Small RNA Profile in Moso Bamboo Root and Leaf Obtained by High Definition Adapters

AbstractNext generation sequencing of small RNA (sRNA) libraries is widely used for studying sRNAs in various biological systems. However, cDNA libraries of sRNAs are biased for molecules that are ligated to adapters more or less efficiently than other molecules. One approach to reduce this ligation bias is to use a pool of adapters instead of a single adapter sequence, which allows many sRNAs to be ligated efficiently. We previously developed High Definition (HD) adapters for the Illumina sequencing platform, which contain degenerate nucleotides at the ligating ends of the adapters. However, the current commercial kits produced a large amount of 5’ adapter – 3’ adapter ligation product without the cDNA insert when HD adapters were used to replace the kit adapters. Here, we report a protocol to generate sRNA libraries using HD adapters with greatly reduced proportion of adapter-adapter products due to the degradation of nonligated 3’ adapters. The libraries can be completed within two days and can be used for various biological and clinical samples. As examples for using this protocol, we constructed sRNA libraries using total RNA extracted from cultured mammalian cells and plant leaf tissue.

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Transcriptionally active LTR retroelement-related sequences and their relationship with small RNA in moso bamboo (Phyllostachys edulis)

Molecular Breeding ◽

10.1007/s11032-017-0733-6 ◽

2017 ◽

Vol 37 (10) ◽

Cited By ~ 4

Author(s):

Mingbing Zhou ◽

Yihang Zhu ◽

Youhuang Bai ◽

Heikki Hänninen ◽

Xianwen Meng

Keyword(s):

Small Rna ◽

Moso Bamboo ◽

Phyllostachys Edulis

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Integrated mRNA, MicroRNA Transcriptome and Degradome Analyses Provide Insights into Stamen Development in Moso Bamboo

Plant and Cell Physiology ◽

10.1093/pcp/pcz179 ◽

2019 ◽

Vol 61 (1) ◽

pp. 76-87 ◽

Cited By ~ 3

Author(s):

Zhanchao Cheng ◽

Dan Hou ◽

Wei Ge ◽

Xiangyu Li ◽

Lihua Xie ◽

...

Keyword(s):

Small Rna ◽

Moso Bamboo ◽

Molecular Networks ◽

Anther Dehiscence ◽

Floral Organs ◽

Stamen Development ◽

Secondary Thickening ◽

Expression Of Genes ◽

Section Result

Abstract A flower is an essential organ for sexual reproduction in flowering plants, which has been extensively studied in model plants. In this study, we used transcriptomic, small RNA and degradome analyses to characterize key microRNAs (miRNAs) and their targets in floral organs of moso bamboo. In total, we identified 13,051 differentially expressed genes and 109 known miRNAs from 26 miRNA families. We aligned the miRNAs to known miRNA databases and revealed some conserved as well as novel miRNAs. Sixteen conserved miRNAs were specifically and highly expressed in stamens, including miRNA159 and miRNA166. In situ hybridization shows that miRNA159 plays a key role in the regulation of stamen development, and the expression levels of its targets PheMYB98 and PheMYB42 were low. Furthermore, Phe-MIRNA159 partially recovers phenotypes of mir159ab double mutant. Overexpression of Phe-MIR159 could cause failure in anther dehisce, and the mature pollens could not be dispersed and further reduce fertility in Arabidopsis. Semi-thin section result shows that anther endothelial layer of Phe-MIRNA159 overexpressing lines is lack of secondary thickening, resulting in limited force for anther opening. Phe-miR159 may regulate the expression of genes related to secondary thickening through negative regulation of AtMYB33, affecting the anther dehiscence. Taken together, this study provides insights regarding molecular networks underlying floral organs development of moso bamboo.

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Routine Digital Processing of Microscope Images

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100181506 ◽

1990 ◽

Vol 48 (1) ◽

pp. 550-551

Author(s):

E. Wisse ◽

A. Geerts ◽

R.B. De Zanger

Keyword(s):

Operating System ◽

Digital Processing ◽

Hard Disks ◽

The Sun ◽

Tape Drive ◽

High Definition ◽

Fluorescent Microscope ◽

Microscope Images ◽

Helical Scan ◽

Ethernet Connection

The slowscan and TV signal of the Philips SEM 505 and the signal of a TV camera attached to a Leitz fluorescent microscope, were digitized by the data acquisition processor of a Masscomp 5520S computer, which is based on a 16.7 MHz 68020 CPU with 10 Mb RAM memory, a graphics processor with two frame buffers for images with 8 bit / 256 grey values, a high definition (HD) monitor (910 × 1150), two hard disks (70 and 663 Mb) and a 60 Mb tape drive. The system is equipped with Imaging Technology video digitizing boards: analog I/O, an ALU, and two memory mapped frame buffers for TV images of the IP 512 series. The Masscomp computer has an ethernet connection to other computers, such as a Vax PDP 11/785, and a Sun 368i with a 327 Mb hard disk and a SCSI interface to an Exabyte 2.3 Gb helical scan tape drive. The operating system for these computers is based on different versions of Unix, such as RTU 4.1 (including NFS) on the acquisition computer, bsd 4.3 for the Vax, and Sun OS 4.0.1 for the Sun (with NFS).

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Enhancing Clinical Supervision Using High-Definition Real-Time Digital Recording, Annotation, and Bluetooth Technology

Perspectives of the ASHA Special Interest Groups ◽

10.1044/2019_pers-sig11-2018-0020 ◽

2019 ◽

Vol 4 (2) ◽

pp. 356-362

Author(s):

Jennifer W. Means ◽

Casey McCaffrey

Keyword(s):

Graduate Students ◽

Data Collection ◽

Real Time ◽

Clinical Supervision ◽

Video Recording ◽

Advanced Technology ◽

High Definition ◽

Recording Technology ◽

Self Confidence ◽

Additional Data Collection

Purpose The use of real-time recording technology for clinical instruction allows student clinicians to more easily collect data, self-reflect, and move toward independence as supervisors continue to provide continuation of supportive methods. This article discusses how the use of high-definition real-time recording, Bluetooth technology, and embedded annotation may enhance the supervisory process. It also reports results of graduate students' perception of the benefits and satisfaction with the types of technology used. Method Survey data were collected from graduate students about their use and perceived benefits of advanced technology to support supervision during their 1st clinical experience. Results Survey results indicate that students found the use of their video recordings useful for self-evaluation, data collection, and therapy preparation. The students also perceived an increase in self-confidence through the use of the Bluetooth headsets as their supervisors could provide guidance and encouragement without interrupting the flow of their therapy sessions by entering the room to redirect them. Conclusions The use of video recording technology can provide opportunities for students to review: videos of prospective clients they will be treating, their treatment videos for self-assessment purposes, and for additional data collection. Bluetooth technology provides immediate communication between the clinical educator and the student. Students reported that the result of that communication can improve their self-confidence, perceived performance, and subsequent shift toward independence.

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