Journal: Genome Research

Article Title: 5?-Transducing SVA retrotransposon groups spread efficiently throughout the human genome

doi: 10.1101/gr.093435.109

Figure Lengend Snippet: Ongoing transcription of SVA_F1 subfamily members is demonstrated by ESTs and RT-PCR analyses. (A) ESTs (arrows) aligning specifically to the source element H10_1 and its descendants (DB277120, AA582071) and to MAST2–SVA junctions of a subset of SVA_F1 subfamily members. Extensions of the queries used to identify ESTs (black bars) are shown. (B) Transcriptional control of transduction group 1 members H20_1 and H1_F_160 is effected by external promoters. Identified ESTs match 5′ junctions of the SVA elements with primary 5′ transductions. MER57A is an internal portion of the nonautonomous retrovirus 1 (ERV1). (C) ESTs indicating ongoing transcription of source element HX_4. Those ESTs that correspond to the 3′-end (BI325030, AW627827) and the 3′ junction (BX110444) of HX_4 are also consistent with transcription of the HX_4 derivative H3_8 (Fig. 7C). 3′-Ends of sense ESTs BI325030 and BX110444 as well as the 5′-end of antisense EST BX373748 are directly at the polyadenylation sites of HX_4 and/or H3_8. SVA copies highlighted in red were verified to be source elements. (D) RT-PCR analyses confirm transcription of distinct SVA_F1 subfamily members. Agarose gel electrophoresis of H20_1 and HX_4/H3_8-specific RT-PCR products derived from total RNA from human tissues and NCCIT cells. Primer binding sites and extension of the RT-PCR products are indicated as short arrows and red bars, respectively, in B and C. To control for both successful cDNA synthesis and DNA-free RNA preparations, PCRs with GAPDH-specific, intron-spanning primers (see Methods) were performed on RNA preparations from each tissue before (−RT) and after (+RT) cDNA synthesis. PCR on genomic HeLa DNA served as a positive control. The 766- and 481-bp products originate from the unspliced GAPDH gene and a processed GAPDH pseudogene, respectively (Harper et al. 2003). Sizes of obtained PCR products are indicated and correspond to expected fragment sizes. RT, reverse transcriptase; M, size marker; NTC, no template control.

Article Snippet: Total RNA was extracted from human teratocarcinoma cell line NCCIT (ATCC CRL-2073) using TRIzol reagent (Invitrogen).

Techniques: Reverse Transcription Polymerase Chain Reaction, Transduction, Agarose Gel Electrophoresis, Derivative Assay, Binding Assay, Positive Control, Marker

Journal: Plant biology (Stuttgart, Germany)

Article Title: The transmembrane domain of the rice small protein OsS1Fa1 is responsible for subcellular localization and drought tolerance.

doi: 10.1111/plb.13711

Figure Lengend Snippet: Fig. 2. Analysis of OsS1Fa1 and OsS1Fa2 expression in rice tissues and detection of the His-tagged recombinant proteins in E. coli. (A) A comparison of the deduced amino acid sequences of OsS1Fa1 and OsS1Fa2. (B) Amino acid sequences of conserved motifs in OsS1Fa1 and OsS1Fa2 are indicated. (C) Total RNA was extracted from leaf, culm, and root tissues of 3-week-old rice seedlings, and the expression levels of OsS1Fa1 and OsS1Fa2 were analysed using qRT-PCR. Data represent mean SD (n = 3). (D) Detection of recombinant His6-OsS1Fa1 and His6-OsS1Fa2 proteins with anti-OsS1Fa1 antibody.

Article Snippet: Rice leaf, culm, and root samples were thoroughly ground, and total RNA was extracted from the ground tissue using the FavorPrepTM Plant Total RNA Mini Kit (Favorgen).

Techniques: Expressing, Recombinant, Comparison, Quantitative RT-PCR

Journal: Plant biology (Stuttgart, Germany)

Article Title: The transmembrane domain of the rice small protein OsS1Fa1 is responsible for subcellular localization and drought tolerance.

doi: 10.1111/plb.13711

Figure Lengend Snippet: Fig. 4. Drought tolerance assay of transgenic Arabidopsis overexpressing OsS1Fa1 and mutant proteins. (A) Examination of OsS1Fa1, OsS1Fa1(TMm1), OsS1Fa1(mNLS ), and OsS1Fa1(K63R) expression in OsS1Fa1-, OsS1Fa1(mNLS)-, OsS1Fa1(K63R)-, and OsS1Fa1(TMm1)-overexpressing Arabidopsis. Total RNA was extracted from the leaves of 15-day-old WT and transgenic Arabidopsis, and then OsS1Fa1, OsS1Fa1(TMm1), OsS1Fa1(mNLS ), OsS1Fa1(K63R) transcripts were examined by RT-PCR using OsS1Fa1- and FLAG-specific primers. (B) Seeds of WT, OsS1Fa1-, OsS1Fa1(mNLS)-, OsS1Fa1(K63R)-, and OsS1Fa1(TMm1)- overexpressing Arabidopsis were grown for 15 days in moist soil, and watering was withheld for 7 days for drought stress treatment. Following the drought stress treatment, the plants were rewatered, and photographs taken after an additional 3 and 5 days.

Article Snippet: Rice leaf, culm, and root samples were thoroughly ground, and total RNA was extracted from the ground tissue using the FavorPrepTM Plant Total RNA Mini Kit (Favorgen).

Techniques: Transgenic Assay, Mutagenesis, Expressing, Reverse Transcription Polymerase Chain Reaction