Codon-precise, synthetic, antibody fragment libraries built using automated hexamer codon additions and validated through next generation sequencing

We have previously described ProxiMAX, a technology that enables the fabrication of precise, combinatorial gene libraries via codon-by-codon saturation mutagenesis. ProxiMAX was originally performed using manual, enzymatic transfer of codons via blunt-end ligation. Here we present Colibra™: an automated, proprietary version of ProxiMAX used specifically for antibody library generation, in which double-codon hexamers are transferred during the saturation cycling process. The reduction in process complexity, resulting library quality and an unprecedented saturation of up to 24 contiguous codons are described. Utility of the method is demonstrated via fabrication of complementarity determining regions (CDR) in antibody fragment libraries and next generation sequencing (NGS) analysis of their quality and diversity.

Green operations strategy of a luxury car manufacturer

This paper investigates the strategic environmental decisions of a luxury car manufacturer. Through case study research, the investigation sheds light on why and how the company is adopting green technologies. Being pressured by different stakeholders to become greener, luxury car manufacturers carry significant opportunities for environmental improvement given the nature of their manufacturing processes and products. Because of their low-volume production, manufacturers may be able to increase output and still reduce overall emissions when compared to high-volume manufacturers. In the case study company this was found to be possible only because of new ideas brought by a change in ownership. Luxury manufacturers may also be a test-bed for the development and experimentation of green technologies as part of a strategic approach to environmental initiatives. This paper contributes to the fields of green technology adoption and operations strategy in automotive manufacturing groups.

Operation sequencing optimization for five-axis prismatic parts using a particle swarm optimization approach

Operation sequencing is one of the crucial tasks in process planning. However, it is an intractable process to identify an optimized operation sequence with minimal machining cost in a vast search space constrained by manufacturing conditions. Also, the information represented by current process plan models for three-axis machining is not sufficient for five-axis machining owing to the two extra degrees of freedom and the difficulty of set-up planning. In this paper, a representation of process plans for five-axis machining is proposed, and the complicated operation sequencing process is modelled as a combinatorial optimization problem. A modern evolutionary algorithm, i.e. the particle swarm optimization (PSO) algorithm, has been employed and modified to solve it effectively. Initial process plan solutions are formed and encoded into particles of the PSO algorithm. The particles 'fly' intelligently in the search space to achieve the best sequence according to the optimization strategies of the PSO algorithm. Meanwhile, to explore the search space comprehensively and to avoid being trapped into local optima, several new operators have been developed to improve the particle movements to form a modified PSO algorithm. A case study used to verify the performance of the modified PSO algorithm shows that the developed PSO can generate satisfactory results in optimizing the process planning problem. © IMechE 2009.

Selection, staging and sequencing in the recent Chinese privatization

Selection in privatization is a decision-making process of choosing state-owned enterprises (SOEs), prioritizing and sequencing privatizing events, and determining the extent of private ownership in partial privatization. We investigate this process in an important but rarely studied case of China. Based on the SOE population over 1998-2008, we track 49,456 wholly SOEs and identify 9,359 privatization cases over time. Our econometric analysis concludes: (i) The privatization selection is a complex decision-making process in which local governments balance between various economic, financial and political objectives. (ii) In the recent Chinese privatization, firm performance relates to the selection, staging and sequencing in privatization in an inverted-U fashion. The worse and the best performing SOEs are more likely to remain state-owned, maintain higher state holding when privatized, and are less likely to be privatized later in time. These patterns suggest the privatization reform slowdown and the underlying changes in the privatization policy.

Manageable Workflows for Processing Parallel Sequencing Data

ACM Computing Classification System (1998): D.2.11, D.1.3, D.3.1, J.3, C.2.4.

Eco-car : a perfect vehicle for technical design teaching?

Design methods and tools are generally best learned and developed experientially [1]. Finding appropriate vehicles for delivering these to students is becoming increasingly challenging, especially when considering only those that will enthuse, intrigue and inspire. This paper traces the development of different eco-car design and build projects which competed in the Shell Eco-Marathon. The cars provided opportunities for experiential learning through a formal learning cycle of CDIO (Conceive, Design, Implement, Operate) or the more traditional understand, explore, create, validate, with both teams developing a functional finished prototype. Lessons learned were applied through the design of a third and fourth eco-car using experimental techniques with bio-composites, combining the knowledge of fibre reinforced composite materials and adhesives with the plywood construction techniques of the two teams. The paper discusses the importance of applying materials and techniques to a real world problem. It will also explore how eco-car and comparing traditional materials and construction techniques with high tech composite materials is an ideal teaching, learning and assessment vehicle for technical design techniques.

The evolution of the car-making industry

Mass-production, cars, pollution – they all have long become well known and well connected phenomena of the modern life. Nowadays the people can also add to the list such items like awareness, scientific approach, long-term thinking, and environmental responsibility. They are surrounded by a multitude of consumer goods, most of which are produced in a scientific manner, and all of which will more sooner than later end up in the garbage. Cars are the most noticeable – both by size and by numbers – and also the most expensive of all the mass products in people’s view. For many of them they are a clear target for reprimand and regulation, and, as a result, the automotive industry is being increasingly brought under bureaucratic control, together with its whole supplier and distributor network. The author started writing this article in an attempt to place the above process under scrutiny, because it is his firm belief that similar measures, similar tough governmental control will inevitably spill over to other industries, which at the moment are producing more inconspicuous, but still polluting products. The present paper shows the relationship between car-making, supply chain management and the efforts of public administration to protect the environment – a connection with clear practical implications.

Tittmann and the 'Tiger Car' : competing conceptions of modernity in Haiti, 1946-50

The purpose of this project was to address the lack of scholarship on mid-twentieth century Haitian history and illustrate its significance. It employs primary and secondary sources in shaping a Gramscian historical narrative. Ideas of "everyday resistance" and internal and external politics are also be of significance to this work. In mid-twentieth century Haiti, the black-nationalist rhetoric of noirisme became the dominant political ideology. Blackness was amorphous and its application to politics was dependent upon class. In proclaiming blackness the average Haitian was attacking the class schism that beleaguered the island. Yet for the elite noirismewas a conduit to modernity and a useful tool for muting the division between rich and poor. With the election of Dumarsais Estimé in 1946, dialogue between the U.S. government, the Haitian elite, and the masses, relative to definitions of modernity played out within the new political reality of noirisme.

Response of spring diatoms to CO2 availability in the Western North Pacific as determined by next-generation sequencing

Next-generation sequencing (NGS) technologies have enabled us to determine phytoplankton community compositions at high resolution. However, few studies have adopted this approach to assess the responses of natural phytoplankton communities to environmental change. Here, we report the impact of different CO2 levels on spring diatoms in the Oyashio region of the western North Pacific as estimated by NGS of the diatom-specific rbcL gene (DNA), which encodes the large subunit of RubisCO. We also examined the abundance and composition of rbcL transcripts (cDNA) in diatoms to assess their physiological responses to changing CO2 levels. A short-term (3-day) incubation experiment was carried out on-deck using surface Oyashio waters under different pCO2 levels (180, 350, 750, and 1000 µatm) in May 2011. During the incubation, the transcript abundance of the diatom-specific rbcL gene decreased with an increase in seawater pCO2 levels. These results suggest that CO2 fixation capacity of diatoms decreased rapidly under elevated CO2 levels. In the high CO2 treatments (750 and 1000 µatm), diversity of diatom-specific rbcL gene and its transcripts decreased relative to the control treatment (350µatm), as well as contributions of Chaetocerataceae, Thalassiosiraceae, and Fragilariaceae to the total population, but the contributions of Bacillariaceae increased. In the low CO2 treatment, contributions of Bacillariaceae also increased together with other eukaryotes. These suggest that changes in CO2 levels can alter the community composition of spring diatoms in the Oyashio region. Overall, the NGS technology provided us a deeper understanding of the response of diatoms to changes in CO2 levels in terms of their community composition, diversity, and photosynthetic physiology.

Targeted sequencing for high-resolution evolutionary analyses following genome duplication in salmonid fish : Proof of concept for key components of the insulin-like growth factor axis

Acknowledgements This study was funded by a Natural Environment Research Council grant (NERC, project code: NBAF704). FML is funded by a NERC Doctoral Training Grant (Project Reference: NE/L50175X/1). RLS was an undergraduate student at the University of Aberdeen and benefitted from financial support from the School of Biological Sciences. DJM is indebted to Dr. Steven Weiss (University of Graz, Austria), Dr. Takashi Yada (National Research Institute of Fisheries Science, Japan), Dr. Robert Devlin (Fisheries and Oceans Canada, Canada), Prof. Samuel Martin (University of Aberdeen, UK), Mr. Neil Lincoln (Environment Agency, UK) and Prof. Colin Adams/Mr. Stuart Wilson (University of Glasgow, UK) for providing salmonid material or assisting with its sampling. We are grateful to staff at the Centre for Genomics Research (University of Liverpool, UK) (i.e. NERC Biomolecular Analysis Facility – Liverpool; NBAF-Liverpool) for performing sequence capture/Illumina sequencing and providing us with details on associated methods that were incorporated into the manuscript. Finally, we are grateful to the organizers of the Society of Experimental Biology Satellite meeting 'Genome-powered perspectives in integrative physiology and evolutionary biology' (held in Prague, July 2015) for inviting us to contribute to this special edition of Marine Genomics and hosting a really stimulating meeting.

Isolation and Characterization of Microsatellite DNA Markers in the Deep-Sea Amphipod Paralicella tenuipes by Illumina MiSeq Sequencing

Funding This work was supported by the HADEEP projects, funded by the Nippon Foundation, Japan (2009765188), the Natural Environmental Research Council, UK (NE/E007171/1) and the Total Foundation, France. We acknowledge additional support from the Marine Alliance for Science and Technology for Scotland (MASTS) funded by the Scottish Funding Council (Ref: HR09011) and contributing institutions. We also acknowledge support from the Leverhulme Trust to SBP. Additional sea time was supported by NIWA’s ‘Impact of Resource Use on Vulnerable Deep-Sea Communities’ project (CO1_0906)

Genome-wide association of multiple complex traits in outbred mice by ultra low-coverage sequencing

We thank the High-Throughput Genomics Group at the Wellcome Trust Centre for Human Genetics and the Wellcome Trust Sanger Institute for the generation of the sequencing data. This work was funded by Wellcome Trust grant 090532/Z/09/Z (J.F.). Primary phenotyping of the mice was supported by the Mary Lyon Centre and Mammalian Genetics Unit (Medical Research Council, UK Hub grant G0900747 91070 and Medical Research Council, UK grant MC U142684172). D.A.B acknowledges support from NIH R01AR056280. The sleep work was supported by the state of Vaud (Switzerland) and the Swiss National Science Foundation (SNF 14694 and 136201 to P.F.). The ECG work was supported by the Netherlands CardioVascular Research Initiative (Dutch Heart Foundation, Dutch Federation of University Medical Centres, the Netherlands Organization for Health Research and Development, and the Royal Netherlands Academy of Sciences) PREDICT project, InterUniversity Cardiology Institute of the Netherlands (ICIN; 061.02; C.A.R., C.R.B). Na Cai is supported by the Agency of Science, Technology and Research (A*STAR) Graduate Academy. The authors wish to acknowledge excellent technical assistance from: Ayako Kurioka, Leo Swadling, Catherine de Lara, James Ussher, Rachel Townsend, Sima Lionikaite, Ausra S. Lionikiene, Rianne Wolswinkel and Inge van der Made. We would like to thank Thomas M Keane and Anthony G Doran for their help in annotating variants and adding the FVB/NJ strain to the Mouse Genomes Project.

A new method to calculate the periodic steady state of sequencing batch reactors for biological wastewater treatment : model development and applications

Peer reviewed

Janet Guthrie, professional race car driver

General note: Title and date provided by Bettye Lane.