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Rapid Homology Search with Two-Stage Extension and Daughter Seeds [chapter]

Miklós Csűrös, Bin Ma
2005 Lecture Notes in Computer Science  
Daughter seeds, especially when combined with the two-stage extension, provide the flexibility to maximize the independence between the seeds, which is a well-known criterion for maximizing sensitivity  ...  Using a seed to rapidly "hit" possible homologies for further examination is a common practice to speed up homology search in molecular sequences.  ...  Acknowledgments This work was supported by grants from the Natural Sciences and Engineering Research Council of Canada, and the Fonds québécois de la recherche sur la nature et les technologies.  ... 
doi:10.1007/11533719_13 fatcat:szlgvb5kpzgopktmxuw6qmk27e

Rapid Homology Search with Neighbor Seeds

Miklos Csuros, Bin Ma
2007 Algorithmica  
By drawing upon the previously studied ideas of vector seed and multiple seeds, we introduce neighbor seeds, which are implemented using two-stage extension.  ...  However, huge memory requirements diminish the advantages of high weight seeds. This paper describes a two-stage extension method, which simulates high weight seeds with modest memory requirements.  ...  Two-stage hit extension In this section we propose the following two-stage extension process, and show that this seemingly simple idea is in fact nontrivial and makes a big difference to the sensitivity  ... 
doi:10.1007/s00453-007-0062-y fatcat:zx6byd4ssbcxxcgnagt6xvf24a

Proteomics of Medicago truncatula Seed Development Establishes the Time Frame of Diverse Metabolic Processes Related to Reserve Accumulation

K. Gallardo
2003 Plant Physiology  
We utilized a proteomic approach to investigate seed development in Medicago truncatula, cv Jemalong, line J5 at specific stages of seed filling corresponding to the acquisition of germination capacity  ...  Correlated with the reserve deposition phase was the accumulation of proteins associated with cell expansion (actin 7 and reversibly glycosylated polypeptide) and of components of the precursor accumulating  ...  ACKNOWLEDGMENTS We thank Gerard Duc (Unité de Gènetique et Ecophysiologie des Legumineuses, INRA, Dijon, France) for initiating this project, for his constant support, and for critical reading of the manuscript  ... 
doi:10.1104/pp.103.025254 pmid:12972662 pmcid:PMC219042 fatcat:k47s2n2dabhofi6xtt4arz3a5m

Maize VKS1 Regulates Mitosis and Cytokinesis during Early Endosperm Development

Yongcai Huang, Haihai Wang, Xing Huang, Qiong Wang, Jiechen Wang, Dong An, Jiqin Li, Wenqin Wang, Yongrui Wu
2019 The Plant Cell  
Rapid mitotic divisions in early endosperm development produce most of the cells that make up the starchy endosperm; however, the mechanisms underlying early endosperm development remain largely unknown  ...  VKS1 dynamically localizes to the nucleus and microtubules and plays key roles in the migration of free nuclei in the coenocyte as well as in mitosis and cytokinesis in early mitotic divisions.  ...  We thank Zhenhua Wang, Lin Zhang, and Xing Zeng from Northeast Agricultural University for assistance with materials planting. We thank Xiaosu Gao for guidance on confocal microscopy.  ... 
doi:10.1105/tpc.18.00966 pmid:30962394 pmcid:PMC6588315 fatcat:g3zf6dcqtbbmvookgzmikhsjni

The Novel Gene HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1 of Rice Encodes a Putative Coiled-Coil Protein Required for Homologous Chromosome Pairing in Meiosis

K.-I. Nonomura
2004 The Plant Cell  
We have identified and characterized a novel gene, PAIR1 (HOMOLOGOUS PAIRING ABERRATION IN RICE MEIOSIS1), required for homologous chromosome pairing and cytokinesis in male and female meiocytes of rice  ...  The PAIR1 gene encodes a 492-amino acid protein, which contains putative coiled-coil motifs in the middle, two basic regions at both termini, and a potential nuclear localization signal at the C terminus  ...  and Fisheries of Japan (Rice Genome Project MP-2133).  ... 
doi:10.1105/tpc.020701 pmid:15031413 pmcid:PMC412873 fatcat:degqwsaqfrhddffnnfahiqxpde

Real-time dynamics of Plasmodium NDC80 as a marker for the kinetochore during atypical mitosis and meiosis [article]

Rajan Pandey, Mohammad Zeeshan, David J.P. Ferguson, Robert Markus, Declan Brady, Emilie Daniel, Rebecca R. Stanway, Anthony A Holder, David S. Guttery, Rita Tewari
2019 biorxiv/medrxiv   pre-print
Eukaryotic cell proliferation requires chromosome replication and precise segregation, followed by cell division, to ensure daughter cells have identical genomic copies.  ...  We show that NDC80 is located at a single cluster of all kinetochores and examine its spatio-temporal dynamics throughout all proliferative stages of the parasite life cycle.  ...  sensitive homology searches using HMM-HMM comparison should be employed to more thoroughly test for homolog presences or absences.  ... 
doi:10.1101/767830 fatcat:pyzaf6hv4jd5nerbnepocmdz3u

Real-time dynamics of Plasmodium NDC80 reveals unusual modes of chromosome segregation during parasite proliferation

Mohammad Zeeshan, Rajan Pandey, David J. P. Ferguson, Eelco C. Tromer, Robert Markus, Steven Abel, Declan Brady, Emilie Daniel, Rebecca Limenitakis, Andrew R. Bottrill, Karine G. Le Roch, Anthony A. Holder (+3 others)
2020 Journal of Cell Science  
The parasite undergoes atypical endomitosis and endoreduplication with an intact nuclear membrane and intranuclear mitotic spindle.  ...  Eukaryotic cell proliferation requires chromosome replication and precise segregation to ensure daughter cells have identical genomic copies.  ...  ChIP-seq data have been deposited in NCBI Sequence Read Archive with accession number PRJNA637024.  ... 
doi:10.1242/jcs.245753 pmid:32501284 pmcid:PMC7340582 fatcat:664k7kt5zjevnpkk2merye7emy

Mre11 Deficiency in Arabidopsis Is Associated with Chromosomal Instability in Somatic Cells and Spo11-Dependent Genome Fragmentation during Meiosis

J. Puizina
2004 The Plant Cell  
Aberrant function of the complex is associated with defects in the DNA checkpoint, double-strand break repair, meiosis, and telomere maintenance.  ...  Cytogenetic examination of pollen mother cells revealed massive chromosome fragmentation and the absence of synapsis in the initial stages of meiosis.  ...  We also thank Mathilde Grelon for providing spo11-1-1 mutants and Paula Bombosi for assistance with scanning electron microscopy.  ... 
doi:10.1105/tpc.104.022749 pmid:15258261 pmcid:PMC519189 fatcat:ona3rz2wc5hjpatiq2by5s5cee

The Conserved Chimeric Transcript UPGRADE2 Is Associated with Unreduced Pollen Formation and Is Exclusively Found in Apomictic Boechera Species

M. Mau, J. M. Corral, H. Vogel, M. Melzer, J. Fuchs, M. Kuhlmann, N. de Storme, D. Geelen, T. F. Sharbel
2013 Plant Physiology  
Here, we have established an early flower developmental staging system and have performed microarray-based comparative gene expression analyses of the pollen mother cell stage in seven diploid sexual and  ...  BspUPG2 is highly conserved among apomictic Boechera spp. genotypes but has no homolog in sexual Boechera spp. or in any other taxa.  ...  Eric Schranz for seed material.  ... 
doi:10.1104/pp.113.222448 pmid:24130193 pmcid:PMC3850206 fatcat:bb5kyd3p3jhnvgregskcsaj5je

Evolutionary crossroads in developmental biology: Physcomitrella patens

M. J. Prigge, M. Bezanilla
2010 Development  
The availability of a complete genome sequence, together with the ability to perform gene targeting efficiently in P. patens has spurred a flurry of elegant reverse genetic studies in this plant model  ...  As a member of the bryophytes, P. patens provides a unique opportunity to study the evolution of a myriad of plant traits, such as polarized cell growth, gametophyte-to-sporophyte transitions, and sperm-to-pollen  ...  Acknowledgements The authors are supported by the National Science Foundation (M.J.P. and M.B.) and by the David and Lucille Packard Foundation (M.B.).  ... 
doi:10.1242/dev.049023 pmid:20940223 fatcat:mpe45d6zm5e6lah767ihmm4bse

Mitotic Spindle Assembly in Land Plants: Molecules and Mechanisms

Moé Yamada, Gohta Goshima
2017 Biology  
Searches of >100 animal spindle assembly factors showed that the genes involved in this process are well conserved in plants, with the exception of two major missing elements: centrosomal components and  ...  Two poles of the metaphase spindle are well focused as spindle MTs remain associated with the centrosome at the pole or crosslinked with each other by motors and MAPs [10, 11] .  ...  The plant research conducted in our laboratory is supported by the TORAY Science Foundation and by JSPS KAKNHI (15K14540 and 15H01227) .  ... 
doi:10.3390/biology6010006 pmid:28125061 pmcid:PMC5371999 fatcat:n4xtcmirwjd5lkqrgk2bkcrroa

The TORMOZ Gene Encodes a Nucleolar Protein Required for Regulated Division Planes and Embryo Development in Arabidopsis

M. E. Griffith, U. Mayer, A. Capron, Q. A. Ngo, A. Surendrarao, R. McClinton, G. Jurgens, V. Sundaresan
2007 The Plant Cell  
We show that mutation of the TORMOZ (TOZ) gene yields embryos with aberrant cell division planes and arrested embryos that appear not to have established normal patterning.  ...  Our study suggests that in plant cells, nucleolar functions might interact with the processes of regulated cell divisions and influence the selection of longitudinal division planes during embryogenesis  ...  Resau (Van Andel Research Institute, Grand Rapids, MI) for support.  ... 
doi:10.1105/tpc.106.042697 pmid:17616738 fatcat:u757smixpvb3nnxfxkt5enruwi

IMC10 and LMF1 mediate membrane contact between the mitochondrion and the inner membrane complex in Toxoplasma gondii [article]

Rodolpho Ornitz Oliveira Souza, Gustavo Arrizabalaga, Kylie N Jacobs
2022 bioRxiv   pre-print
Using reciprocal immunoprecipitation and proximity ligation assays, we confirmed the interaction of LMF1 with the pellicle protein IMC10, with a hypothetical protein known to be part of the conoid, and  ...  Conditional knockdown of IMC10 does not affect parasite viability but severely affects mitochondrial morphology in intracellular parasites and mitochondrial distribution to the daughter cells during division  ...  As the two nascent IMCs form during endodyogeny, the mitochondrion develops extensions along its length, which continue to grow as the daughter IMCs elongate.  ... 
doi:10.1101/2022.04.01.486766 fatcat:oo2ewm2f6jcepbd4zxyddfo4iu

Cytological and Proteomic Analyses ofOsmunda cinnamomeaGerminating Spores Reveal Characteristics of Fern Spore Germination and Rhizoid Tip Growth

Jinwei Suo, Qi Zhao, Zhengxiu Zhang, Sixue Chen, Jian'guo Cao, Guanjun Liu, Xing Wei, Tai Wang, Chuanping Yang, Shaojun Dai
2015 Molecular & Cellular Proteomics  
spores, rehydrated spores, double-celled spores, germinated spores, and spores with protonemal cells).  ...  Osmunda cinnamomea L. var. asiatica is one of the oldest fern species with typical separate-growing trophophyll and sporophyll.  ...  Katherine Tran and Baozhen Shan from Bioinformatics Solutions Inc. for assistance with de novo sequencing of the MS/MS spectra.  ... 
doi:10.1074/mcp.m114.047225 pmid:26091698 pmcid:PMC4563732 fatcat:ukxqoggx4vfitdp76wtf7ojynu

A Transcript and Metabolite Atlas of Blackcurrant Fruit Development Highlights Hormonal Regulation and Reveals the Role of Key Transcription Factors

Dorota A. Jarret, Jenny Morris, Danny W. Cullen, Sandra L. Gordon, Susan R. Verrall, Linda Milne, Pete E. Hedley, J. William Allwood, Rex M. Brennan, Robert D. Hancock
2018 Frontiers in Plant Science  
During mid fruit development, fatty acids accumulated and transcript profiles were consistent with seed and embryo development.  ...  At the later stages, sugars and anthocyanins accumulated consistent with transcript profiles that were associated with secondary metabolism.  ...  The importance of seed development processes in middle stages was also underpinned by the presence of transcription factors encoding proteins homologous to those with functions in seed and embryo development  ... 
doi:10.3389/fpls.2018.01235 pmid:30210515 pmcid:PMC6119775 fatcat:7kgjwvtwija2dcufxaisyrgiqu
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