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Characterisation of full-length cDNA sequences provides insights into the Eimeria tenellatranscriptome
Nadzirah Amiruddin, Xin-Wei Lee, Damer P Blake, Yutaka Suzuki, Yea-Ling Tay, Lik-Sin Lim, Fiona M Tomley, Junichi Watanabe, Chihiro Sugimoto, Kiew-Lian Wan
BMC Genomics , 2012, DOI: 10.1186/1471-2164-13-21
Abstract: More than 15,000 partial sequences were generated from the 5' and 3' ends of clones randomly selected from an E. tenella second generation merozoite full-length cDNA library. Clustering of these sequences produced 1,529 unique transcripts (UTs). Based on the transcript assembly and subsequently primer walking, 433 full-length cDNA sequences were successfully generated. These sequences varied in length, ranging from 441 bp to 3,083 bp, with an average size of 1,647 bp. Simple sequence repeat (SSR) analysis identified CAG as the most abundant trinucleotide motif, while codon usage analysis revealed that the ten most infrequently used codons in E. tenella are UAU, UGU, GUA, CAU, AUA, CGA, UUA, CUA, CGU and AGU. Subsequent analysis of the E. tenella complete coding sequences identified 25 putative secretory and 60 putative surface proteins, all of which are now rational candidates for development as recombinant vaccines or drug targets in the effort to control avian coccidiosis.This paper describes the generation and characterisation of full-length cDNA sequences from E. tenella second generation merozoites and provides new insights into the E. tenella transcriptome. The data generated will be useful for the development and validation of diagnostic and control strategies for coccidiosis and will be of value in annotation of the E. tenella genome sequence.Coccidiosis is an economically important intestinal disease of poultry caused by parasitic Eimeria species. The annual cost of coccidiosis to the poultry industry worldwide has been estimated to exceed £2 billion [1]. Control of this disease in intensively reared poultry is accomplished principally by prophylactic chemotherapy with specific anticoccidial drugs, although drug-resistance is a serious problem that has to be constantly managed. No new drugs have been introduced in recent years and alternative methods of control are now required. Vaccination using live vaccines is a viable option, though it is hampered by th
Automatic detection of shared fragments model
共享片段自动检测模型

SHI Lei,CHENG Gang-yun,
石磊
,程刚运

计算机应用 , 2009,
Abstract: A model of automatic online detection of shared fragments was described including its architecture and implementation schemes. Besides, a scalable algorithm for detecting shared fragments was proposed. The online detection algorithm could run automatically in the model. The model took the Web pages that were more popular than others as detection objects, and could get a set of maximal shared fragments from a large collection of Web pages. Experimental results show that it not only provides veracity of detection but also improves the efficiency.
Cloning and Sequencing of Two Acetylcholinesterase cDNA Fragments from Cotton Aphid, Aphis gossypii Glover
棉蚜2个乙酰胆碱酯酶cDNA片段的基因克隆与序列分析

Abstract,
李飞
,韩召军

动物学研究 , 2002,
Abstract: Two acetylcholinesterase (AChE) genes cDNA fragments,Ag.acel and Ag.ace2,have been cloned from cotton aphid,Aphis gossypii Glover using degenerate primers with RT-PCR technique.Ag.acel gene cDNA fragment is of 282?bp encoding 94 amino acids,and Ag.ace2 gene cDNA fragment is of 264?bp encoding 88 amino acids.Both two putative AChE genes cDNA fragments share numerous similarities with those cloned from other insects.This is the first report of two AChE cDNA fragment sequences in the insect species,which provided the direct evidence of multiple AChE existence in insects.
Effect of cDNA fragments in different length derived from Potato Virus Y coat protein gene on the induction of RNA-mediated virus resistance
Zhu Junhua,Zhu Xiaoping,Wen Fujiang,Bai Qingrong,Zhu Changxiang,Song Yunzhi
Science China Life Sciences , 2004, DOI: 10.1360/03yc0066
Abstract: We have reported that cDNA derived from entire coat protein (CP) gene of potato virus Y (PVY) could induce resistance to PVY infection in transgenic tobacco plants, and the resistance was further demonstrated to be RNA-mediated rather than coat protein-mediated. In this study, we cloned cDNA fragments of 202 bp, 417 bp, and 603 bp in length derived from the 3′ end of the PVY CP gene, and the cDNA fragments were introduced into tobacco (var. NC89) plants via Agrobacterium- mediated transformation system. The results of resistance assay showed that the CP cDNA fragments of 417 bp and 603 bp could confer resistance of the transgenic plants to PVY infection, but the fragment of 202 bp in length could not. Molecular analysis revealed that the resistance was RNA-mediated, which is believed to be a result of post-transcriptional gene silencing. The results indicate that the length of cDNA fragments needed for resistance induction was located somewhere between 202 bp and 417 bp from the 3′ end of PVY CP gene.
mRNA differential display between sterile and fertile anther of rice and analysis of cDNA differential fragments
Xuede Wang,Yingguo Zhu
Science China Life Sciences , 1998, DOI: 10.1007/BF02882730
Abstract: Rice anther and leaf mRNAs from two cytoplasmic male sterile lines (Maxie A and Congguong 41A) were compared with those from their maintainers and F1 hybrids by using mRNA differential display to study gene expression pattern in sterile anther during pollen abortion. Anther cDNA differential bands between sterile and fertile plants were more than those of leaf. It was indicated that the expression of fertility gene(s) in the anther was more activable and sufficient than in the leaf. The gene transcript pattern in one of different types of anther was not only associated with its pollen sterility degree but also with its stage of pollen abortion. The anthers with full or partial sterility or with early abortion produced more cDNA differential bands than those fertile or late abortion anthers. In twelve recovered differential cDNA fragments, two were probably associated with male sterility, i. e. one is (AB4A5), which was specifically expressed in the sterile anther, and the other (AB3B2), which contained some sequence homologous to a mitochondrial gene (coxII) and whose expression was partially suppressed in the sterile anther.
Identifying and mapping cDNA fragments related to rice photoperiod sensitive genic male sterility
Shuye Jiang,Qifeng Chen,Xuanjun Fang
Chinese Science Bulletin , 2000, DOI: 10.1007/BF02887101
Abstract: The differentially expressed cDNA fragments have been obtained by differential screening with cDNA-RAPD technique in photoperiod sensitive genic male sterile (PGMS) rice. Some of them have been reassessed with Northern blot hybridization, from which a PGMS-related positive fragment,RPG43, has been identified. Further analysis onRPG43 with Southern blot and RAPD indicates that the fragment is a single-copy sequence and its mRNA has been processed after transcription. Sequence analysis reveals thatRPG43 is 744 bp in length and contains a 60 bp region (from 126th to 185th bp) showing 72% homology to a human DNA sequence, pac pDJ-356d6, on chromosome 11. So it is a new sequence found in plant and its GenBank access number is AF126027. In addition,RPG43 has been mapped to a position 3.8 cM away from RFLP marker R1553 on chromosome 5 of rice.
GOGOT: a method for the identification of differentially expressed fragments from cDNA-AFLP data
Koji Kadota, Ryoko Araki, Yuji Nakai, Masumi Abe
Algorithms for Molecular Biology , 2007, DOI: 10.1186/1748-7188-2-5
Abstract: We describe a method, GOGOT, which automatically detects the differentially expressed TDFs in a set of time-course electropherograms. Analysis by GOGOT is conducted as follows: correction of fragment lengths of TDFs, alignment of identical TDFs across different electropherograms, normalization of peak heights, and identification of differentially expressed TDFs using a special statistic. The output of the analysis is a highly reduced list of differentially expressed TDFs. Visual evaluation confirmed that the peak alignment was performed perfectly for the TDFs by virtue of the correction of peak fragment lengths before alignment in step 1. The validity of the automated ranking of TDFs by the special statistic was confirmed by the visual evaluation of a third party.GOGOT is useful for the automated detection of differentially expressed TDFs from cDNA-AFLP temporal electrophoretic data. The current algorithm may be applied to other electrophoretic data and temporal microarray data.Expression analysis based on comparison of one-dimensional (1-D) electrophoretic patterns is one of the few genome-wide approaches that don't require sequence information. There are a few methods such as differential display [1], amplified fragment length polymorphism (AFLP) [2], and its variants like cDNA-AFLP, an AFLP-derived technique for RNA fingerprinting [3]. The cDNA-AFLP method and related techniques such as HiCEP have been widely used for gene discovery and monitoring temporal expression changes of transcript-derived fragments (TDFs) by comparing sets of time-course electropherograms [4-15]. However, inaccurate DNA fragment sizing often interferes with high-throughput analysis.A major source of incorrect estimation of fragment lengths is the use of wrong size marker peaks when the true peaks are masked by intense peaks nearby [12,16]. Such electropherograms are locally expanded or compressed and the deviation from the true electropherogram reaches a maximum around the length of the w
A fully automatic gridding method for cDNA microarray images
Luis Rueda, Iman Rezaeian
BMC Bioinformatics , 2011, DOI: 10.1186/1471-2105-12-113
Abstract: We propose a parameterless and fully automatic approach that first detects the sub-grids given the entire microarray image, and then detects the locations of the spots in each sub-grid. The approach, first, detects and corrects rotations in the images by applying an affine transformation, followed by a polynomial-time optimal multi-level thresholding algorithm used to find the positions of the sub-grids in the image and the positions of the spots in each sub-grid. Additionally, a new validity index is proposed in order to find the correct number of sub-grids in the image, and the correct number of spots in each sub-grid. Moreover, a refinement procedure is used to correct possible misalignments and increase the accuracy of the method.Extensive experiments on real-life microarray images and a comparison to other methods show that the proposed method performs these tasks fully automatically and with a very high degree of accuracy. Moreover, unlike previous methods, the proposed approach can be used in various type of microarray images with different resolutions and spot sizes and does not need any parameter to be adjusted.Microarrays are one of the most important technologies used in molecular biology to massively explore how the genes express themselves into proteins and other molecular machines responsible for the different functions in an organism. These expressions are monitored in cells and organisms under specific conditions, and have many applications in medical diagnosis, pharmacology, disease treatment, just to mention a few. We consider cDNA microarrays which are produced on a chip (slide) by hybridizing sample DNA on the slide, typically in two channels. Scanning the slides at a very high resolution produces images composed of sub-grids of spots. Image processing and analysis are two important aspects of microarrays, since the aim of the whole experimental procedure is to obtain meaningful biological conclusions, which depends on the accuracy of the differe
Conversion of cDNA differential display results (DDRT-PCR) into quantitative transcription profiles
Balakrishnan Venkatesh, Ursula Hettwer, Birger Koopmann, Petr Karlovsky
BMC Genomics , 2005, DOI: 10.1186/1471-2164-6-51
Abstract: We developed procedures for the conversion of cDNA Differential Display data into quantitative transcription profiles. Amplified cDNA fragments are separated on a DNA sequencer and detector signals are converted into virtual gel images suitable for semi-automatic analysis. Data processing consists of four steps: (i) cDNA bands in lanes corresponding to samples treated with the same primer combination are matched in order to identify fragments originating from the same transcript, (ii) intensity of bands is determined by densitometry, (iii) densitometric values are normalized, and (iv) intensity ratio is calculated for each pair of corresponding bands. Transcription profiles are represented by sets of intensity ratios (control vs. treatment) for cDNA fragments defined by primer combination and DNA mobility. We demonstrated the procedure by analyzing DDRT-PCR data on the effect of secondary metabolites of oilseed rape Brassica napus on the transcriptome of the pathogenic fungus Leptosphaeria maculans.We developed a data processing procedure for the quantitative analysis of amplified cDNA fragments separated by electrophoresis. The system utilizes common software and provides an open-end alternative to DNA microarray analysis of the transcriptome. It is expected to work equally well with DDRT-PCR and cDNA-AFLP data and be useful particularly in reseach on organisms for which microarray analysis is not available or economical.Transcriptome analysis is a common way of discovering differences in gene expression because regulation of gene activity occurs primarily on transcription level. Numerous low-cost, simple methods are available for gene discovery projects, providing a limited set of transcripts more or less randomly selected from a pool of genes expressed differently between two samples (for example treated sample/control or diseased/healthy tissue). These methods include differential hybridization, subtractive hybridization, EST sequencing and other gene discovery
Characterisation of immune responses and protective efficacy in mice after immunisation with Rift Valley Fever virus cDNA constructs
Nina Lagerqvist, Jonas N?slund, ?ke Lundkvist, Michèle Bouloy, Clas Ahlm, G?ran Bucht
Virology Journal , 2009, DOI: 10.1186/1743-422x-6-6
Abstract: Immunisation with cDNA encoding the nucleocapsid protein induced strong humoral and lymphocyte proliferative immune responses, and virus neutralising antibodies were acquired after vaccination with cDNA encoding the glycoproteins. Even though complete protection was not achieved by genetic immunisation, four out of eight, and five out of eight mice vaccinated with cDNA encoding the nucleocapsid protein or the glycoproteins, respectively, displayed no clinical signs of infection after challenge. In contrast, all fourteen control animals displayed clinical manifestations of Rift Valley Fever after challenge.The appearance of Rift Valley Fever associated clinical signs were significantly decreased among the DNA vaccinated mice and further adjustment of this strategy may result in full protection against Rift Valley Fever.Rift Valley Fever virus (RVFV) is a mosquito-borne Phlebovirus in the Bunyaviridae family. RVFV infects domesticated ruminants and humans and regularly induces epizootics with concomitant epidemics throughout the African continent and on the Arabian Peninsula [1,2]. Outbreaks among domesticated ruminants are characterised by a large increase of spontaneous abortions and the case fatality rate may reach 100% in young animals [3]. While Rift Valley Fever (RVF) is generally benign in man, more severe clinical manifestations such as hemorrhagic fever, encephalitis and retinitis are regulary observed [4].Despite the fact that RVF is an important viral zoonosis, and the risk for emergence in new susceptible areas has been emphasized [1], effective and safe vaccines are not commercially available. However, formalin inactivated vaccines have been developed for human use, but the distribution is limited to high-risk occupation staff [5,6]. Currently there are a few vaccines available for use in livestock: vaccines based on the live-attenuated Smithburn strain [7] and formalin inactivated virus preparations [8]. The Smithburn virus vaccine is suggested to induce
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