A microfluidic oligonucleotide synthesizer

De novo gene and genome synthesis enables the design of any sequence without the requirement of a pre-existing template as in traditional genetic engineering methods. The ability to mass produce synthetic genes holds great potential for biological research, but widespread availability of de novo DNA constructs is currently hampered by their high cost. In this work, we describe a microfluidic platform for parallel solid phase synthesis of oligonucleotides that can greatly reduce the cost of gene synthesis by reducing reagent consumption (by 100-fold) while maintaining a 100 pmol synthesis scale so there is no need for amplification before assembly. Sixteen oligonucleotides were synthesized in parallel on this platform and then successfully used in a ligation-mediated assembly method to generate DNA constructs 200 bp in length

Synthesis from specifications : basic concepts

The need has evolved for a synthesis tool at the computer system level. SpecSyn is one such tool. Basically, it will view the world as a set of chips communicating via protocols. Thus, an abstract specification would get synthesized into a set of one or more interconnected chips. From that point, detail is added to each chip's specification until its structure is synthesized or it is determined that a prefabricated chip similar in functionality can be used.Features of such a tool include executable specifications from which to synthesize, constraint driven partitioning of the specifications into components (chips) and synthesis of interfaces between them, translation into VHDL and synthesis into VHDL structures of micro-architectural components, and the use of other tools (e.g. MILO, a micro-architecture and logic optimizer, and LES, a layout expert system) to evaluate the quality of the chip layout generated from VHDL description.A major component of SpecSyn is SpecCharts, a high level specification language amenable to system level synthesis, able to represent designs from system to register transfer levels. The language consists of a hierarchy of states, represented in combined graphical and textual form, at the same time catering to the expression of concurrent behavior and specification of constraints. With it we have specified several Intel chips as well as higher level systems, and have found it to be quite powerful and easy to use.SpecSyn will have a graphical interface, from which the user can at any time view or edit a SpecChart, translate to VHDL and simulate, view statistics provided by estimators (such as area, speed, and pins), store and retrieve SpecCharts, apply basic Spec Chart operations, as well as apply the partitioning algorithms or interface synthesizer. Providing access to a wide range of tools, having a single language represent the design throughout the synthesis process, and having user specified constraints allow the user to have varying amounts of control over the synthesis process

A computational framework for aesthetical navigation in musical search space

Paper presented at 3rd AISB symposium on computational creativity, AISB 2016, 4-6th April, Sheffield. Abstract. This article addresses aspects of an ongoing project in the generation of artificial Persian (-like) music. Liquid Persian Music software (LPM) is a cellular automata based audio generator. In this paper LPM is discussed from the view point of future potentials of algorithmic composition and creativity. Liquid Persian Music is a creative tool, enabling exploration of emergent audio through new dimensions of music composition. Various configurations of the system produce different voices which resemble musical motives in many respects. Aesthetical measurements are determined by Zipf’s law in an evolutionary environment. Arranging these voices together for producing a musical corpus can be considered as a search problem in the LPM outputs space of musical possibilities. On this account, the issues toward defining the search space for LPM is studied throughout this paper

Position location and data collection system and method Patent

Development of telemetry system for position location and data acquisitio

SNAC-tag for sequence-specific chemical protein cleavage.

Site-specific protein cleavage is essential for many protein-production protocols and typically requires proteases. We report the development of a chemical protein-cleavage method that is achieved through the use of a sequence-specific nickel-assisted cleavage (SNAC)-tag. We demonstrate that the SNAC-tag can be inserted before both water-soluble and membrane proteins to achieve fusion protein cleavage under biocompatible conditions with efficiency comparable to that of enzymes, and that the method works even when enzymatic cleavages fail

Automatic generation of audio content for open learning resources

This paper describes how digital talking books (DTBs) with embedded functionality for learners can be generated from content structured according to the OU OpenLearn schema. It includes examples showing how a software transformation developed from open source components can be used to remix OpenLearn content, and discusses issues concerning the generation of synthesised speech for educational purposes. Factors which may affect the quality of a learner's experience with open educational audio resources are identified, and in conclusion plans for testing the effect of these factors are outlined

Identification of a Carcinoembryonic Antigen Gene Family in the Rat

The existence of a carcinoembryonic antigen (CEA)-like gene family in rat has been demonstrated through isolation and sequencing of the N- terminal domain exons of presumably five discrete genes (rnCGM1-5). This finding will allow for the first time the study of functional and clinical aspects of the tumor marker CEA and related antigens in an animal model. Sequence comparison with the corresponding regions of members of the human CEA gene family revealed a relatively low similarity at the amino acid level, which indicates rapid divergence of the CEA gene family during evolution and explains the lack of cross- reactivity of rat CEA-like antigens with antibodies directed against human CEA. The N-terminal domains of the rat CEA-like proteins show structural similarity to immunoglobulin variable domains, including the presence of hypervariable regions, which points to a possible receptor function of the CEA family members. Although so far only one of the five rat CEA-like genes could be shown to be transcriptionally active, multiple mRNA species derived from other members of the rat CEA-like gene family have been found to be differentially expressed in rat placenta and liver

Analysis of the Size of the Carcinoembryonic Antigen (CEA) Gene Family

Five members of the human CEA gene family [human pregnancy-specific β1-glycoprotein (PSβG), hsCGM1, 2, 3 and 4] have been isolated and identified through sequencing the exons containing their N-terminal domains. Sequence comparisons with published data for CEA and related molecules reveal the existence of highly-conserved gene subgroups within the CEA family. Together with published data eleven CEA family members have so far been determined. Apart from the highly conserved coding sequences, these genes also show strong sequence conservation in their introns, indicating a duplication of whole gene units during the evolution of the CEA gene family

Linguistic unit discovery from multi-modal inputs in unwritten languages: Summary of the "Speaking Rosetta" JSALT 2017 Workshop

We summarize the accomplishments of a multi-disciplinary workshop exploring the computational and scientific issues surrounding the discovery of linguistic units (subwords and words) in a language without orthography. We study the replacement of orthographic transcriptions by images and/or translated text in a well-resourced language to help unsupervised discovery from raw speech.Comment: Accepted to ICASSP 201