Defining synonymous codon compression schemes by genome recoding

Synthetic recoding of genomes, to remove targeted sense codons, may facilitate the encoded cellular synthesis of unnatural polymers by orthogonal translation systems. However, our limited understanding of allowed synonymous codon substitutions, and the absence of methods that enable the stepwise replacement of the Escherichia coli genome with long synthetic DNA and provide feedback on allowed and disallowed design features in synthetic genomes, have restricted progress towards this goal. Here we endow E. coli with a system for efficient, programmable replacement of genomic DNA with long (>100-kb) synthetic DNA, through the in vivo excision of double-stranded DNA from an episomal replicon by CRISPR/Cas9, coupled to lambda-red-mediated recombination and simultaneous positive and negative selection. We iterate the approach, providing a basis for stepwise whole-genome replacement. We attempt systematic recoding in an essential operon using eight synonymous recoding schemes. Each scheme systematically replaces target codons with defined synonyms and is compatible with codon reassignment. Our results define allowed and disallowed synonymous recoding schemes, and enable the identification and repair of recoding at idiosyncratic positions in the genome

Influence of monsoon regime and microclimate on soil respiration in the tropical forests

The consequence of precipitation and how environmental factors influence soil respiration remain poorly understood in the tropical forest ecosystems under a monsoon climate in Malaysia. This study was conducted in a recovering tropical lowland Dipterocarpus forest in Peninsular Malaysia, and its monthly variations were examined in association with changing precipitation. Soil respiration was measured using a continuous open flow chamber system connected to a multi gas-handling unit and an infrared gas analyser. The aim of this study was to determine the effects of the monsoon period and microclimate of the tropical region on soil respiration. The average monthly soil respiration rates were 152.79 to 528.67, 120.97 to 500.73, 106.77 to 472.89, 122.89 to 453.89 and 120.33 to 434.89 mg m⁻² h⁻¹ in the respective months from September to January. The emission rate varied across the days and months, with the highest value recorded between September and October, and then gradually decreasing from November to January. Soil temperature explained more than 90% of the soil respiration rate whereas precipitation had a major effect during the monsoon regime. Soil organic carbon (SOC), total organic carbon (TOC), soil organic carbon stock (SOCstock), forest biomass, carbon to nitrogen ratio (C/N) and soil pH were found to vary in considerable amounts, provide nutrients and the environment favourable for microorganism activities, leading to emission of soil CO₂. The low values of soil respiration rate between November and January were due not only on the amount of soil moisture and water potential but also on the intensity and frequency of precipitation. Therefore, these results indicate that the monsoon regime can significantly alter the emission of soil CO₂ and influence the microclimatic conditions and other environmental factors

Defining synonymous codon compression schemes by genome recoding

Synthetic recoding of genomes, to remove targeted sense codons, may facilitate the encoded cellular synthesis of unnatural polymers by orthogonal translation systems. However, our limited understanding of allowed synonymous codon substitutions, and the absence of methods that enable the stepwise replacement of the Escherichia coli genome with long synthetic DNA and provide feedback on allowed and disallowed design features in synthetic genomes, have restricted progress towards this goal. Here we endow E. coli with a system for efficient, programmable replacement of genomic DNA with long (>100-kb) synthetic DNA, through the in vivo excision of double-stranded DNA from an episomal replicon by CRISPR/Cas9, coupled to lambda-red-mediated recombination and simultaneous positive and negative selection. We iterate the approach, providing a basis for stepwise whole-genome replacement. We attempt systematic recoding in an essential operon using eight synonymous recoding schemes. Each scheme systematically replaces target codons with defined synonyms and is compatible with codon reassignment. Our results define allowed and disallowed synonymous recoding schemes, and enable the identification and repair of recoding at idiosyncratic positions in the genome

Total synthesis of Escherichia coli with a recoded genome

Nature uses 64 codons to encode the synthesis of proteins from the genome, and chooses 1 sense codon—out of up to 6 synonyms—to encode each amino acid. Synonymous codon choice has diverse and important roles, and many synonymous substitutions are detrimental. Here we demonstrate that the number of codons used to encode the canonical amino acids can be reduced, through the genome-wide substitution of target codons by defined synonyms. We create a variant of Escherichia coli with a four-megabase synthetic genome through a high-fidelity convergent total synthesis. Our synthetic genome implements a defined recoding and refactoring scheme—with simple corrections at just seven positions—to replace every known occurrence of two sense codons and a stop codon in the genome. Thus, we recode 18,214 codons to create an organism with a 61-codon genome; this organism uses 59 codons to encode the 20 amino acids, and enables the deletion of a previously essential transfer RNA

The Physics of the B Factories

This work is on the Physics of the B Factories. Part A of this book contains a brief description of the SLAC and KEK B Factories as well as their detectors, BaBar and Belle, and data taking related issues. Part B discusses tools and methods used by the experiments in order to obtain results. The results themselves can be found in Part C

Influences of housing attributes on house purchase intention, mediated by housing preference and gender as a moderator among consumers in Kota Kinabalu

This study has been done as partial fulfilment of the requirements for the postgraduate degree of Master in Business Administration (MBA) at the School of Business, Economics and Accountancy, University Malaysia Sabah (UMS). It dealt with issues related to the housing industry, within the study area, which was the district of Kota Kinabalu (KK), Sabah. The basis of the study was the Theory of Buyer Behaviour Model by Howard & Sheth (1973) and Loudon & Dell Bitta (1993). The Perception Construct of the Model consisted of the Independent Variables called Housing Attributes (House Features, Living Space, Distance and Environment). The Learning Construct consisted of the Mediating Variable (Housing Preference). The Output Construct consisted of the Dependent Variable (House Purchase Intention). The so called Exogenous Variables of the model consisted of four Independent Variables (Superstition-Numbers, Superstition-Ghosts, Developer and Financing) and a demographic factor (Gender). The results of the study found that: Five of the eight Independent Variables (House Features, Financing, Distance, Environment and Superstition-Numbers) have significant relationships with the Dependent Variable (House Purchase Intention); Housing Preference (Mediator) mediates on the relationships between two Independent Variables (House Features and Financing) and the Dependent Variable (House Purchase Intention); and the demographic factor of Gender (Moderator) moderates on the relationships between two Independent Variables (Distance and Developer) and the Dependent Variable (House Purchase Intention)