Certain Non-Standard Coding Tables Appear to be More Robust to Error Than the Standard Genetic Code

Since the identification of the Standard Coding Table as a “universal” method to translate genetic information into amino acids, exceptions to this rule have been reported, and to date there are nearly 20 alternative genetic coding tables deployed by either nuclear genomes or organelles of organisms. Why are these codes still in use and why are new codon reassignments occurring? This present study aims to provide a new method to address these questions and to analyze whether these alternative codes present any advantages or disadvantages to the organisms or organelles in terms of robustness to error. We show that two of the alternative coding tables, The Ciliate, Dasycladacean and Hexamita Nuclear Code (CDH) and The Flatworm Mitochondrial Code (FMC), exhibit an advantage, while others such as The Yeast Mitochondrial Code (YMC) are at a significant disadvantage. We propose that the Standard Code is likely to have emerged as a “local minimum” and that the “coding landscape” is still being searched for a “global” minimum.     

Effects of ovariectomy and tamoxifen on rat bone tissue: histomorphometric and histopathologic study

OBJECTIVE: To investigate possible detrimental effects on bone tissue induced by ovariectomy and tamoxifen (TMX) using bone densitometry and histomorphologic analysis. STUDY DESIGN: Twenty-four rats were allocated into 4 groups: group 1, intact normal rats (n = 6); group 2, ovariectomized rats (n = 6); group 3, normal female rats that received 1 mg/kg/day TMX dissolved in dimethyl sulfoxide (DMSO) for 2 months (n = 6); group 4, normal female rats that received DMSO for the same duration and with a volume equal to that of TMX (n = 6). Results of histomorphometric analysis for trabecular thickness, number of osteoblasts and osteoclasts, trabecular number, and area and cortical thickness were compared. RESULTS: No significant effects of ovariectomy on femoral or lumbar bone mineral density (BMD) were found. In the TMX group, the value of femoral BMD increased significantly compared to control group cellular and pathologic changes. TMX caused significant decrease in osteoblasts compared to the control group. CONCLUSION: TMX has a positive effect on inorganic bone tissue, but a negative effect on number of osteoblasts and osteoclasts. Future studies investigating estrogenic and antiestrogenic effects of TMX should include cellular parameters related to proliferation using histopathologic and histomorphometric analyses.     

Temperature dependence of accuracy of DNA polymerase I from Geobacillus anatolicus

Klenow-like DNA polymerase I fragment from Geobacillus anatolicus (GF) was cloned and purified. The accuracy of GF was measured in vitro at three different temperatures under single turnover conditions as well as using a forward mutation assay. In pre-steady-state kinetic measurements, when temperature was raised from 22 °C to 50 °C, the rate (k_pol) for cognate dTTP and non-cognate dATP nucleotide incorporations increased six- and four-fold, respectively, whereas the K_d for both nucleotide incorporations changed only slightly. As a result, the error frequency was remained constant (∼4 × 10⁻⁴) over this temperature range. The accuracy of GF was also measured using a forward mutation assay during a single cycle of DNA synthesis of the lacZα complementation gene in M13mp2 DNA. In this assay, which scores various types of replication errors, mutant frequency of GF was 5 × 10⁻³ at 72 °C which is four-fold higher than that of 37 °C.     

Multiscale feature analysis of salivary gland branching morphogenesis

Pattern formation in developing tissues involves dynamic spatio-temporal changes in cellular organization and subsequent evolution of functional adult structures. Branching morphogenesis is a developmental mechanism by which patterns are generated in many developing organs, which is controlled by underlying molecular pathways. Understanding the relationship between molecular signaling, cellular behavior and resulting morphological change requires quantification and categorization of the cellular behavior. In this study, tissue-level and cellular changes in developing salivary gland in response to disruption of ROCK-mediated signaling by are modeled by building cell-graphs to compute mathematical features capturing structural properties at multiple scales. These features were used to generate multiscale cell-graph signatures of untreated and ROCK signaling disrupted salivary gland organ explants. From confocal images of mouse submandibular salivary gland organ explants in which epithelial and mesenchymal nuclei were marked, a multiscale feature set capturing global structural properties, local structural properties, spectral, and morphological properties of the tissues was derived. Six feature selection algorithms and multiway modeling of the data was performed to identify distinct subsets of cell graph features that can uniquely classify and differentiate between different cell populations. Multiscale cell-graph analysis was most effective in classification of the tissue state. Cellular and tissue organization, as defined by a multiscale subset of cell-graph features, are both quantitatively distinct in epithelial and mesenchymal cell types both in the presence and absence of ROCK inhibitors. Whereas tensor analysis demonstrate that epithelial tissue was affected the most by inhibition of ROCK signaling, significant multiscale changes in mesenchymal tissue organization were identified with this analysis that were not identified in previous biological studies. We here show how to define and calculate a multiscale feature set as an effective computational approach to identify and quantify changes at multiple biological scales and to distinguish between different states in developing tissues.     

Design and analysis of a distributed grid resource discovery protocol

Computational grids have been emerging as a new paradigm for solving large complex problems over the recent years. The problem space and data set are divided into smaller pieces that are processed in parallel over the grid network and reassembled upon completion. Typically, resources are logged into a resource broker that is somewhat aware of all of the participants available on the grid. The resource broker scheme can be a bottleneck because of the amount of computational power and network bandwidth needed to maintain a fresh view of the grid. In this paper, we propose to place the load of managing the network resource discovery on to the network itself: inside of the routers. In the proposed protocol, the routers contain tables for resources similar to routing tables. These resource tables map IP addresses to the available computing resource values, which are provided through a scoring mechanism. Each resource provider is scored based on the attributes they provide such as the number of processors, processor frequency, amount of memory, hard drive space, and the network bandwidth. The resources are discovered on the grid by the protocol’s discovery packets, which are encapsulated within the TCP/IP packets. The discovery packet visits the routers and look up in the resource tables until a satisfactory resource is found. The protocol is validated by simulations with five different deployment environments.     

Multiple Origins of kdr-type Resistance in the House Fly,Musca domestica

Insecticide resistance is a model phenotype that can be used to investigate evolutionary processes underlying the spread of alleles across a global landscape, while offering valuable insights into solving the problems that resistant pests present to human health and agriculture. Pyrethroids are one of the most widely used classes of insecticides world-wide and they exert their toxic effects through interactions with the voltage-sensitive sodium channel (Vssc). Specific mutations in Vssc (kdr, kdr-his and super-kdr) are known to cause resistance to pyrethroid insecticides in house flies. In order to determine the number of evolutionary origins of kdr, kdr-his and super-kdr, we sequenced a region of Vssc from house flies collected in the USA, Turkey and China. Our phylogenetic analysis of Vssc unequivocally supports the hypothesis of multiple independent origins of kdr, super-kdr and kdr-his on an unprecedented geographic scale. The implications of these evolutionary processes on pest management are discussed.     

Environmental margin and island evolution in Middle Eastern populations of the Egyptian fruit bat

Here, we present a study of the population genetic architecture and microevolution of the Egyptian fruit bat (Rousettus aegyptiacus) at the environmental margins in the Middle East using mitochondrial sequences and nuclear microsatellites. In contrast to the rather homogenous population structure typical of cave‐dwelling bats in climax tropical ecosystems, a relatively pronounced isolation by distance and population diversification was observed. The evolution of this pattern could be ascribed to the complicated demographic history at higher latitudes related to the range margin fragmentation and complex geomorphology of the studied area. Lineages from East Africa and Arabia show divergent positions. Within the northwestern unit, the most marked pattern of the microsatellite data set is connected with insularity, as demonstrated by the separate status of populations from Saharan oases and Cyprus. These demes also exhibit a reduction in genetic variability, which is presumably connected with founder effects, drift and other potential factors related to island evolution as site‐specific selection. Genetic clustering indicates a semipermeability of the desert barriers in the Sahara and Arabian Peninsula and a corridor role of the Nile Valley. The results emphasize the role of the island environment in restricting the gene flow in megabats, which is also corroborated by biogeographic patterns within the family, and suggests the possibility of nascent island speciation on Cyprus. Demographic analyses suggest that the colonization of the region was connected to the spread of agricultural plants; therefore, the peripatric processes described above might be because of or strengthened by anthropogenic changes in the environment.     

Production of (R)‐1‐phenylethanols through bioreduction of acetophenones by a new fungus isolate Trichothecium roseum

A total of 120 fungal strains were isolated from soil samples and evaluated in the bioreduction of substituted acetophenones to the corresponding (R)‐alcohols. Among these strains, isolate Trichothecium roseum EBK‐18 was highly effective in the production of (R)‐alcohols with excellent enantioselectivity (ee > 99%). Gram scale preparation of (R)‐1‐phenylethanol is reported. Chirality 2010. © 2009 Wiley‐Liss, Inc.