International Journal of Molecular Sciences

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Open AccessCorrection

by Shu-Kun Lin

Int. J. Mol. Sci. 2008, 9(5), 905; https://doi.org/10.3390/ijms9050905 - 1 Jun 2008

Viewed by 4664

Publisher's Note added on 29 September 2008: There is a pagination error in the Int. J. Mol. Sci. 2008, 9(5) with page 905 missing. Thus, page 905 is taken as a blank page. Full article

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Open AccessArticle

Concerted Solvent Processes for Common Sulfonyl Chloride Precursors used in the Synthesis of Sulfonamide-based Drugs

by Malcolm J. D’Souza, Lamia Yaakoubd, Stacey L. Mlynarski and Dennis N. Kevill

Int. J. Mol. Sci. 2008, 9(5), 914-925; https://doi.org/10.3390/ijms9050914 - 24 May 2008

Cited by 16 | Viewed by 10033

Abstract

Specific rates of solvolysis in hydroxylic solvents available for the solvolysis of 2-thiophenesulfonyl chloride and phenylmethanesulfonyl chloride are supplemented by determining the values in fluoroalcohol-containing solvents. The data sets are then correlated using the extended Grunwald-Winstein equation. For both substrates, it is found [...] Read more.

Specific rates of solvolysis in hydroxylic solvents available for the solvolysis of 2-thiophenesulfonyl chloride and phenylmethanesulfonyl chloride are supplemented by determining the values in fluoroalcohol-containing solvents. The data sets are then correlated using the extended Grunwald-Winstein equation. For both substrates, it is found that a single correlation controls the influence of solvent over the full range of solvent composition. The sensitivities to solvent nucleophilicity and solvent ionizing power are compared to values available for other substrates. Three of these previous studies are upgraded by the incorporation of additional specific rate values from the recent literature. With a methyl, isopropyl, benzyl, aromatic or heteroaromatic group as the R group of RSO₂Cl, a concerted S_N2 mechanism is proposed for the solvolysis. Full article

(This article belongs to the Special Issue Grunwald-Winstein Equations – 60 Years & Counting)

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Open AccessArticle

Headspace Solid Phase Micro Extraction Gas Chromatographic Determination of Fenthion in Human Serum

by Konstantinos M. Kasiotis, Helen Souki, Angelos N. Tsakirakis, Haris Carageorgiou, Spiridon A. Theotokatos, Serkos A. Haroutounian and Kyriaki Machera

Int. J. Mol. Sci. 2008, 9(5), 906-913; https://doi.org/10.3390/ijms9050906 - 23 May 2008

Cited by 12 | Viewed by 9382

Abstract

A simple and effective analytical procedure was developed for the determination of fenthion residues in human serum samples. The sample treatment was performed using the headspace solid-phase micro extraction with polyacrylate fiber, which has the advantage to require low amount of serum (1 [...] Read more.

A simple and effective analytical procedure was developed for the determination of fenthion residues in human serum samples. The sample treatment was performed using the headspace solid-phase micro extraction with polyacrylate fiber, which has the advantage to require low amount of serum (1 mL) without tedious pre-treatment. The quantification of fenthion was carried out by gas chromatography-mass spectrometry and the recoveries ranged from 79 to 104% at two spiking levels for 6 replicates. Detection and quantification limits were calculated as 1.51 and 4.54 ng/mL of serum respectively. Two fenthion metabolites − fenoxon and fenthion–sulfoxide − were also identified. Full article

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Open AccessArticle

Remarks on Muscle Contraction Mechanism

by Toshio Mitsui and Hiroyuki Ohshima

Int. J. Mol. Sci. 2008, 9(5), 872-904; https://doi.org/10.3390/ijms9050872 - 23 May 2008

Cited by 5 | Viewed by 9110

Abstract

Muscle contraction mechanism is discussed by reforming the model described in an article by Mitsui (Adv. Biophys. 1999, 36, 107-158). A simple thermodynamic relationship is presented, which indicates that there is an inconsistency in the power stroke model or the swinging [...] Read more.

Muscle contraction mechanism is discussed by reforming the model described in an article by Mitsui (Adv. Biophys. 1999, 36, 107-158). A simple thermodynamic relationship is presented, which indicates that there is an inconsistency in the power stroke model or the swinging lever model. To avoid this difficulty, a new model is proposed. It is assumed that a myosin head forms a polaron-like complex with about three actin molecules when it attaches to an actin filament and the complex translates along the actin filament producing force. Various experimental data on the muscle contraction are well explained based upon the model. Full article

(This article belongs to the Special Issue Muscle Contraction Mechanism, Motor Proteins Function and Molecular Aspects of Water)

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Open AccessArticle

Newly Synthesized Water Soluble Cholinium-Purpurin Photosensitizers and Their Stabilized Gold Nanoparticles as Promising Anticancer Agents

by Dorjnamjin Demberelnyamba, Mama Ariunaa and Young Key Shim

Int. J. Mol. Sci. 2008, 9(5), 864-871; https://doi.org/10.3390/ijms9050864 - 23 May 2008

Cited by 39 | Viewed by 11554

Abstract

For possible future use in Photodynamic Therapy (PDT) and/or Photothermal Therapy (PTT) of cancer and screening of cancer cells a new type of ionic liquid photosensitizer –Cholinium-Purpurin-18 (Chol-Pu-18) – was synthesized and small gold (Au) nanoparticles, stabilized by this photosensitizer were prepared without [...] Read more.

For possible future use in Photodynamic Therapy (PDT) and/or Photothermal Therapy (PTT) of cancer and screening of cancer cells a new type of ionic liquid photosensitizer –Cholinium-Purpurin-18 (Chol-Pu-18) – was synthesized and small gold (Au) nanoparticles, stabilized by this photosensitizer were prepared without adding any particular reducing agents and CTAB. UV-Vis spectroscopy and Transmission Electron Microscopy (TEM) were used for characterization of the nanoparticles and FAB-MS and NMR of the ionic liquid choline hydroxide, purpurin carboxylate and their ionic liquid type of photosensitizer were obtained. Full article

(This article belongs to the Special Issue Natural Compounds for Cancer Treatment and Prevention)

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Open AccessReview

Roles of Probiotics and Prebiotics in Colon Cancer Prevention: Postulated Mechanisms and In-vivo Evidence

by Min-Tze Liong

Int. J. Mol. Sci. 2008, 9(5), 854-863; https://doi.org/10.3390/ijms9050854 - 20 May 2008

Cited by 191 | Viewed by 24765

Abstract

Probiotics are live bacteria that could exert health beneficial effects upon consumption. In additional to their conventional use as gut modulators, probiotics are investigated for their role to prevent cancer. In-vivo and molecular studies have demonstrated encouraging outcomes, mainly attributed to its antimicrobial [...] Read more.

Probiotics are live bacteria that could exert health beneficial effects upon consumption. In additional to their conventional use as gut modulators, probiotics are investigated for their role to prevent cancer. In-vivo and molecular studies have demonstrated encouraging outcomes, mainly attributed to its antimicrobial effects against carcinogen-producing microorganisms, antimutagenic properties, and alteration of the tumor differentiation processes. Prebiotics are indigestible food components that could promote the growth of beneficial bacteria including probiotics. Present studies have suggested that prebiotics also possess protective effect against colon carcinogenesis, mainly attributed to the production of short chain fatty acids upon its fermentation by gut microflora, and alteration of gene-expressions in tumor cells. Synbiotic (combination of probiotic and prebiotic) has been found to exert a synergistic effect in improving colon carcinogenesis compared to when both were used individually. This paper highlights the colon cancer preventive effects by probiotics, prebiotics and synbiotics. In addition, the controversial outcomes on the insignificant effect of these food adjuncts will be discussed. Full article

(This article belongs to the Special Issue Natural Compounds for Cancer Treatment and Prevention)

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Open AccessReview

Red Wine Polyphenols for Cancer Prevention

by Shan He, Cuirong Sun and Yuanjiang Pan

Int. J. Mol. Sci. 2008, 9(5), 842-853; https://doi.org/10.3390/ijms9050842 - 20 May 2008

Cited by 69 | Viewed by 16341

Abstract

Conventional cancer therapies, the second leading cause of death worldwide, result in serious side effects and, at best, merely extend the patient's lifespan by a few years. Searching for effective prevention is of high priority in both basic and clinical sciences. In recent [...] Read more.

Conventional cancer therapies, the second leading cause of death worldwide, result in serious side effects and, at best, merely extend the patient's lifespan by a few years. Searching for effective prevention is of high priority in both basic and clinical sciences. In recent decades natural products have been considered to be an important source of cancer chemopreventive agents. Red wine polyphenols, which consisted of various powerful antioxidants such as flavonoids and stilbenes, have been implicated in cancer prevention and that promote human health without recognizable side effects. Since resveratrol, a major component of red wine polyphenols, has been studied and reviewed extensively for its chemopreventive activity to interfere with the multi-stage carcinogenesis, this review focuses on recent progress in studies on cancer chemopreventive activities of red wine polyphenol extracts and fractions as well as other red wine polyphenols, like procyanidin B5 analogues and myricetin. Full article

(This article belongs to the Special Issue Natural Compounds for Cancer Treatment and Prevention)

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Open AccessArticle

Synthesis and Biological Evaluation of a Novel Pentagastrin- Toxin Conjugate Designed for a Targeted Prodrug Monotherapy of Cancer

by Lutz F. Tietze, Olaf Panknin, Birgit Krewer, Felix Major and Ingrid Schuberth

Int. J. Mol. Sci. 2008, 9(5), 821-837; https://doi.org/10.3390/ijms9050821 - 20 May 2008

Cited by 11 | Viewed by 11600

Abstract

A novel carbamate prodrug 2 containing a pentagastrin moiety was synthesized. 2 was designed as a detoxified analogue of the highly cytotoxic natural antibiotic duocarmycin SA (1) for the use in a targeted prodrug monotherapy of cancers expressing cholecystokinin (CCK-B)/gastrin receptors. The synthesis [...] Read more.

A novel carbamate prodrug 2 containing a pentagastrin moiety was synthesized. 2 was designed as a detoxified analogue of the highly cytotoxic natural antibiotic duocarmycin SA (1) for the use in a targeted prodrug monotherapy of cancers expressing cholecystokinin (CCK-B)/gastrin receptors. The synthesis of prodrug 2 was performed using a palladium-catalyzed carbonylation of bromide 6, followed by a radical cyclisation to give the pharmacophoric unit 10, coupling of 10 to the DNA-binding subunit 15 and transformation of the resulting seco-drug 3b into the carbamate 2 via addition of a pentagastrin moiety. Full article

(This article belongs to the Special Issue Natural Compounds for Cancer Treatment and Prevention)

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Open AccessArticle

Synthesis of Silver Nanoparticles Using Hydroxyl Functionalized Ionic Liquids and Their Antimicrobial Activity

by Demberelnyamba Dorjnamjin, Maamaa Ariunaa and Young Key Shim

Int. J. Mol. Sci. 2008, 9(5), 807-820; https://doi.org/10.3390/ijms9050807 - 20 May 2008

Cited by 133 | Viewed by 15316

Abstract

We report a new one phase method for the synthesis of uniform monodisperse crystalline Ag nanoparticles in aqueous systems that has been developed by using newly synthesized mono and dihydroxylated ionic liquids and cationic surfactants based on 1,3-disubstituted imidazolium cations and halogens anions. [...] Read more.

We report a new one phase method for the synthesis of uniform monodisperse crystalline Ag nanoparticles in aqueous systems that has been developed by using newly synthesized mono and dihydroxylated ionic liquids and cationic surfactants based on 1,3-disubstituted imidazolium cations and halogens anions. The hydroxyl functionalized ionic liquids (HFILs) and hydroxyl functionalized cationic surfactants (HFCSs) also simultaneously acts both as the reductant and protective agent. By changing the carbon chain length, alcohol structure and anion of the 1,3-imidazolium based HFILs and HFCSs the particle size, uniform and dispersibility of nanoparticles in aqueous solvents could be controlled. Transmission electron microscopy (TEM), electron diffraction, UV-Vis and NMR, were used for characterization of HFILs, HFCSs and silver nanoparticles. TEM studies on the solution showed representative spherical silver nanoparticles with average sizes 2-8 nm, particularly 2.2 nm and 4.5 nm in size range and reasonable narrow particle size distributions (SD-standard distribution) 0.2 nm and 0.5 nm respectively. The all metal nanoparticles are single crystals with face centered cubic (fcc) structure. The silver nanoparticles surface of plasmon resonance band (λ_max) around 420 nm broadened and little moved to the long wavelength region that indicating the formation of silver nanoparticles dispersion with broad absorption around infrared (IR) region. Silver complexes of these HFILs as well as different silver nanoparticles dispersions have been tested in vitro against several gram positive and gram negative bacteria and fungus. The silver nanoparticles providing environmentally friendly and high antimicrobial activity agents. Full article

(This article belongs to the Special Issue Ionic Liquids)

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Open AccessReview

Sublethal RNA Oxidation as a Mechanism for Neurodegenerative Disease

by Rudy J. Castellani, Akihiko Nunomura, Raj K. Rolston, Paula I. Moreira, Atsushi Takeda, George Perry and Mark A. Smith

Int. J. Mol. Sci. 2008, 9(5), 789-806; https://doi.org/10.3390/ijms9050789 - 20 May 2008

Cited by 37 | Viewed by 14365

Abstract

Although cellular RNA is subjected to the same oxidative insults as DNA and other cellular macromolecules, oxidative damage to RNA has not been a major focus in investigations of the biological consequences of free radical damage. In fact, because it is largely single-stranded [...] Read more.

Although cellular RNA is subjected to the same oxidative insults as DNA and other cellular macromolecules, oxidative damage to RNA has not been a major focus in investigations of the biological consequences of free radical damage. In fact, because it is largely single-stranded and its bases lack the protection of hydrogen bonding and binding by specific proteins, RNA may be more susceptible to oxidative insults than is DNA. Oxidative damage to protein-coding RNA or non-coding RNA will, in turn, potentially cause errors in proteins and/or dysregulation of gene expression. While less lethal than mutations in the genome, such sublethal insults to cells might be associated with underlying mechanisms of several chronic diseases, including neurodegenerative disease. Recently, oxidative RNA damage has been described in several neurodegenerative diseases including Alzheimer disease, Parkinson disease, dementia with Lewy bodies, and prion diseases. Of particular interest, oxidative RNA damage can be demonstrated in vulnerable neurons early in disease, suggesting that RNA oxidation may actively contribute to the onset of the disease. An increasing body of evidence suggests that, mechanistically speaking, the detrimental effects of oxidative RNA damage to protein synthesis are attenuated, at least in part, by the existence of protective mechanisms that prevent the incorporation of the damaged ribonucleotides into the translational machinery. Further investigations aimed at understanding the processing mechanisms related to oxidative RNA damage and its consequences may provide significant insights into the pathogenesis of neurodegenerative and other degenerative diseases and lead to better therapeutic strategies. Full article

(This article belongs to the Special Issue Nucleic Acid Derivatives in Emerging Technologies)

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Open AccessReview

Perennial Forages as Second Generation Bioenergy Crops

by Matt A. Sanderson and Paul R. Adler

Int. J. Mol. Sci. 2008, 9(5), 768-788; https://doi.org/10.3390/ijms9050768 - 20 May 2008

Cited by 203 | Viewed by 17255

Abstract

The lignocellulose in forage crops represents a second generation of biomass feedstock for conversion into energy-related end products. Some of the most extensively studied species for cellulosic feedstock production include forages such as switchgrass (Panicum virgatum L.), reed canarygrass (Phalaris [...] Read more.

The lignocellulose in forage crops represents a second generation of biomass feedstock for conversion into energy-related end products. Some of the most extensively studied species for cellulosic feedstock production include forages such as switchgrass (Panicum virgatum L.), reed canarygrass (Phalaris arundinacea L.), and alfalfa (Medicago sativa L.). An advantage of using forages as bioenergy crops is that farmers are familiar with their management and already have the capacity to grow, harvest, store, and transport them. Forage crops offer additional flexibility in management because they can be used for biomass or forage and the land can be returned to other uses or put into crop rotation. Estimates indicate about 22.3 million ha of cropland, idle cropland, and cropland pasture will be needed for biomass production in 2030. Converting these lands to large scale cellulosic energy farming could push the traditional forage-livestock industry to ever more marginal lands. Furthermore, encouraging bioenergy production from marginal lands could directly compete with forage-livestock production. Full article

(This article belongs to the Special Issue Biofuels R&D: Securing the Planet's Future Energy Needs)

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Open AccessEditorial

Cellulosic Ethanol: Securing the Planet Future Energy Needs

by Clifford Louime and Hannah Uckelmann

Int. J. Mol. Sci. 2008, 9(5), 838-841; https://doi.org/10.3390/ijms9050838 - 17 May 2008

Cited by 21 | Viewed by 8970

Abstract

Bioenergy is fairly recognized as not only a necessity, but an inevitable path to secure the planet future energy needs. There is however a global consensus that the overall feasibility of bioenergy will require an integrated approach based on diversified feedstocks and conversion [...] Read more.

Bioenergy is fairly recognized as not only a necessity, but an inevitable path to secure the planet future energy needs. There is however a global consensus that the overall feasibility of bioenergy will require an integrated approach based on diversified feedstocks and conversion processes. As illustrated in the Brazilian experience, the thrust of any bioenergy program should be centered on the principles and criteria of sustainable production. In general the trends are towards exploiting low value cellulosic materials to obtain high-end value energy products. To this end, it is expected that scientific or technical innovation will come to play a critical role on the future prospects and potential of any bioenergy initiative. Full article

(This article belongs to the Special Issue Biofuels R&D: Securing the Planet's Future Energy Needs)

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Open AccessReview

Metabolic Compartmentation – A System Level Property of Muscle Cells

by Valdur Saks, Nathalie Beraud and Theo Wallimann

Int. J. Mol. Sci. 2008, 9(5), 751-767; https://doi.org/10.3390/ijms9050751 - 9 May 2008

Cited by 76 | Viewed by 13527

Abstract

Problems of quantitative investigation of intracellular diffusion and compartmentation of metabolites are analyzed. Principal controversies in recently published analyses of these problems for the living cells are discussed. It is shown that the formal theoretical analysis of diffusion of metabolites based on Fick’s [...] Read more.

Problems of quantitative investigation of intracellular diffusion and compartmentation of metabolites are analyzed. Principal controversies in recently published analyses of these problems for the living cells are discussed. It is shown that the formal theoretical analysis of diffusion of metabolites based on Fick’s equation and using fixed diffusion coefficients for diluted homogenous aqueous solutions, but applied for biological systems in vivo without any comparison with experimental results, may lead to misleading conclusions, which are contradictory to most biological observations. However, if the same theoretical methods are used for analysis of actual experimental data, the apparent diffusion constants obtained are orders of magnitude lower than those in diluted aqueous solutions. Thus, it can be concluded that local restrictions of diffusion of metabolites in a cell are a system-level properties caused by complex structural organization of the cells, macromolecular crowding, cytoskeletal networks and organization of metabolic pathways into multienzyme complexes and metabolons. This results in microcompartmentation of metabolites, their channeling between enzymes and in modular organization of cellular metabolic networks. The perspectives of further studies of these complex intracellular interactions in the framework of Systems Biology are discussed. Full article

(This article belongs to the Special Issue Muscle Contraction Mechanism, Motor Proteins Function and Molecular Aspects of Water)

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Open AccessArticle

Purification and Preliminary Crystallographic Analysis of a New Lys49-PLA2 from B. Jararacussu

by Marcelo L. Dos Santos, Fábio H. R. Fagundes, Bruno R. F. Teixeira, Marcos H. Toyama and Ricardo Aparicio

Int. J. Mol. Sci. 2008, 9(5), 736-750; https://doi.org/10.3390/ijms9050736 - 8 May 2008

Cited by 8 | Viewed by 10012

Abstract

BjVIII is a new myotoxic Lys49-PLA2 isolated from Bothrops jararacussu venom that exhibits atypical effects on human platelet aggregation. To better understand the mode of action of BjVIII, crystallographic studies were initiated. Two crystal forms were obtained, both containing two molecules in the [...] Read more.

BjVIII is a new myotoxic Lys49-PLA2 isolated from Bothrops jararacussu venom that exhibits atypical effects on human platelet aggregation. To better understand the mode of action of BjVIII, crystallographic studies were initiated. Two crystal forms were obtained, both containing two molecules in the asymmetric unit (ASU). Synchrotron radiation diffraction data were collected to 2.0 °A resolution and 1.9 °A resolution for crystals belonging to the space group P2₁2₁2₁(a = 48:4 A° , b = 65:3 A° , c = 84:3 A° ) and space group P3₁2₁ (a = b = 55:7 A° , c = 127:9 A° ), respectively. Refinement is currently in progress and the refined structures are expected to shed light on the unusual platelet aggregation activity observed for BjVIII. Full article

(This article belongs to the Special Issue Protein Crystallography)

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Open AccessArticle

Binding of Ochratoxin A to a Urinary Globulin: A New Concept to Account for Gender Difference in Rat Nephrocarcinogenic Responses

by Peter G. Mantle and Judit Nagy

Int. J. Mol. Sci. 2008, 9(5), 719-735; https://doi.org/10.3390/ijms9050719 - 8 May 2008

Cited by 24 | Viewed by 12251

Abstract

SDS-gradient mini-gel electrophoresis and immunoblotting of urine of rats given ochratoxin A (OTA), showed OTA binding to an α2u-globulin. Perceived potential internalised delivery of OTA to proximal tubule epithelia by the carrier, specific only to adult male rats and augmenting other uptake mechanisms, [...] Read more.

SDS-gradient mini-gel electrophoresis and immunoblotting of urine of rats given ochratoxin A (OTA), showed OTA binding to an α2u-globulin. Perceived potential internalised delivery of OTA to proximal tubule epithelia by the carrier, specific only to adult male rats and augmenting other uptake mechanisms, suggests that some experimental nephrotoxicological data may not be appropriate for human risk assessment. Reexamination of female rat renal tumour histopathology of the NTP high dose OTA study showed all carcinomas were solitary, unilateral, microscopic and clinically insignificant at the 2-year end-stage. The novel concept, when consolidated further from our archived material, may moderate current perceptions of the human risk of traces of dietary OTA. Full article

(This article belongs to the Special Issue Mycotoxins: Mechanisms of Toxicological Activity - Treatment and Prevention)

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Open AccessArticle

Caffeine Induces Cell Death via Activation of Apoptotic Signal and Inactivation of Survival Signal in Human Osteoblasts

by Pin-Zhen Lu, Ching-Yu Lai and Wen-Hsiung Chan

Int. J. Mol. Sci. 2008, 9(5), 698-718; https://doi.org/10.3390/ijms9050698 - 8 May 2008

Cited by 89 | Viewed by 15521

Abstract

Caffeine consumption is a risk factor for osteoporosis, but the precise regulatory mechanisms are currently unknown. Here, we show that cell viability decreases in osteoblasts treated with caffeine in a dose-dependent manner. This cell death is attributed primarily to apoptosis and to a [...] Read more.

Caffeine consumption is a risk factor for osteoporosis, but the precise regulatory mechanisms are currently unknown. Here, we show that cell viability decreases in osteoblasts treated with caffeine in a dose-dependent manner. This cell death is attributed primarily to apoptosis and to a smaller extent, necrosis. Moreover, caffeine directly stimulates intracellular oxidative stress. Our data support caffeine-induced apoptosis in osteoblasts via a mitochondria-dependent pathway. The apoptotic biochemical changes were effectively prevented upon pretreatment with ROS scavengers, indicating that ROS plays a critical role as an upstream controller in the caffeine-induced apoptotic cascade. Additionally, p21-activated protein kinase 2 (PAK2) and c-Jun N-terminal kinase (JNK) were activated in caffeine-treated osteoblasts. Experiments further found that PAK2 activity is required for caffeine-induced JNK activation and apoptosis. Importantly, our data also show that caffeine triggers cell death via inactivation of the survival signal, including the ERK- and Akt-mediated anti-apoptotic pathways. Finally, exposure of rats to dietary water containing 10~20 μM caffeine led to bone mineral density loss. These results demonstrate for the first time that caffeine triggers apoptosis in osteoblasts via activation of mitochondria-dependent cell death signaling and inactivation of the survival signal, and causes bone mineral density loss in vivo. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

A Statistical Analysis of the Robustness of Alternate Genetic Coding Tables

by Mehmet Levent Kurnaz and Isil Aksan Kurnaz

Int. J. Mol. Sci. 2008, 9(5), 679-697; https://doi.org/10.3390/ijms9050679 - 2 May 2008

Cited by 1 | Viewed by 10358

Abstract

The rules that specify how the information contained in DNA is translated into amino acid “language” during protein synthesis are called “the genetic code”, commonly called the “Standard” or “Universal” Genetic Code Table. As a matter of fact, this coding table is not [...] Read more.

The rules that specify how the information contained in DNA is translated into amino acid “language” during protein synthesis are called “the genetic code”, commonly called the “Standard” or “Universal” Genetic Code Table. As a matter of fact, this coding table is not at all “universal”: in addition to different genetic code tables used by different organisms, even within the same organism the nuclear and mitochondrial genes may be subject to two different coding tables. Results In an attempt to understand the advantages and disadvantages these coding tables may bring to an organism, we have decided to analyze various coding tables on genes subject to mutations, and have estimated how these genes “survive” over generations. We have used this as indicative of the “evolutionary” success of that particular coding table. We find that the “standard” genetic code is not actually the most robust of all coding tables, and interestingly, Flatworm Mitochondrial Code (FMC) appears to be the highest ranking coding table given our assumptions. Conclusions It is commonly hypothesized that the more robust a genetic code, the better suited it is for maintenance of the genome. Our study shows that, given the assumptions in our model, Standard Genetic Code is quite poor when compared to other alternate code tables in terms of robustness. This brings about the question of why Standard Code has been so widely accepted by a wider variety of organisms instead of FMC, which needs to be addressed for a thorough understanding of genetic code evolution. Full article

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Int. J. Mol. Sci., Volume 9, Issue 5 (May 2008) – 17 articles , Pages 679-925

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