High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides

Homologous DNA recombination is a fundamental, regenerative process within living organisms. However, in most organisms, homologous recombination is a rare event, requiring a complex set of reactions and extensive homology. We demonstrate in this paper that Beta protein of phage λ generates recombinants in chromosomal DNA by using synthetic single-stranded DNAs (ssDNA) as short as 30 bases long. This ssDNA recombination can be used to mutagenize or repair the chromosome with efficiencies that generate up to 6% recombinants among treated cells. Mechanistically, it appears that Beta protein, a Rad52-like protein, binds and anneals the ssDNA donor to a complementary single-strand near the DNA replication fork to generate the recombinant. This type of homologous recombination with ssDNA provides new avenues for studying and modifying genomes ranging from bacterial pathogens to eukaryotes. Beta protein and ssDNA may prove generally applicable for repairing DNA in many organisms.

4-Coumarate:Coenzyme A Ligase in Hybrid Poplar1 : Properties of Native Enzymes, cDNA Cloning, and Analysis of Recombinant Enzymes

The enzyme 4-coumarate:coenzyme A ligase (4CL) is important in providing activated thioester substrates for phenylpropanoid natural product biosynthesis. We tested different hybrid poplar (Populus trichocarpa × Populus deltoides) tissues for the presence of 4CL isoforms by fast-protein liquid chromatography and detected a minimum of three 4CL isoforms. These isoforms shared similar hydroxycinnamic acid substrate-utilization profiles and were all inactive against sinapic acid, but instability of the native forms precluded extensive further analysis. 4CL cDNA clones were isolated and grouped into two major classes, the predicted amino acid sequences of which were 86% identical. Genomic Southern blots showed that the cDNA classes represent two poplar 4CL genes, and northern blots provided evidence for their differential expression. Recombinant enzymes corresponding to the two genes were expressed using a baculovirus system. The two recombinant proteins had substrate utilization profiles similar to each other and to the native poplar 4CL isoforms (4-coumaric acid > ferulic acid > caffeic acid; there was no conversion of sinapic acid), except that both had relatively high activity toward cinnamic acid. These results are discussed with respect to the role of 4CL in the partitioning of carbon in phenylpropanoid metabolism.

Mass extinctions and supernova explosions.

In a recent contribution to this journal Ellis and Schramm [Ellis, J. & Schramm, D. N. (1995) Proc. Natl. Acad. Sci. USA 92, 235-238] claim that supernova explosions can cause massive biological extinctions as a result of strongly enhanced stratospheric NOx (NO + NO2) production by accompanying galactic cosmic rays. They suggested that these NOx productions which would last over several centuries and occur once every few hundred million years would result in ozone depletions of about 95%, leading to vastly increased levels of biologically damaging solar ultraviolet radiation. Our detailed model calculations show, however, substantially smaller ozone depletions ranging from at most 60% at high latitudes to below 20% at the equator.

Functional domain analysis of glass, a zinc-finger-containing transcription factor in Drosophila.

The glass gene is required for proper photo-receptor differentiation during development of the Drosophila eye glass codes for a DNA-binding protein containing five zinc fingers that we show is a transcriptional activator. A comparison of the sequences of the glass genes from two species of Drosophila and a detailed functional domain analysis of the Drosophila melanogaster glass gene reveal that both the DNA-binding domain and the transcriptional-activation domain are highly conserved between the two species. Analysis of the DNA-binding domain of glass indicates that the three carboxyl-terminal zinc fingers alone are necessary and sufficient for DNA binding. We also show that a deletion mutant of glass containing only the DNA-binding domain can behave in a dominant-negative manner both in vivo and in a cell culture assay that measures transcriptional activation.

Contrasting complexity of two rust resistance loci in flax.

DNA probes from the L6 rust resistance gene of flax (Linum usitatissimum) hybridize to resistance genes at the unlinked M locus, indicating sequence similarities between genes at the two loci. Genetic and molecular data indicate that the L locus is simple and contains a single gene with 13 alleles and that the M locus is complex and contains a tandem array of genes of similar sequence. Thus the evolution of these two related loci has been different. The consequence of the contrasting structures of the L and M loci on the evolution of different rust resistance specificities can now be investigated at the molecular level

How one juvenile court helps to make child labor legislation effective

by Mabel Brown Ellis.

Student lecture notes of Benjamin Peirce, 1797-1798

This collection contains approximately twenty-three handwritten lecture summaries on six leaves made by Harvard undergraduate Benjamin Peirce between September 1797 and November 22, 1798. The summaries generally provide a few sentences describing the topic covered and primarily pertain to lectures on English grammar delivered by Eliphalet Pearson, the Hollis Professor of Hebrew and other Oriental Languages. There are also summaries for single lectures by David Tappan, the Hollis Professor Divinity; Samuel Webber, the Hollis Professor of Mathematics and Natural Philosophy; and John Snelling Popkin, the Greek Tutor from 1795 to 1798, and later the Eliot Professor of Greek Literature. There is also an undated summary of a lecture by Benjamin Waterhouse, the Hersey Professor of Theory and Practice of Physic.

Massachusetts, Rhode Island, and Connecticut, Postal Statistics Map, 1876 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: The "centennial" postal statistical map of Massachusetts, Rhode Island and Connecticut : showing railroads, post routes and offices together with population and valuation of cities and towns. It compiled and published by M.G. Cook and Frank O. Ellis in 1876. Scale [ca. 1:422,400]. Covers also portions of New York, Vermont, and New Hampshire. The image inside the map neatline is georeferenced to the surface of the earth and fit to the USA Contiguous Albers Equal Area Conic projection (Meters). All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, or other information associated with the principal map. This map shows features such as railroads, post routes and offices together with population and valuation of cities and towns, distances between post offices, drainage, state, county, and town boundaries, and more. Includes table of population and valuation by county and cities of Boston and vicinity, and table of distances. This layer is part of a selection of digitally scanned and georeferenced historic maps of New England from the Harvard Map Collection. These maps typically portray both natural and manmade features. The selection represents a range of regions, originators, ground condition dates, scales, and purposes.

London, England, 1767 (Raster Image)

This layer is a georeferenced raster image of the historic paper map entitled: The London guide, or, a pocket plan of the cities of London & Westminster & borough of Southwark : with the new buildings &c. to the year 1767, by J. Ellis. It was printed for Carington Bowles in 1767. Scale [ca. 1:15,200]. Covers City of London and portions of Westminster, Camden, Islington, Hackney, Tower Hamlets, Southwark, and Lambeth. The image inside the map neatline is georeferenced to the surface of the earth and fit to the British National Grid coordinate system (British National Grid, Airy Spheroid OSGB (1936) Datum). All map collar and inset information is also available as part of the raster image, including any inset maps, profiles, statistical tables, directories, text, illustrations, index maps, legends, or other information associated with the principal map. This map shows features such as roads, bridges, drainage, land cover, built-up areas, selected public buildings, and more. Includes "A Table of References to the Churches and Principal Buildings shewing their Situation in the above Plan." This layer is part of a selection of digitally scanned and georeferenced historic maps from The Harvard Map Collection as part of the Imaging the Urban Environment project. Maps selected for this project represent major urban areas and cities of the world, at various time periods. These maps typically portray both natural and manmade features at a large scale. The selection represents a range of regions, originators, ground condition dates, scales, and purposes.

Panjāh bāb-i sulṭānī : manuscript, undated

According to the colophon (f. 76r), written on 5 Shawwāl 860 AH [September 5, 1456 AD]. There is a note in a later hand that says, "Hādhā al-kitāb bi-khaṭṭ al-muʼallif" (f. 75r).

Need To Be Adored

Faced with a diagnosis of multiple sclerosis, I began with the objective of discovering methods for creating art that were still accessible to me. Along the way, I encountered others who had travelled this road before me. Their experiences led me to examine, not only my art, but also my political orientations, my love obligations and my transitioning self. In my varied art pieces, I conjure something from diverse sources and different worldviews, including contemporary feminist performance art and disability cultural theory. My thesis is a project. I make things: puppets, videos and performances, which included the exhibition, Need to be Adored (2014), staged in the digital media lab of the Isabel Bader Centre for the Performing Arts in Kingston, Ontario, Canada. The exhibition introduced thirteen of my puppets and a thirty-two-minute looped video. Following the exhibition, I put the puppets away and spent two years reading. Finally, taking my inspiration from Carolyn Ellis’s The Autoethnographic I (Ellis 2004), I turned my processes into words. I wrote out my experiences. I created an alternative text of my identity from an able-bodied cis-identified woman into a disabled trans-feminist artist academic. The writing required an uncomfortably intimate examination of my life. Nothing less than complete honesty would allow me to understand my new location. The resulting text is a lyrical and sometimes whimsical flow of consciousness that invites the reader to imagine what it might be like to engage in such a candid review of everything one holds close to one’s heart. Contained within are all my identities. In this text I let some out. This is a story of unsettling. I am working on my art practices, creating a cast of characters from cloth. Puppets. El becomes the exulted main character of a fictional accounting. She uncovers her queer roots and begins to see that she is at the centre of a very strange geography. Her desire to make film is revealed as she re-remembers her childhood through a disability lens.

Comparisons between analogue and numerical models of thrust wedge development

Analogue and finite element numerical models with frictional and viscous properties are used to model thrust wedge development. Comparison between model types yields valuable information about analogue model evolution, scaling laws and the relative strengths and limitations of the techniques. Both model types show a marked contrast in structural style between ‘frictional-viscous domains’ underlain by a thin viscous layer and purely ‘frictional domains’. Closely spaced thrusts form a narrow and highly asymmetric fold-and-thrust belt in the frictional domain, characterized by in-sequence propagation of forward thrusts. In contrast, the frictional-viscous domain shows a wide and low taper wedge and a thrust belt with a more symmetrical vergence, with both forward and back thrusts. The frictional-viscous domain numerical models show that the viscous layer initially simple shears as deformation propagates along it, while localized deformation resulting in the formation of a pop-up structure occurs in the overlying frictional layers. In both domains, thrust shear zones in the numerical model are generally steeper than the equivalent faults in the analogue model, because the finite element code uses a non-associated plasticity flow law. Nevertheless, the qualitative agreement between analogue and numerical models is encouraging. It shows that the continuum approximation used in numerical models can be used to model frictional materials, such as sand, provided caution is taken to properly scale the experiments, and some of the limitations are taken into account.