"Per cell" normalization method for mRNA measurement by quantitative PCR and microarrays

BACKGROUND: Transcriptome data from quantitative PCR (Q-PCR) and DNA microarrays are typically obtained from a fixed amount of RNA collected per sample. Therefore, variations in tissue cellularity and RNA yield across samples in an experimental series compromise accurate determination of the absolute level of each mRNA species per cell in any sample. Since mRNAs are copied from genomic DNA, the simplest way to express mRNA level would be as copy number per template DNA, or more practically, as copy number per cell. RESULTS: Here we report a method (designated the "Percellome" method) for normalizing the expression of mRNA values in biological samples. It provides a "per cell" readout in mRNA copy number and is applicable to both quantitative PCR (Q-PCR) and DNA microarray studies. The genomic DNA content of each sample homogenate was measured from a small aliquot to derive the number of cells in the sample. A cocktail of five external spike RNAs admixed in a dose-graded manner (dose-graded spike cocktail; GSC) was prepared and added to each homogenate in proportion to its DNA content. In this way, the spike mRNAs represented absolute copy numbers per cell in the sample. The signals from the five spike mRNAs were used as a dose-response standard curve for each sample, enabling us to convert all the signals measured to copy numbers per cell in an expression profile-independent manner. A series of samples was measured by Q-PCR and Affymetrix GeneChip microarrays using this Percellome method, and the results showed up to 90 % concordance. CONCLUSION: Percellome data can be compared directly among samples and among different studies, and between different platforms, without further normalization. Therefore, "percellome" normalization can serve as a standard method for exchanging and comparing data across different platforms and among different laboratories

Terahertz wireless communication at 560-GHz band using Kerr micro-resonator soliton comb

Terahertz (THz) waves have attracted attention as carrier waves for next-generation wireless communications (6G). Electronic THz emitters are widely used in current mobile communications; however, they may face technical limitations in 6G with upper-frequency limits. We demonstrate wireless communication in a 560-GHz band by using a photonic THz emitter based on photomixing of a 560-GHz-spacing soliton microcomb in a uni-travelling carrier photodiode together with a THz receiver of Schottky barrier diode. The on-off keying data transfer with 2-Gbit/s achieves a Q-factor of 3.4, thus, satisfying the limit of forward error correction.Comment: 17 pages, 4 figur

Terahertz wireless communication in a 560-GHz band using a Kerr micro-resonator soliton comb

Terahertz (THz) waves have attracted attention as carrier waves for next-generation wireless communications (6 G). Electronic THz emitters are widely used in current mobile communications; however, they may face technical limitations in 6 G with upper-frequency limits. We demonstrate wireless communication in a 560-GHz band by using a photonic THz emitter based on photomixing of a 560-GHz-spacing soliton microcomb in a uni-travelling carrier photodiode together with a THz receiver of Schottky barrier diode. The on-off keying data transfer with 2-Gbit/s achieves a Q-factor of 3.4, thus, satisfying the limit of forward error correction

Wireless data transmission in a 560-GHz band using low-phase-noise terahertz wave generated by photomixing of a pair of distributed feedback lasers injection-locking to Kerr micro-resonator soliton comb

The demand for higher data rates in next-generation mobile wireless communication systems (6G) has led to significant interest in terahertz (THz) waves as a high-frequency, broad modulation bandwidth carrier wave. In this study, we propose and demonstrate a wireless data transfer in the 560-GHz band using low-phase-noise THz waves generated by photomixing of a pair of distributed feedback lasers injection-locking to Kerr micro-resonator soliton comb. Experimental results showed near-error-free on-off keying (OOK) data transfer at 1 Gbit/s in the 560-GHz band, with a Q-factor of 6.23, surpassing the error-free limit. Also, modulation formats of binary phase shift keying (BPSK) and quadrature phase shift keying (QPSK) were successfully used, showing clear constellation diagrams and relatively low root mean squared error vector magnitude (rms EVM) values of 23.9% and 23.6%, respectively. Moreover, data transfer at 0.4 Gbit/s in 16 quadrature amplitude modulation (16QAM) demonstrated clear isolated symbols and achieved a low rms EVM value of 8.1%, complying with the IEEE 802.15.3d standard amendment. These demonstrations highlight the potential of using injection-locked DFB lasers with the Kerr micro-resonator soliton comb to achieve high-quality, high-speed wireless data transfer in the 560-GHz band. These findings contribute significantly to the advancement of wireless communication technology in the THz frequency range and pave the way for the realization of 6G wireless communication systems

Carrier conversion from terahertz wave to dual-wavelength near-infrared light injection-locking to optical comb using asynchronous nonpolarimetric electro-optic downconversion with electro-optic polymer modulator

THz waves are promising wireless carriers for next-generation wireless communications, where a seamless connection from wireless to optical communication is required. In this study, we demonstrate carrier conversion from THz waves to dual-wavelength NIR light injection-locking to an optical frequency comb using asynchronous nonpolarimetric electro-optic downconversion with an electro-optic polymer modulator. THz wave in the W band was obtained as a stable photonic RF beat signal of 1 GHz with a signal-to-noise ratio of 25 dB via the proposed THz-to-NIR carrier conversion. In addition, the results imply the potential of the photonic detection of THz waves for wireless-to-optical seamless communication.Comment: 15 pages, 5 figure

Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene

Minichromosome Maintenance 2 Bound with Retroviral Gp70 Is Localized to Cytoplasm and Enhances DNA-Damage-Induced Apoptosis

The interaction of viral proteins with host-cellular proteins elicits the activation of cellular signal transduction pathways and possibly leads to viral pathogenesis as well as cellular biological events. Apoptotic signals induced by DNA-damage are remarkably up-regulated by Friend leukemia virus (FLV) exclusively in C3H hosts; however, the mechanisms underlying the apoptosis enhancement and host-specificity are unknown. Here, we show that C3H mouse-derived hematopoietic cells originally express higher levels of the minichromosome maintenance (MCM) 2 protein than BALB/c- or C57BL/6-deriverd cells, and undergo more frequent apoptosis following doxorubicin-induced DNA-damage in the presence of the FLV envelope protein gp70. Dual transfection with gp70/Mcm2 reproduced doxorubicin-induced apoptosis even in BALB/c-derived 3T3 cells. Immunoprecipitation assays using various deletion mutants of MCM2 revealed that gp70 bound to the nuclear localization signal (NLS) 1 (amino acids 18–24) of MCM2, interfered with the function of NLS2 (amino acids 132–152), and suppressed the normal nuclear-import of MCM2. Cytoplasmic MCM2 reduced the activity of protein phosphatase 2A (PP2A) leading to the subsequent hyperphosphorylation of DNA-dependent protein kinase (DNA-PK). Phosphorylated DNA-PK exhibited elevated kinase activity to phosphorylate P53, thereby up-regulating p53-dependent apoptosis. An apoptosis-enhancing domain was identified in the C-terminal portion (amino acids 703–904) of MCM2. Furthermore, simultaneous treatment with FLV and doxorubicin extended the survival of SCID mice bearing 8047 leukemia cells expressing high levels of MCM2. Thus, depending on its subcellular localization, MCM2 plays different roles. It participates in DNA replication in the nucleus as shown previously, and enhances apoptosis in the cytoplasm