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51.
O'Rourke SM Yochem J Connolly AA Price MH Carter L Lowry JB Turnbull DW Kamps-Hughes N Stiffler N Miller MR Johnson EA Bowerman B 《Genetics》2011,189(3):767-778
Forward genetic screens provide a powerful approach for inferring gene function on the basis of the phenotypes associated with mutated genes. However, determining the causal mutation by traditional mapping and candidate gene sequencing is often the rate-limiting step, especially when analyzing many mutants. We report two genomic approaches for more rapidly determining the identity of the affected genes in Caenorhabditis elegans mutants. First, we report our use of restriction site-associated DNA (RAD) polymorphism markers for rapidly mapping mutations after chemical mutagenesis and mutant isolation. Second, we describe our use of genomic interval pull-down sequencing (GIPS) to selectively capture and sequence megabase-sized portions of a mutant genome. Together, these two methods provide a rapid and cost-effective approach for positional cloning of C. elegans mutant loci, and are also applicable to other genetic model systems. 相似文献
52.
Xiao-Qi Zhang Chengdao Li Joe Panozzo Sharon Westcott Guoping Zhang Amy Tay Rudi Appels Mike Jones Reg Lance 《Molecular breeding : new strategies in plant improvement》2011,27(1):1-9
The terminal region of barley chromosome 5HL controls malt extract, diastatic power, free amino acid nitrogen, alpha-amylase activity, seed dormancy and pre-harvest sprouting. Comparative analysis of the barley and rice maps has established that the terminal region of barley chromosome 5HL is syntenic to rice chromosome 3L near the telomere end. The rice BAC (Bacterial Artificial Chromosome) sequences covering the region of chromosome 3L were used to search barley expressed sequenced tags database. Thirty-three genes were amplified by PCR (polymerase chain reaction) with the primers designed from barley ESTs (expressed sequence tag). Comparison of the sequences of the PCR generated DNA fragments revealed polymorphisms including single nucleotide polymorphism (SNP), insertions or deletions between the barley varieties. Seven new PCR based molecular markers were developed and mapped within 10 cM in three doubled haploid barley populations (Stirling × Harrington, Baudin × AC Metcalfe and Chebec × Harrington). The mapped genes maintain the micro-syntenic relationship between barley and rice. These gene specific markers provide simple and efficient tools for germplasm characterization and marker-assisted selection for barley malting quality, and ultimately lead to isolation and identification of the major gene(s) controlling multiple quality traits on barley chromosome 5HL. 相似文献
53.
Rylie B. Walsh Erica C. Dresselhaus Agata N. Becalska Matthew J. Zunitch Cassandra R. Blanchette Amy L. Scalera Tania Lemos So Min Lee Julia Apiki ShiYu Wang Berith Isaac Anna Yeh Kate Koles Avital A. Rodal 《The Journal of cell biology》2021,220(8)
Neuronal extracellular vesicles (EVs) play important roles in intercellular communication and pathogenic protein propagation in neurological disease. However, it remains unclear how cargoes are selectively packaged into neuronal EVs. Here, we show that loss of the endosomal retromer complex leads to accumulation of EV cargoes including amyloid precursor protein (APP), synaptotagmin-4 (Syt4), and neuroglian (Nrg) at Drosophila motor neuron presynaptic terminals, resulting in increased release of these cargoes in EVs. By systematically exploring known retromer-dependent trafficking mechanisms, we show that EV regulation is separable from several previously identified roles of neuronal retromer. Conversely, mutations in rab11 and rab4, regulators of endosome-plasma membrane recycling, cause reduced EV cargo levels, and rab11 suppresses cargo accumulation in retromer mutants. Thus, EV traffic reflects a balance between Rab4/Rab11 recycling and retromer-dependent removal from EV precursor compartments. Our data shed light on previous studies implicating Rab11 and retromer in competing pathways in Alzheimer’s disease, and suggest that misregulated EV traffic may be an underlying defect. 相似文献
54.
Colleran A Ryan A O'Gorman A Mureau C Liptrot C Dockery P Fearnhead H Egan LJ 《The Journal of biological chemistry》2011,286(26):22886-22893
55.
GRP78, a master regulator of the unfolded protein response (UPR) and cell signaling, is required for inner cell mass survival during early embryonic development. However, little is known about its role in adult hematopoietic stem cells (HSCs) and hematopoiesis. Here we generated a conditional knockout mouse model that acutely deletes Grp78 in the adult hematopoietic system. Acute GRP78 ablation resulted in a significant reduction of HSCs, common lymphoid and myeloid progenitors, and lymphoid cell populations in the mutant mice. The GRP78-null induced reduction of the HSC pool could be attributed to increased apoptosis. Chimeric mice with Grp78 deletion only in the hematopoietic cells also showed a loss of HSCs and lymphopenia, suggesting a cell intrinsic effect. Analysis of GRP78 deficient bone marrow (BM) cells showed constitutive activation of all the major UPR signaling pathways, including activation of eIF2α, ATF6, xbp-1 splicing, as well as caspase activation. A multiplex cytokine assay further revealed alteration in select cytokine and chemokine serum levels in the mutant mice. Collectively, these studies demonstrate that GRP78 plays a pleiotropic role in BM cells and contributes to HSC survival and the maintenance of the lymphoid lineage. 相似文献
56.
Clotfelter ED Pedersen AB Cranford JA Ram N Snajdr EA Nolan V Ketterson ED 《Oecologia》2007,154(3):493-503
Resource pulses can have cascading effects on the dynamics of multiple trophic levels. Acorn mast is a pulsed resource in
oak-dominated forests that has significant direct effects on acorn predators and indirect effects on their predators, prey,
and pathogens. We evaluated changes in acorn mast, rodent abundance, raptor abundance, and reproductive success of a ground-nesting
songbird over a 24-year period (1980–2004) in the southern Appalachian Mountains in an effort to determine the relationships
among the four trophic levels. In particular, we examined the following: acorn mast from red oaks (Quercus rubra) and white oaks (Q. alba), abundance of white-footed mice (Peromyscus leucopus) and deer mice (P. maniculatus), population estimates of seven raptor species from three feeding guilds, and nest failure and number of juveniles of dark-eyed
juncos (Junco hyemalis). Finally, we recorded seasonal temperature and precipitation to determine the effects of weather on each trophic level.
We found that weather patterns had delayed effects of up to 3 years on these trophic interactions. Variation in acorn mast,
the keystone resource in this community, was explained by weather conditions as far back as 2 years before the mast event.
Acorn mast, in turn, was a strongly positive predictor of rodent abundance the following year, whereas spring and summer temperature
and raptor abundance negatively affected rodent abundance. Dark-eyed junco nests were more likely to fail in years in which
there were more rodents and raptors. Nest failure rate was a strong predictor of the number of juvenile juncos caught at the
end of the summer. Our results improve our understanding of the complex ecological interactions in oak-dominated forests by
illustrating the importance of abiotic and biotic factors at different trophic levels.
Ethan D. Clotfelter and Amy B. Pedersen contributed equally to the writing of this paper. 相似文献
57.
Stan D. Wullschleger Amy L. Breen Colleen M. Iversen Matthew S. Olson Torgny Näsholm Ulrika Ganeteg Matthew D. Wallenstein David J. Weston 《Molecular ecology》2015,24(10):2301-2309
Molecular ecology is poised to tackle a host of interesting questions in the coming years. The Arctic provides a unique and rapidly changing environment with a suite of emerging research needs that can be addressed through genetics and genomics. Here we highlight recent research on boreal and tundra ecosystems and put forth a series of questions related to plant and microbial responses to climate change that can benefit from technologies and analytical approaches contained within the molecular ecologist's toolbox. These questions include understanding (i) the mechanisms of plant acquisition and uptake of N in cold soils, (ii) how these processes are mediated by root traits, (iii) the role played by the plant microbiome in cycling C and nutrients within high‐latitude ecosystems and (iv) plant adaptation to extreme Arctic climates. We highlight how contributions can be made in these areas through studies that target model and nonmodel organisms and emphasize that the sequencing of the Populus and Salix genomes provides a valuable resource for scientific discoveries related to the plant microbiome and plant adaptation in the Arctic. Moreover, there exists an exciting role to play in model development, including incorporating genetic and evolutionary knowledge into ecosystem and Earth System Models. In this regard, the molecular ecologist provides a valuable perspective on plant genetics as a driver for community biodiversity, and how ecological and evolutionary forces govern community dynamics in a rapidly changing climate. 相似文献
58.
The initiative role of XPC protein in cisplatin DNA damaging treatment-mediated cell cycle regulation 总被引:5,自引:0,他引:5
Wang G Chuang L Zhang X Colton S Dombkowski A Reiners J Diakiw A Xu XS 《Nucleic acids research》2004,32(7):2231-2240
XPC is an important DNA damage recognition protein involved in DNA nucleotide excision repair. We have studied the role of the XPC protein in cisplatin treatment-mediated cell cycle regulation. Through the comparison of microarray data obtained from human normal fibroblasts and two individual XPC-defective cell lines, 486 genes were identified as XPC-responsive genes in the cisplatin treatment (with a minimal 1.5-fold change) and 297 of these genes were further mapped to biological pathways and gene ontologies. The cell cycle and cell proliferation-related genes were the most affected genes by the XPC defect in the cisplatin treatment. Many other cellular function genes were also affected by the XPC defect in the treatment. Western blot hybridization results revealed that the XPC defect reduced the p53 responses to the cisplatin treatment. The ability to activate caspase-3 was also attenuated in the XPC cells with the treatment. These results suggest that the XPC protein plays a critical role in initiating the cisplatin DNA damaging treatment-mediated signal transduction process, resulting in activation of the p53 pathway and cell cycle arrest that allow DNA repair and apoptosis to take place. These results reveal an important role of the XPC protein in the cancer prevention. 相似文献
59.
60.
William K. Cornwell William D. Pearse Rhiannon L. Dalrymple Amy E. Zanne 《Ecography》2019,42(11):1819-1831
The era of big biodiversity data has led to rapid, exciting advances in the theoretical and applied biological, ecological and conservation sciences. While large genetic, geographic and trait databases are available, these are neither complete nor random samples of the globe. Gaps and biases in these databases reduce our inferential and predictive power, and this incompleteness is even more worrisome because we are ignorant of both its kind and magnitude. We performed a comprehensive examination of the taxonomic and spatial sampling in the most complete current databases for plant genes, locations and functional traits. To do this, we downloaded data from The Plant List (taxonomy), the Global Biodiversity Information Facility (locations), TRY (traits) and GenBank (genes). Only 17.7% of the world's described and accepted land plant species feature in all three databases, meaning that more than 82% of known plant biodiversity lacks representation in at least one database. Species coverage is highest for location data and lowest for genetic data. Bryophytes and orchids stand out taxonomically and the equatorial region stands out spatially as poorly represented in all databases. We have highlighted a number of clades and regions about which we know little functionally, spatially and genetically, on which we should set research targets. The scientific community should recognize and reward the significant value, both for biodiversity science and conservation, of filling in these gaps in our knowledge of the plant tree of life. 相似文献