Abstract: Provided herein are methods for manipulating nucleotide sequences that permit greater control of sequence recombination compared to traditional methods, and related compositions. In one such method, a set of oligonucleotides and at least one primer are provided, where the primer has a first region uniquely complementary to a sequence of a first oligonucleotide of the set and a second region uniquely complementary to a second oligonucleotide of the set, combining the primer with an oligonucleotide comprising the first region of said first polynucleotide and an oligonucleotide comprising the second region of said second polynucleotide, and PCR amplifying to create a chimeric polynucleotide having some sequence from the first oligonucleotide and some sequence from the second oligonucleotide.

Abstract: Provided are methods for creating a synthetic gene for expression in a host organism, by providing a data set representative of codon pair translational kinetics for the host organism which includes translational kinetics values of the codon pairs utilized by the host organism, providing a desired polypeptide sequence for expression in the host organism, and generating a polynucleotide sequence encoding the polypeptide sequence by analyzing candidate nucleotides to select, where possible, codon pairs that are predicted not to cause a translational pause in the host organism, with reference to the data set, thereby providing a candidate polynucleotide sequence encoding the desired polypeptide. The methods can be performed using multiple parameter nucleotide sequence optimization methods, such as branch-and-bound methods for nucleotide sequence refinement.

Abstract: Graphical displays are provided of translational kinetics values of codon pairs in a host organism plotted as a function of polypeptide-encoding nucleotide sequence. Such translational kinetics values of codon pair frequencies correspond to the predicted translational pausing properties of a codon pair in a host organism. The graphical displays provided reflect the relative over-representation or under-representation of each codon pair in an organism, thereby facilitating analysis of translational kinetics of an mRNA into polypeptide by comparing graphical displays of different codon pairs in sequences encoding the polypeptide. The graphical displays of translational kinetics values also can display codon pair properties on comparable numerical scales, thereby facilitating analysis of translational kinetics of an mRNA into polypeptide in different organisms by comparing comparably scaled graphical displays of the same or different codon pairs in sequences encoding the polypeptide.

Abstract: Provided are methods for calculating codon pair translational kinetics values, creating a synthetic gene for expression in a host organism, and providing codon pair translational kinetic values. The methods typically are directed to refinement of statistical observed versus expected codon pair frequencies using one of several factors such as amino acid sequence homology, secondary or tertiary structural considerations, and empirical measurements. In some synthetic genes codon pairs are predicted not to cause a translational pause in the host organism, thereby providing a polynucleotide sequence encoding the desired polypeptide with desired translational kinetics properties. The methods can be performed using multiple parameter nucleotide sequence optimization methods, such as branch-and-bound methods for nucleotide sequence refinement.

Abstract: A method and system for synthesizing one or more pieces of DNA with desired sequences using pooled DNA, the method comprising a hierarchical division phase and a hierarchical assembly phase. In the division phase, the sequences of one or more pieces of DNA with desired nucleic acid sequences are recursively: divided into partially overlapping resulting pieces of DNA, and the resulting pieces of DNA assigned to a plurality of pools except after the after the final division step, wherein overlapping, adjacent resulting pieces of DNA are assigned to different pools. In the assembly phase, pools of oligonucleotides are obtained corresponding to the pools of the resulting pieces of DNA, and one or more pieces of DNA with desired sequences are assembled by overlap extension in the reverse order of the hierarchical division. Embodiments of the method combine the advantages of hierarchical assembly with the advantages of pooled oligonucleotides.

Abstract: A device is designed to facilitate operation of a separable slide fastener having a pair of stringers, respectively carrying first and second rows of interlocking elements, the rows respectively terminating at a stop member and a lug, the fastener including at least one slider moveable along the first row and having an aperture therethrough alignable with an aperture in the stop member when the slider is disposed in a terminal position. The device includes a handle and retention structure receivable in an aligning position in the apertures when the slider is in or is moved to its terminal position and engageable with the slider and the stop member to hold the slider in its terminal position so that the user does not have to manually do so during insertion of the lug into the apertures to join the stringers. When the lug is inserted it displaces the retention structure from the apertures. Several embodiments of the device are disclosed.

Abstract: Disclosed herein is a method for synthesizing a desired nucleic acid sequence. The method comprises dividing the desired sequence into a plurality of partially overlapping segments; optimizing the melting temperatures of the overlapping regions of each segment to disfavor hybridization to the overlapping segments which are non-adjacent in the desired sequence; allowing the overlapping regions of single stranded segments which are adjacent to one another in the desired sequence to hybridize to one another under conditions which disfavor hybridization of non-adjacent segments; and filling in, ligating, or repairing the gaps between the overlapping regions, thereby forming a double-stranded DNA with the desired sequence. Also disclosed is a method for preventing errors in the synthesis of the nucleic acid sequence.

Abstract: A network transmits viewable data objects to viewer receivers. The network includes a plurality of local servers to store subsets of the viewable data objects, a plurality of links to couple each local server to a set of viewer receivers without coupling the viewer receivers together, and at least, one storage server. Each local server transmits viewable data objects to viewer receivers. The storage server stores the viewable data objects and transmits a subset of the stored data objects to the local servers responsive to different expected demands there present.