kreier in Infection, Resistance, and Immunity, 2022
There is a phenomenal variety of shapes and groupings of cells among the prokaryotes. Shapes include the forms historically described as: spherical (cocci), cylindrical (bacilli), either straight or curved (vibrio). The organisms may grow singly or in pairs (diplococci or diplobacilli), in chains (streptococci or streptoba-cilli), in three-dimensional cubes of spheres (sarcinae), or in randomly arranged clusters (staphylococci); in more or less tightly coiled spirals (e.g., spirochaetes), in long sometimes branched filaments (found in Streptomyces and Actinomyces species, among others), in squares, and in irregular clusters. In addition to those already described, groupings of cells include: rosette clusters, flexible gliding clusters, and tightly packed films. It seems reasonable to assume that any possible form, shape or arrangement of bacterial cells may exist somewhere in nature awaiting discovery.
Introduction to Genomics
Altuna Akalin in Computational Genomics with R, 2020
There might be several chromosomes depending on the organism. However, in some species (such as most prokaryotes) DNA is stored in a circular form. The size of the genome between species differs too. The human genome has 46 chromosomes and over 3 billion base-pairs, whereas the wheat genome has 42 chromosomes and 17 billion base-pairs; both genome size and chromosome numbers are variable between different organisms. Genome sequences of organisms are obtained using sequencing technology. With this technology, fragments of the DNA sequence from the genome, called reads, are obtained. Larger chunks of the genome sequence are later obtained by stitching the initial fragments to larger ones by using the overlapping reads. The latest sequencing technologies made genome sequencing cheaper and faster. These technologies output more reads, longer reads and more accurate reads.
Steps to address anti-microbial drug resistance in today’s drug discovery
Published in Expert Opinion on Drug Discovery, 2019
Tanya Parish
The low success of many phenotypic screening campaigns in discovering antibacterials is likely to be related to both the quality of the libraries, representing limited chemical space, and the inherent difficulty of finding compounds that selectively target bacteria. Large pharma libraries are biased toward compounds that target eukaryotic cells and are largely comprised of compounds made for a small number of therapeutic areas (which no longer includes antimicrobials). Thus, the types of molecules that have whole cell activity against prokaryotes are missing from these sets. The mining of natural products has been limited by the relatively small number of purified products available for screening; complex, diverse, extracts can be screened but deconvolution of activity coupled with repeated identification of the same compounds has limited its usefulness. However, more effort is being made to access previously untapped sources of natural products, for example, isolating organisms from inaccessible locations, e.g. deep sea vents, or from currently non-culturable sources, e.g. soil in order to find novel chemical entities that can form the starting points for drug development. In the latter case, technology used to identify the novel antibiotic teixobactin holds the promise of finding more active natural products from accessible sources [3].
Gut microbes from the phylogenetically diverse genus Eubacterium and their various contributions to gut health
Published in Gut Microbes, 2020
Arghya Mukherjee, Cathy Lordan, R. Paul Ross, Paul D. Cotter
Understandably, taxonomic reassignments proposed have not been universally accepted yet and indeed, as noted, care must be taken while considering taxonomic classification and reporting of any member of genus Eubacterium. Further efforts relating to the classification of the genus should have a primarily genotypic focus with an emphasis on genomic characteristics. The prokaryotic taxonomy devised by Parks et al.33 in the GTDB, where a battery of universal, single copy marker genes derived from whole/draft genomes, are used to classify microorganisms, can be used as a model. Such an approach standardizes taxonomic assignments through normalization of taxonomic ranks on the basis of relative evolutionary divergence and has been shown to be capable of deconvoluting polyphyletic groups. Combined with rapidly declining sequencing prices, the increasing and ample availability of prokaryotic genomes can contribute greatly to such an exercise. With assembly of high-resolution draft genomes from metagenomes also now routine, microbiologists can glean information from truly uncultivable organisms and a definitive reclassification of the genus Eubacterium should be possible in the near future. Until then, there is likely to continue to be those who will view Eubacterium as a combined group – Eubacterium et rel. – when discussing human health, especially in relation to the gut. We will adopt this approach for the remainder of this review.
DNA electromagnetic properties and interactions -An investigation on intrinsic bioelectromagnetism within DNA
Published in Electromagnetic Biology and Medicine, 2018
Masroor Hassan Bukhari, Salma Batool, Dr Yasir Raza, Omar Bagasra, Abbas Rizvi, Asifa Shah, Tashmeem Razzaki, Tipu Sultan
In order to carry out this study, we prepared and isolated seven samples of prokaryotic and eukaryotic DNA for our measurements. Samples 1–3, the eukaryotic DNA batch, was obtained from mesenchymal stem cells (MSC) from murine bone marrow, which is one of the most viable models for MSC extraction (Anjos-Afonso et al., 2004; Friedenstein et al., 1970). We prepared and isolated the samples following the protocols described elsewhere (Eslaminejad et al., 2006; Nadri et al., 2007) mainly using standard scientific-grade kits. Alternatively, for a simpler extraction, the MSC DNA can also be obtained from dental pulp (Gronthos et al., 2000). Samples 4–7 constituted the prokaryotic DNA batch, obtained from E.coli chromosomal DNA with the help of a standard commercial DNA isolation kit (Qiagen, www.qiagen.com). The protocols used were modified forms of those ones as found in the literature (He, 2011; Maniatis et al., 1982). The samples were suspended in a buffer and kept in DNA lock-seal vials (Fisher Thermoscientific) at 280K. For experiments, the samples were naturally thawed and immediately used as soon as they reached the ambient room temperature. We used two kinds of sample preparations in our studies, at first, a DNA suspension in a buffer, and second, the same DNA suspension diluted in water.
Related Knowledge Centers
- Archaea
- Bacteria
- Cytoplasm
- Eukaryote
- Evolution
- Cell Membrane
- Cell Nucleus
- Organelle
- Mitochondrion
- Molecular Phylogenetics