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Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato
Erwin Datema, Lukas A Mueller, Robert Buels, James J Giovannoni, Richard GF Visser, Willem J Stiekema, Roeland CHJ van Ham
BMC Plant Biology , 2008, DOI: 10.1186/1471-2229-8-34
Abstract: The tomato genome has a higher repeat content than the potato genome, primarily due to a higher number of retrotransposon insertions in the tomato genome. On the other hand, simple sequence repeats are more abundant in potato than in tomato. The two genomes also differ in the frequency distribution of SSR motifs. Based on EST and protein alignments, potato appears to contain up to 6,400 more putative coding regions than tomato. Major gene families such as cytochrome P450 mono-oxygenases and serine-threonine protein kinases are significantly overrepresented in potato, compared to tomato. Moreover, the P450 superfamily appears to have expanded spectacularly in both species compared to Arabidopsis thaliana, suggesting an expanded network of secondary metabolic pathways in the Solanaceae. Both tomato and potato appear to have a low level of microsynteny with A. thaliana. A higher degree of synteny was observed with Populus trichocarpa, specifically in the region between 15.2 and 19.4 Mb on P. trichocarpa chromosome 10.The findings in this paper present a first glimpse into the evolution of Solanaceous genomes, both within the family and relative to other plant species. When the complete genome sequences of these species become available, whole-genome comparisons and protein- or repeat-family specific studies may shed more light on the observations made here.The Solanaceae, or Nightshade family, is a dicot plant family that includes many economically important genera that are used in agriculture, horticulture, and other industries. Family members include the tuber bearing potato (Solanum tuberosum); a large number of fruit-bearing vegetables, such as peppers (Capsicum spp), tomatoes (S. lycopersicum), and eggplant (S. melongena); leafy tobacco (Nicotiana tabacum); and ornamental flowers from the Petunia and Solanum genera.Tomato is generally considered to be a model crop plant species, for which many high-quality genetic and genomic resources are available, such as high-
Aperiodic linearly repetitive Delone sets are densely repetitive  [PDF]
Daniel Lenz
Mathematics , 2002,
Abstract: We show that aperiodic linearly repetitive Delone sets are densely repetitive. This confirms a conjecture of Lagarias and Pleasants.
Colonization of Potato Rhizosphere by GFP-Tagged Bacillus subtilis MB73/2, Pseudomonas sp. P482 and Ochrobactrum sp. A44 Shown on Large Sections of Roots Using Enrichment Sample Preparation and Confocal Laser Scanning Microscopy  [PDF]
Dorota Krzyzanowska,Michal Obuchowski,Mariusz Bikowski,Michal Rychlowski,Sylwia Jafra
Sensors , 2012, DOI: 10.3390/s121217608
Abstract: The ability to colonize the host plants’ rhizospheres is a crucial feature to study in the case of Plant Growth Promoting Rhizobacteria (PGPRs) with potential agricultural applications. In this work, we have created GFP-tagged derivatives of three candidate PGPRs: Bacillus subtilis MB73/2, Pseudomonas sp. P482 and Ochrobactrum sp. A44. The presence of these strains in the rhizosphere of soil-grown potato (Solanum tuberosum L.) was detected with a classical fluorescence microscope and a confocal laser scanning microscope (CLSM). In this work, we have used a broad-field-of-view CLMS device, dedicated to in vivo analysis of macroscopic objects, equipped with an automated optical zoom system and tunable excitation and detection spectra. We show that features of this type of CLSM microscopes make them particularly well suited to study root colonization by microorganisms. To facilitate the detection of small and scattered bacterial populations, we have developed a fast and user-friendly enrichment method for root sample preparation. The described method, thanks to the in situ formation of mini-colonies, enables visualization of bacterial colonization sites on large root fragments. This approach can be easily modified to study colonization patterns of other fluorescently tagged strains. Additionally, dilution plating of the root extracts was performed to estimate the cell number of MB73/2, P482 and A44 in the rhizosphere of the inoculated plants.
hsp90抑制剂?如酸对乳腺癌mda-mb-231细胞增殖、侵袭、迁移的影响  [PDF]
李红梅,聂丽娟,霍强,赵素容,马涛,吴成柱,刘浩
南方医科大学学报 , 2015,
Abstract: 目的探讨热休克蛋白90(hsp90)抑制剂?如酸对人乳腺癌mda-mb-231细胞增殖、侵袭、迁移的影响。方法采用体外malachitegreen-molybdate显色反应和atp-琼脂糖凝胶结合实验检测?如酸对hsp90抑制活性;mtt法检测药物对mda-mb-231增殖抑制效应;transwell小室法检测药物对细胞侵袭和迁移影响;免疫印迹法检测药物对相关蛋白基质金属蛋白酶-9(mmp-9)、基质金属蛋白酶组织抑制剂-1(timp-1)、hsp90、热休克蛋白70(hsp70)表达的影响。结果?如酸为特异性的hsp90抑制剂,其抑制ic50值为82.5μmol/l。mtt结果显示,?如酸具有明显抑制细胞增殖的作用,且呈现浓度依赖关系,其ic50值为29.3μmol/l。不同浓度的?如酸(12.5,25.0,50.0μmol/l)处理36h后,与对照组相比,药物对细胞侵袭抑制率分别为:23.6%、56.6%、67.0%,p<0.05。?如酸(12.5,25.0,50.0μmol/l)处理24h后,与对照组相比,药物对细胞迁移抑制率分别为:30.0%、45.5%、77.5%,p<0.05。免疫印迹法结果显示,?如酸随着浓度的增加,诱导mmp-9降解越明显,而对hsp90和hsp70蛋白表达均没有影响。结论?如酸能明显抑制乳腺癌细胞增殖、侵袭、迁移能力,其机制可能是通过抑制hsp90atpase活性以及导致下游的顾客蛋白的mmp-9表达下调有关。
Genomic Resources and Tools for Gene Function Analysis in Potato  [PDF]
Glenn J. Bryan,Ingo Hein
International Journal of Plant Genomics , 2008, DOI: 10.1155/2008/216513
Abstract: Potato, a highly heterozygous tetraploid, is undergoing an exciting phase of genomics resource development. The potato research community has established extensive genomic resources, such as large expressed sequence tag (EST) data collections, microarrays and other expression profiling platforms, and large-insert genomic libraries. Moreover, potato will now benefit from a global potato physical mapping effort, which is serving as the underlying resource for a full potato genome sequencing project, now well underway. These tools and resources are having a major impact on potato breeding and genetics. The genome sequence will provide an invaluable comparative genomics resource for cross-referencing to the other Solanaceae, notably tomato, whose sequence is also being determined. Most importantly perhaps, a potato genome sequence will pave the way for the functional analysis of the large numbers of potato genes that await discovery. Potato, being easily transformable, is highly amenable to the investigation of gene function by biotechnological approaches. Recent advances in the development of Virus Induced Gene Silencing (VIGS) and related methods will facilitate rapid progress in the analysis of gene function in this important crop.
Occurrence of Pospiviroid in potato, tomato and some ornamental plants in Turkey
H Bostan, M Gazel, IO Elibuyuk, K Calayan
African Journal of Biotechnology , 2010,
Abstract: In order to investigate the Pospiviroid in potato, tomato and some ornamental plants in Turkey, a survey study was carried out from 2006 to 2009. During this survey study, a total of 1766 samples (1047 potato samples, 258 tomato leaves and 461 ornamental plants) were tested by reverse transcriptionpolymerase chain reaction (RT-PCR) and, the samples found to be positive in RT-PCR were also checked in return polyacrylamide gel electrophoresis (R-PAGE). Of these samples, potato tubers were collected from markets, leaf samples from potato fields (Erzurum), tomato samples from field (Tokat, Amasya, Balykesir and Bursa) and greenhouses (Antalya and Mula), leaves and vines of ornamental plants from greenhouses (Yalova) and florists (Erzurum) and recreation areas (Ankara, zmir and Trabzon). In the result of RT-PCR test, PSTVd was detected in 6 out of 891 potato tubers and CSVd in 2 out of 154 chrysanthemums. On the other side, tomato, citrus and most ornamental plants belonging to different families were found to be free from pospiviroid. This is the first report of CSVd in Turkey.
Mycoplasma pneumoniae Large DNA Repetitive Elements RepMP1 Show Type Specific Organization among Strains  [PDF]
Oxana Musatovova, T. R. Kannan, Joel B. Baseman
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0047625
Abstract: Mycoplasma pneumoniae is the smallest self-replicating bacterium with a streamlined genome of 0.81 Mb. Complete genome analysis revealed the presence of multiple copies of four large repetitive elements (designated RepMP1, RepMP2/3, RepMP4 and RepMP5) that are implicated in creating sequence variations among individual strains. Recently, we described RepMP1-associated sequence variations between reference strain M129 and clinical isolate S1 that involved three RepMP1-genes (i.e. mpn130, mpn137 and mpn138). Using PCR and sequencing we analyze 28 additional M. pneumoniae strains and demonstrate the existence of S1-like sequence variants in nine strains and M129-like variants in the remaining nineteen strains. We propose a series of recombination steps that facilitates transition from M129- to S1-like sequence variants. Next we examined the remaining RepMP1-genes and observed no other rearrangements related to the repeat element. The only other detected difference was varying numbers of the 21-nucleotide tandem repeats within mpn127, mpn137, mpn501 and mpn524. Furthermore, typing of strains through analysis of large RepMPs localized within the adhesin P1 operon revealed that sequence divergence involving RepMP1-genes mpn130, mpn137 and mpn138 is strictly type-specific. Once more our analysis confirmed existence of two highly conserved groups of M. pneumoniae strains.
Repetitive Delone Sets and Quasicrystals  [PDF]
Jeffery C. Lagarias,Peter A. B. Pleasants
Physics , 1999,
Abstract: This paper considers the problem of characterizing the simplest discrete point sets that are aperiodic, using invariants based on topological dynamics. A Delone set whose patch-counting function N(T), for radius T, is finite for all T is called repetitive if there is a function M(T) such that every ball of radius M(T)+T contains a copy of each kind of patch of radius T that occurs in the set. This is equivalent to the minimality of an associated topological dynamical system with R^n-action. There is a lower bound for M(T) in terms of N(T), namely N(T) = O(M(T)^n), but no general upper bound. The complexity of a repetitive Delone set can be measured by the growth rate of its repetitivity function M(T). For example, M(T) is bounded if and only if the set is a crystal. A set is called is linearly repetitive if M(T) = O(T) and densely repetitive if M(T) = O(N(T))^{1/n}). We show that linearly repetitive sets and densely repetitive sets have strict uniform patch frequencies, i.e. the associated topological dynamical system is strictly ergodic. It follows that such sets are diffractive. In the reverse direction, we construct a repetitive Delone set in R^n which has M(T) = O(T(log T)^{2/n}(log log log T)^{4/n}), but does not have uniform patch frequencies. Aperiodic linearly repetitive sets have many claims to be the simplest class of aperiodic sets, and we propose considering them as a notion of "perfectly ordered quasicrystal".
Nakajima varieties and repetitive algebras  [PDF]
Bernard Leclerc,Pierre-Guy Plamondon
Mathematics , 2012,
Abstract: We realize certain graded Nakajima varieties of finite Dynkin type as orbit closures of repetitive algebras of Dynkin quivers. As an application, we obtain that the perverse sheaves introduced by Nakajima for describing irreducible characters of quantum loop algebras are isomorphic to the intersection cohomology sheaves of these orbit closures.
Repetitive elements in parasitic protozoa
Christine Clayton
BMC Biology , 2010, DOI: 10.1186/1741-7007-8-64
Abstract: See research article http://www.biomedcentral.com/1471-2164/11/321 webciteThe genomes of eukaryotes contain numerous types of repetitive element with a wide variety of functions. Some are within coding regions; others are in untranslated regions of mRNAs or are located in regions that are important for chromosome maintenance; and many may have no function at all beyond self-perpetuation. Repetitive elements fall into three broad classes. Simple repeats can change in copy number, but do not move to new locations; DNA 'cut-and-paste' transposons are able to 'jump' to a new location; and retroposons move via an RNA intermediate, leaving an intact retroposon at the original location. Changes in the numbers, or locations, of repetitive elements can alter the structures of proteins, influence gene expression and affect chromosome segregation and karyotypes. Repetitive elements are therefore significant drivers of diversity.There is currently little direct evidence for active transposition of the elements present in the genomes of parasitic protists but a genome-wide bioinformatic screen of the sequenced genome of the gut parasite Entamoeba histolytica published recently in BMC Genomics by Huntley et al. [1] has found indirect evidence of recent transposition events involving the SINE (short interspersed nuclear element) class of retroposon.The numbers of simple repeats and transposons in the genomes of parasitic protists vary considerably, with estimates of the proportion of repetitive DNA in genomes varying from 11% to 65%. These numbers are unreliable, however, as repetitive regions usually become compressed during alignment, and sequences present in multiple locations cause difficulties in assembly of contiguous chromosomes. Within species, variations between isolates in the numbers of simple repeats, and in the locations of transposable elements, are useful for epidemiological studies. Multicopy sequences are also ideal targets for amplification-based diagnostics.Simp
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