Mutation discovery in the mouse using genetically guided array capture and resequencing

Forward genetics (phenotype-driven approaches) remain the primary source for allelic variants in the mouse. Unfortunately, the gap between observable phenotype and causative genotype limits the widespread use of spontaneous and induced mouse mutants. As alternatives to traditional positional cloning and mutation detection approaches, sequence capture and next-generation sequencing technologies can be used to rapidly sequence subsets of the genome. Application of these technologies to mutation detection efforts in the mouse has the potential to significantly reduce the time and resources required for mutation identification by abrogating the need for high-resolution genetic mapping, long-range PCR, and sequencing of individual PCR amplimers. As proof of principle, we used array-based sequence capture and pyrosequencing to sequence an allelic series from the classically defined Kit locus (~200 kb) from each of five noncomplementing Kit mutants (one known allele and four unknown alleles) and have successfully identified and validated a nonsynonymous coding mutation for each allele. These data represent the first documentation and validation that these new technologies can be used to efficiently discover causative mutations. Importantly, these data also provide a specific methodological foundation for the development of large-scale mutation detection efforts in the laboratory mouse. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users. M. D’Ascenzo and C. Meacham contributed equally to this work.     

Photosynthetic pathways in a midwestern rock outcrop succulent,Sedum nuttallianum Raf. (Crassulaceae)

Shoots of Sedum nuttallianum exhibited CAM^* acid fluctuations in the field. These nocturnal acid accumulations persisted in the laboratory under well-watered and water-stressed conditions. Simultaneous measurements of transpiration, however, indicated daytime stomatal opening and nocturnal stomatal closure. Measurements of CO₂ and H₂O vapor exchange continuously for six days after watering substantiated these results in part: the majority of CO₂ uptake occurred during the day early in the experiment; however, after several days without water, nighttime CO₂ uptake was stimulated and eventually was greater than the drastically reduced daytime CO₂ uptake. This nighttime uptake was never quite sufficient to account for all estimated increases in tissue acidity. Thus, a combination of CAM and CAM-cycling occurred early in the desiccation experiment. Evidence for CAM and a form of CAM-idling was found later in the experiment. Though nighttime CO₂ uptake occurred and persisted after only one day without water, rates were too low to alter the tissue ¹³C/¹²C value from a C₃-like number (–30). Thus, although CAM and CAM-idling may have survival value during extended droughts, shoots of S. nuttallianum apparently utilize the C₃ pathway to obtain most of their carbon.Abbreviations C₃ pathway - CO₂ fixation pathway in which an intermediate containing 3 carbon atoms is formed - CAM Crassulacean acid metabolism - Chl Chlorophyll - c_i internal CO₂ concentration - DW Dry weight - g_c mean conductance to CO₂ - FW Fresh weight - PAR Photosynthetically active radiation - SD Standard deviation - vpd Vapor pressure deficit - WUE Water use efficiency     

Purification of fatty acid methyl esters by high-performance liquid chromatography

The determination by gas chromatography (GC) of fatty acid methyl esters (FAMEs) prepared from complex biological samples is subject to interference from cholesterol. During sample injection on the GC system of FAMEs prepared from tissues that contain cholesterol, we observed a major contaminant that co-eluted with docosahexaenoic acid (DHA, 22:6n-3). To address this problem, FAMEs were purified on an amino-phase high-performance liquid chromatography (HPLC) column using a hexane–isopropanol gradient. The HPLC retention times for both the FAME fraction and cholesterol were stable and reproducible when the amino column was used for sample purification. The purified extracts were analyzed by GC without artifacts or impurity peaks after 50 analytical runs. The method described here will be useful for measurement of 22:6n-3 and other fatty acids important for studies of nutrition or pathology.     

NH(4)OH-KOH pulping mechanisms and kinetics of rice straw

The mechanisms and kinetics of NH(4)OH-KOH mixture pulping rice straw were studied. When aqueous ammonia was mixed with a small amount of caustic potash (ratio of 1:5), three distinct delignification phases were observed in the pulping process: a bulk delignification phase from the beginning of the cooking period to 100 degrees C, a supplementary delignification phase from 100 degrees C to 155 degrees C lasting a further 45 min, and a residual delignification phase until the end of the cooking period. There were two silica removal phases; the first phase was from the beginning of the cooking period to 100 degrees C and the second phase was from 100 degrees C to the end of the cooking period. The rate of delignification reaction was first order with respect to residual lignin and 0.3 order with respect to [OH(-)]. The silica removal was pseudo-first-order with respect to residual silica and 0.6 order with respect to [OH(-)]. The activation energies of the delignification and removal of silica reactions were 35.6 and 30.9 kJ/mol, respectively.     

Btn2, a Hook1 ortholog and potential Batten disease-related protein, mediates late endosome-Golgi protein sorting in yeast

BTN2 gene expression in the yeast Saccharomyces cerevisiae is up-regulated in response to the deletion of BTN1, which encodes the ortholog of a human Batten disease protein. We isolated Btn2 as a Snc1 v-SNARE binding protein using the two-hybrid assay and examined its role in intracellular protein trafficking. We show that Btn2 is an ortholog of the Drosophila and mammalian Hook1 proteins that interact with SNAREs, cargo proteins, and coat components involved in endosome-Golgi protein sorting. By immunoprecipitation, it was found that Btn2 bound the yeast endocytic SNARE complex (e.g., Snc1 and Snc2 [Snc1/2], Tlg1, Tlg2, and Vti1), the Snx4 sorting nexin, and retromer (e.g., Vps26 and Vps35). In in vitro binding assays, recombinant His(6)-tagged Btn2 bound glutathione S-transferase (GST)-Snc1 and GST-Vps26. Btn2-green fluorescent protein and Btn2-red fluorescent protein colocalize with Tlg2, Snx4, and Vps27 to a compartment adjacent to the vacuole that corresponds to a late endosome. The deletion of BTN2 blocks Yif1 retrieval back to the Golgi apparatus, while the localization of Ste2, Fur4, Snc1, Vps10, carboxypeptidases Y (CPY) and S (CPS), Sed5, and Sec7 is unaltered in btn2Delta cells. Yif1 delivery to the vacuole was observed in other late endosome-Golgi trafficking mutants, including ypt6Delta, snx4Delta, and vps26Delta cells. Thus, Btn2 facilitates specific protein retrieval from a late endosome to the Golgi apparatus, a process which may be adversely affected in patients with Batten disease.     

A WNTer wonderland in Snowbird

The Keystone Symposium on ;Wnt and beta-catenin signaling in development and disease' was held recently in Snowbird, UT, USA. Organized by Mariann Bienz and Hans Clevers, this meeting covered a wide range of topics, including Wnt protein biogenesis, Wnt receptors and signaling pathways, beta-catenin/Tcf complexes and gene expression, Wnt signaling in development, cancer, stem cell biology and regeneration, and therapeutics that target the Wnt/beta-catenin pathway.     

Tissue-specific differences in human transfer RNA expression

Over 450 transfer RNA (tRNA) genes have been annotated in the human genome. Reliable quantitation of tRNA levels in human samples using microarray methods presents a technical challenge. We have developed a microarray method to quantify tRNAs based on a fluorescent dye-labeling technique. The first-generation tRNA microarray consists of 42 probes for nuclear encoded tRNAs and 21 probes for mitochondrial encoded tRNAs. These probes cover tRNAs for all 20 amino acids and 11 isoacceptor families. Using this array, we report that the amounts of tRNA within the total cellular RNA vary widely among eight different human tissues. The brain expresses higher overall levels of nuclear encoded tRNAs than every tissue examined but one and higher levels of mitochondrial encoded tRNAs than every tissue examined. We found tissue-specific differences in the expression of individual tRNA species, and tRNAs decoding amino acids with similar chemical properties exhibited coordinated expression in distinct tissue types. Relative tRNA abundance exhibits a statistically significant correlation to the codon usage of a collection of highly expressed, tissue-specific genes in a subset of tissues or tRNA isoacceptors. Our findings demonstrate the existence of tissue-specific expression of tRNA species that strongly implicates a role for tRNA heterogeneity in regulating translation and possibly additional processes in vertebrate organisms.     

Preparation of a protected phosphoramidon precursor via an H-phosphonate coupling strategy

The preparation of a phosphoramidon precursor is described using a phosphorus(III) coupling protocol.     

Proteomic analysis of mouse growth plate cartilage

Cartilage is a highly specialized load-bearing tissue with a small number of cells and a high proportion of extracellular matrix (ECM). The abundance of heavily sulfated proteoglycans and a poorly soluble collagenous ECM presents a major technical challenge to 2-DE. Here we report proteomic analysis of mouse growth plate cartilage using novel methodology for tissue dissection and sample prefractionation. We have successfully resolved cartilage tissue extracts by 2-DE for the first time and identified cartilage ECM proteins by Western blotting and MS/MS.