scholarly journals Unusual Codon Bias in Vinyl Chloride Reductase Genes of Dehalococcoides Species

2007 ◽  
Vol 73 (8) ◽  
pp. 2744-2747 ◽  
Author(s):  
Paul J. McMurdie ◽  
Sebastian F. Behrens ◽  
Susan Holmes ◽  
Alfred M. Spormann

ABSTRACT Vinyl chloride reductases (VC-RDase) are the key enzymes for complete microbial reductive dehalogenation of chloroethenes, including the groundwater pollutants tetrachloroethene and trichloroethene. Analysis of the codon usage of the VC-RDase genes vcrA and bvcA showed that these genes are highly unusual and are characterized by a low G+C fraction at the third position. The third position of codons in VC-RDase genes is biased toward the nucleotide T, even though available Dehalococcoides genome sequences indicate the absence of any tRNAs matching codons that end in T. The comparatively high level of abnormality in the codon usage of VC-RDase genes suggests an evolutionary history that is different from that of most other Dehalococcoides genes.

1989 ◽  
Vol 28 (04) ◽  
pp. 124-128 ◽  
Author(s):  
J. Spitz ◽  
N. Clemenz ◽  
K. Tittel ◽  
H. Weigand

In addition to its established oncological indications the sensitivity of bone scintigraphy is of steadily increasing significance in traumatology. Inactivity- induced osteoporosis plays a major role during the immobilization period in the plaster cast. In the region of the joints remodelling intensity may reach such a high level that the non-injured bone shows a higher rate of accumulation than the fracture. This process already begins between the third and fourth week of immobilization. The highest uptake is found after fracture of the scaphoid bone at the end of twelve weeks of immobilization. Control scintigraphies at intervals of several days are indicated to differentiate between various clinical conditions (pseudoarthrosis, activated osteoarthrosis, algodystrophy in case of doubtful x-ray results).


Author(s):  
Martin Krzywdzinski

This chapter deals with the dependent variable of the study: consent. It analyses workplace consent in Russia and China using three indicators that refer to the core requirements of the production systems in automotive companies regarding employee behavior: first, standardized work; and second, compliance with expectations in terms of flexibility, cooperation, and a commitment to improving processes. The third indicator of consent (or the lack of it) is the absence or presence of open criticism, resistance, and labor disputes. The chapter reveals significant and unexpected differences between the Chinese and Russian sites on all three indicators. While the Chinese factories exhibit (with some variance between the companies), a relatively high level of consent, the Russian plants have problems with standardized work, the acceptance of performance expectations, and to some extent with labor disputes.


1944 ◽  
Vol 151 (1) ◽  
pp. 70-86
Author(s):  
W. Littlejohn Philip

The paper is limited to the application of hydraulic power to lathes designed for shell making although, in the author's opinion, there is an immense field for the application of the same principles in other directions. Self-contained hydraulic machine tools have been dealt with by Mr. H. C. Town,† but in the system to be described all the machines are operated from a central hydraulic plant. Three complete installations on this principle have been established by the author, and the present paper contains an account of this work from the first experiments in 1915 until about four years ago. The first plant was constructed in 1915 for the production of 3·29-inch shells, known as “18-pounders”, from the solid bar. The output was 2,000 shells per week of 135 hours, with girl operators working on three shifts. The second plant was put down in 1916–17 for an output of 500 9·2-inch howitzer shells per week of 135 hours, also with girls working on three shifts. The third plant is of recent design. It was started in 1938 for the production of 3·45-inch shells, known as “25-pounders”; and was laid out for an output of 1,000 shells per week of 47 hours. This plant included four types of hydraulic lathes which the author was engaged to design for the War Office. Soon after the commencement of the last war in 1914 it became evident that shell production would have to be greatly increased, and engineering firms were pressed to take up shell manufacture. The author, on behalf of his firm, undertook to help in the movement, and he at once set about the construction of some simple machines for the job. These conformed on general lines to the practice of the period as regards design and operation. He soon realized, however, that drastic changes would have to be made if production was to reach the high level that circumstances demanded. Although quite familiar with hydraulic machinery of various types and of many applications in presses and certain types of heavy tools, he was not aware of any instance in which hydraulic power had been applied to the movements of a lathe. It appeared to him, nevertheless, that it would be possible to construct a very useful machine on these lines, and he accordingly started immediately to carry out experiments and to prepare designs. It was considered essential that machines for the duty which the author had in mind should be much heavier and more rigid than the ordinary machines of the time, so that they should be free from vibration and “chatter” or spring with the heaviest possible cutting. The standard of rigidity aimed at was that which would permit a half-crown coin to remain balanced on edge on the moving saddle or turret while the tools were making the heaviest cuts. This object was achieved, and the demonstration was frequently made in the presence of those who came to see the lathes at work.


Genetics ◽  
2001 ◽  
Vol 159 (3) ◽  
pp. 1191-1199
Author(s):  
Araxi O Urrutia ◽  
Laurence D Hurst

Abstract In numerous species, from bacteria to Drosophila, evidence suggests that selection acts even on synonymous codon usage: codon bias is greater in more abundantly expressed genes, the rate of synonymous evolution is lower in genes with greater codon bias, and there is consistency between genes in the same species in which codons are preferred. In contrast, in mammals, while nonequal use of alternative codons is observed, the bias is attributed to the background variance in nucleotide concentrations, reflected in the similar nucleotide composition of flanking noncoding and exonic third sites. However, a systematic examination of the covariants of codon usage controlling for background nucleotide content has yet to be performed. Here we present a new method to measure codon bias that corrects for background nucleotide content and apply this to 2396 human genes. Nearly all (99%) exhibit a higher amount of codon bias than expected by chance. The patterns associated with selectively driven codon bias are weakly recovered: Broadly expressed genes have a higher level of bias than do tissue-specific genes, the bias is higher for genes with lower rates of synonymous substitutions, and certain codons are repeatedly preferred. However, while these patterns are suggestive, the first two patterns appear to be methodological artifacts. The last pattern reflects in part biases in usage of nucleotide pairs. We conclude that we find no evidence for selection on codon usage in humans.


BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Giovanni Franzo ◽  
Claudia Maria Tucciarone ◽  
Matteo Legnardi ◽  
Mattia Cecchinato

Abstract Background Infectious bronchitis virus (IBV) is one of the most relevant viruses affecting the poultry industry, and several studies have investigated the factors involved in its biological cycle and evolution. However, very few of those studies focused on the effect of genome composition and the codon bias of different IBV proteins, despite the remarkable increase in available complete genomes. In the present study, all IBV complete genomes were downloaded (n = 383), and several statistics representative of genome composition and codon bias were calculated for each protein-coding sequence, including but not limited to, the nucleotide odds ratio, relative synonymous codon usage and effective number of codons. Additionally, viral codon usage was compared to host codon usage based on a collection of highly expressed genes in IBV target and nontarget tissues. Results The results obtained demonstrated a significant difference among structural, non-structural and accessory proteins, especially regarding dinucleotide composition, which appears under strong selective forces. In particular, some dinucleotide pairs, such as CpG, a probable target of the host innate immune response, are underrepresented in genes coding for pp1a, pp1ab, S and N. Although genome composition and dinucleotide bias appear to affect codon usage, additional selective forces may act directly on codon bias. Variability in relative synonymous codon usage and effective number of codons was found for different proteins, with structural proteins and polyproteins being more adapted to the codon bias of host target tissues. In contrast, accessory proteins had a more biased codon usage (i.e., lower number of preferred codons), which might contribute to the regulation of their expression level and timing throughout the cell cycle. Conclusions The present study confirms the existence of selective forces acting directly on the genome and not only indirectly through phenotype selection. This evidence might help understanding IBV biology and in developing attenuated strains without affecting the protein phenotype and therefore immunogenicity.


AoB Plants ◽  
2021 ◽  
Author(s):  
Min-Jie Li ◽  
Huan-Xi Yu ◽  
Xian-Lin Guo ◽  
Xing-Jin He

Abstract The disjunctive distribution (Europe-Caucasus-Asia) and species diversification across Eurasia for the genus Allium sect. Daghestanica has fascinating attractions for researchers aiming to understanding the development and history of the modern Eurasia flora. However, no any studies have been carried out to address the evolutionary history of this section. Based on the nrITS and cpDNA fragments (trnL-trnF and rpl32-trnL), the evolutionary history of the third evolutionary line (EL3) of the genus Allium was reconstructed and we further elucidate the evolutionary line of sect. Daghestanica under this background. Our molecular phylogeny recovered two highly supported clades in sect. Daghestanica: the Clade I includes Caucasian-European species and Asian A. maowenense, A. xinlongense and A. carolinianum collected in Qinghai; the Clade II comprises Asian yellowish tepal species, A. chrysanthum, A. chrysocephalum, A. herderianum, A. rude and A. xichuanense. The divergence time estimation and biogeography inference indicated that Asian ancestor located in the QTP and the adjacent region could have migrated to Caucasus and Europe distributions around the Late Miocene and resulted in further divergence and speciation; Asian ancestor underwent the rapid radiation in the QTP and the adjacent region most likely due to the heterogeneous ecology of the QTP resulted from the orogeneses around 4–3 Mya. Our study provides a picture to understand the origin and species diversification across Eurasia for sect. Daghestanica.


Genetics ◽  
2003 ◽  
Vol 165 (2) ◽  
pp. 613-621 ◽  
Author(s):  
Douglas R Dorer ◽  
Jamie A Rudnick ◽  
Etsuko N Moriyama ◽  
Alan C Christensen

Abstract Within the unique Triplo-lethal region (Tpl) of the Drosophila melanogaster genome we have found a cluster of 20 genes encoding a novel family of proteins. This family is also present in the Anopheles gambiae genome and displays remarkable synteny and sequence conservation with the Drosophila cluster. The family is also present in the sequenced genome of D. pseudoobscura, and homologs have been found in Aedes aegypti mosquitoes and in four other insect orders, but it is not present in the sequenced genome of any noninsect species. Phylogenetic analysis suggests that the cluster evolved prior to the divergence of Drosophila and Anopheles (250 MYA) and has been highly conserved since. The ratio of synonymous to nonsynonymous substitutions and the high codon bias suggest that there has been selection on this family both for expression level and function. We hypothesize that this gene family is Tpl, name it the Osiris family, and consider possible functions. We also predict that this family of proteins, due to the unique dosage sensitivity and the lack of homologs in noninsect species, would be a good target for genetic engineering or novel insecticides.


Author(s):  
H. Danin-Mankowitz ◽  
A. Ugarph-Morawski ◽  
F. Braunschweig ◽  
P. Wändell

AbstractVenous thromboembolism (VTE) is the third most common cause of cardiovascular disease. Connection between high level of physical activity (PA) and the onset of VTE is unknown. We searched the literature on the possible association between PA level, especially high levels, and the risk of VTE. A systematic review was carried out to identify relevant articles on the relation between PA level and VTE. The initial search was conducted together with the Karolinska Institutet University Library in February 2018, with follow-up searches after that. In total, 4383 records were found and then screened for exclusion of duplicates and articles outside the area of interest. In total, 16 articles with data on 3 or more levels of PA were included. Of these, 12 were cohort and 4 were case-control studies. Totally 13 studies aimed at investigating VTE cases primarily, while three studies had other primary outcomes. Of the 16 studies, five found a U-shaped association between PA level and VTE risk, although non-significant in three of them. Two articles described an association between a more intense physical activity and a higher risk of VTE, which was significant in one. Nine studies found associations between increasing PA levels and a decreasing VTE risk. Available literature provides diverging results as to the association between high levels of PA and the risk of venous thromboembolism, but with several studies showing an association. Further research is warranted to clarify the relationship between high level PA and VTE.


Genetics ◽  
1987 ◽  
Vol 115 (2) ◽  
pp. 247-253
Author(s):  
Lenore Neigeborn ◽  
Marian Carlson

ABSTRACT We have selected 210 mutants able to grow on sucrose in the presence of 2-deoxyglucose. We identified recessive mutations in three major complementation groups that cause constitutive (glucose-insensitive) secreted invertase synthesis. Two groups comprise alleles of the previously identified HXK2 and REG1 genes, and the third group was designated cid1 (constitutive invertase derepression). The effect of cid1 on SUC2 expression is mediated by the SUC2 upstream regulatory region, as judged by the constitutive expression of a SUC2-LEU2-lacZ fusion in which the LEU2 promoter is under control of SUC2 upstream sequences. A cid1 mutation also causes glucose-insensitive expression of maltase. The previously isolated constitutive mutation ssn6 is epistatic to cid1, reg1 and hxk2 for very high level constitutive invertase expression. Mutations in SNF genes that prevent derepression of invertase are epistatic to cid1, reg1 and hxk2; we have previously shown that ssn6 has different epistasis relationships with snf mutations. The constitutive mutation tup1 was found to resemble ssn6 in its genetic interactions with snf mutations. These findings suggest that CID1, REG1 and HXK2 are functionally distinct from SSN6 and TUP1.


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