Drop deployment system for crystal growth apparatus

A crystal growth apparatus is presented. It utilizes a vapor diffusion method for growing protein crystals, and particularly such an apparatus wherein a ball mixer is used to mix the fluids that form a drop within which crystals are grown. Particular novelty of this invention lies in utilizing a ball mixer to completely mix the precipitate and protein solutions prior to forming the drop. Additional novelty lies in details of construction of the vials, the fluid deployment system, and the fluid storage system of the preferred embodiment

X ray sensitive area detection device

A radiation sensitive area detection device is disclosed which comprises a phosphor-containing film capable of receiving and storing an image formed by a pattern of incoming x rays, UV, or other radiation falling on the film. The device is capable of fluorescing in response to stimulation by a light source in a manner directly proportional to the stored radiation pattern. The device includes: (1) a light source capable of projecting light or other appropriate electromagnetic wave on the film so as to cause it to fluoresce; (2) a means to focus the fluoresced light coming from the phosphor-containing film after light stimulation; and (3) at least one charged coupled detector or other detecting element capable of receiving and digitizing the pattern of fluoresced light coming from the phosphor-containing film. The device will be able to generate superior x ray images of high resolution from a crystal or other sample and will be particularly advantageous in that instantaneous near-real-time images of rapidly deteriorating samples can be obtained. Furthermore, the device can be made compact and sturdy, thus capable of carrying out x ray or other radiation imaging under a variety of conditions, including those experienced in space

Drop deployment system for crystal growth apparatus

This invention relates to a crystal growth apparatus (10) generally used for growing protein crystals wherein a vapor diffusion method is used for growing the crystals. In this apparatus, a precipitating solution and a solution containing dissolved crystalline material are stored in separate vials (12, 14), each having a resilient diaphragm (28) across one end and an opening (24) with a puncturable septum (26) thereacross at an opposite end. The vials are placed in receptacles (30) having a manifold (41) with a manifold diaphragm (42) in contact with the vial diaphragm at one end of the receptacle and a hollow needle (36) for puncturing the septum at the other end of the manifold. The needles of each vial communicate with a ball mixer (40) that mixes the precipitate and protein solutions and directs the mixed solution to a drop support (64) disposed in a crystal growth chamber (16), the drop support being a tube with an inner bevelled surface (66) that provides more support for the drop (68) than the tubes of the prior art. A sealable storage region (70) intermediate the drop support and mixer provides storage of the drop (68) and the grown crystals

The time scale of recombination rate evolution in great apes

We present three linkage-disequilibrium (LD)-based recombination maps generated using whole-genome sequence data from 10 Nigerian chimpanzees, 13 bonobos, and 15 western gorillas, collected as part of the Great Ape Genome Project (Prado-Martinez J, et al. 2013. Great ape genetic diversity and population history. Nature 499:471-475). We also identified species-specific recombination hotspots in each group using a modified LDhot framework, which greatly improves statistical power to detect hotspots at varying strengths. We show that fewer hotspots are shared among chimpanzee subspecies than within human populations, further narrowing the time scale of complete hotspot turnover. Further, using species-specific PRDM9 sequences to predict potential binding sites (PBS), we show higher predicted PRDM9 binding in recombination hotspots as compared to matched cold spot regions in multiple great ape species, including at least one chimpanzee subspecies. We found that correlations between broad-scale recombination rates decline more rapidly than nucleotide divergence between species. We also compared the skew of recombination rates at centromeres and telomeres between species and show a skew from chromosome means extending as far as 10-15Mb from chromosome ends. Further, we examined broad-scale recombination rate changes near a translocation in gorillas and found minimal differences as compared to other great ape species perhaps because the coordinates relative to the chromosome ends were unaffected. Finally, on the basis of multiple linear regression analysis, we found that various correlates of recombination rate persist throughout the African great apes including repeats, diversity, and divergence. Our study is the first to analyze within- And between-species genome-wide recombination rate variation in several close relatives

Anurans from the Lower Cretaceous Jehol Group of western Liaoning, China

BACKGROUND: To date, the Lower Cretaceous Jehol Group of western Liaoning, China has yielded five monotypic genera of anurans, including Liaobatrachus grabaui, Callobatrachus sanyanensis, Mesophryne beipiaoensis, Dalianbatrachus mengi, and Yizhoubatrachus macilentus. However, the validity and distinctness of these taxa have been questioned. METHODOLOGY/PRINCIPAL FINDING: We provide a comprehensive analysis of the Jehol frogs that includes a re-examination of the published taxa as well as an examination of a number of new specimens that have been collected over the past 10 years. The results show that the five previously named taxa can be referred to three species of one genus-Liaobatrachus grabaui, L. beipiaoensis comb. nov. and L. macilentus comb. nov.. The diagnosis of Liaobatrachus is revised, and a new diagnosis is provided for each species of this genus. We also establish Liaobatrachus zhaoi sp. nov., on the basis of a dozen well-preserved specimens from a new locality. This taxon is distinguished by a unique combination of characteristics, including relatively long hind limbs, a rounded rather than triangular acetabulum, and a gradually-tapering cultriform process of the parasphenoid. In addition, an unnamed frog from a higher horizon, which has narrow sacral diapophyses and particularly long legs, is different from Liaobatrachus and represents another form of anuran in the Jehol Biota. CONCLUSION/SIGNIFICANCE: Comparisons with other Mesozoic and extant anurans and the primary phylogenetic analysis both suggest that Liaobatrachus is a member of the anuran crown-group and forms a polytomy with leiopelmatids (Ascaphus and Leiopelma) and the remaining crown-group anurans (Lalagobatrachia).Liping Dong, Zbyněk Roček, Yuan Wang, Marc E H. Jone

Fluorescent Approaches to High Throughput Crystallography

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, 51%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear hits. Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality

Ionic Liquids as Protein Crystallization Additives

Among its attributes, the mythical philosopher’s stone is supposedly capable of turning base metals to gold or silver. In an analogous fashion, we are finding that protein crystallization optimization using ionic liquids (ILs) often results in the conversion of base protein precipitate to crystals. Recombinant inorganic pyrophosphatases (8 of the 11 proteins) from pathogenic bacteria as well as several other proteins were tested for optimization by 23 ILs, plus a dH2O control, at IL concentrations of 0.1, 0.2, and 0.4 M. The ILs were used as additives, and all proteins were crystallized in the presence of at least one IL. For 9 of the 11 proteins, precipitation conditions were converted to crystals with at least one IL. The ILs could be ranked in order of effectiveness, and it was found that ~83% of the precipitation-derived crystallization conditions could be obtained with a suite of just eight ILs, with the top two ILs accounting for ~50% of the hits. Structural trends were found in the effectiveness of the ILs, with shorter-alkyl-chain ILs being more effective. The two top ILs, accounting for ~50% of the unique crystallization results, were choline dihydrogen phosphate and 1-butyl-3-methylimidazolium tetrafluoroborate. Curiously, however, a butyl group was present on the cation of four of the top eight ILs

A Dialysis Technique for Determining Aggregate Concentrations in Crystallizing Protein Solutions

We have adapted a dialysis technique which provides aggregate concentrations of protein molecules in solutions which lead to crystal growth. In dialysis, the flux across a semipermeable membrane is directly proportional to the concentration of the diffusible solute inside the bag provided that the solute concentration in the bulk solution is infinitely dilute. Using membranes of varying porosity, the concentrations of different size solutes can be measured by measuring the flux rate across the membrane. We have used this technique to independently measure the concentrations of monomers, dimers, trimers and higher aggregates of lysozyme in both 1% NaCI and 3% NaCI (0.1 M NaAc, pH4) using 25 K and 50 K molecular weight cut-off membranes. We compare these concentration profiles with (110) face growth rate data under the same conditions

Fluorescent Applications to Crystallization

By covalently modifying a subpopulation, less than or equal to 1%, of a macromolecule with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification, and tests with model proteins have shown that labeling u to 5 percent of the protein molecules does not affect the X-ray data quality obtained . The presence of the trace fluorescent label gives a number of advantages. Since the label is covalently attached to the protein molecules, it "tracks" the protein s response to the crystallization conditions. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination crystals show up as bright objects against a darker background. Non-protein structures, such as salt crystals, do not show up under fluorescent illumination. Crystals have the highest protein concentration and are readily observed against less bright precipitated phases, which under white light illumination may obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries as the protein or protein structures is all that shows up. Fluorescence intensity is a faster search parameter, whether visually or by automated methods, than looking for crystalline features. Preliminary tests, using model proteins, indicates that we can use high fluorescence intensity regions, in the absence of clear crystalline features or "hits", as a means for determining potential lead conditions. A working hypothesis is that more rapid amorphous precipitation kinetics may overwhelm and trap more slowly formed ordered assemblies, which subsequently show up as regions of brighter fluorescence intensity. Experiments are now being carried out to test this approach using a wider range, of proteins. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons