Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR

<p>Abstract</p> <p>Background</p> <p>The wild grass species <it>Brachypodium distachyon </it>(Brachypodium hereafter) is emerging as a new model system for grass crop genomics research and biofuel grass biology. A draft nuclear genome sequence is expected to be publicly available in the near future; an explosion of gene expression studies will undoubtedly follow. Therefore, stable reference genes are necessary to normalize the gene expression data.</p> <p>Results</p> <p>A systematic exploration of suitable reference genes in Brachypodium is presented here. Nine reference gene candidates were chosen, and their gene sequences were obtained from the Brachypodium expressed sequence tag (EST) databases. Their expression levels were examined by quantitative real-time PCR (qRT-PCR) using 21 different Brachypodium plant samples, including those from different plant tissues and grown under various growth conditions. Effects of plant growth hormones were also visualized in the assays. The expression stability of the candidate genes was evaluated using two analysis software packages, geNorm and NormFinder. In conclusion, the ubiquitin-conjugating enzyme 18 gene (<it>UBC18</it>) was validated as a suitable reference gene across all the plant samples examined. While the expression of the polyubiquitin genes (<it>Ubi4 </it>and <it>Ubi10</it>) was most stable in different plant tissues and growth hormone-treated plant samples, the expression of the S-adenosylmethionine decarboxylase gene (<it>SamDC</it>) ranked was most stable in plants grown under various environmental stresses.</p> <p>Conclusion</p> <p>This study identified the reference genes that are most suitable for normalizing the gene expression data in Brachypodium. These reference genes will be particularly useful when stress-responsive genes are analyzed in order to produce transgenic plants that exhibit enhanced stress resistance.</p

Perovskite-polymer composite cross-linker approach for highly-stable and efficient perovskite solar cells.

Manipulation of grain boundaries in polycrystalline perovskite is an essential consideration for both the optoelectronic properties and environmental stability of solar cells as the solution-processing of perovskite films inevitably introduces many defects at grain boundaries. Though small molecule-based additives have proven to be effective defect passivating agents, their high volatility and diffusivity cannot render perovskite films robust enough against harsh environments. Here we suggest design rules for effective molecules by considering their molecular structure. From these, we introduce a strategy to form macromolecular intermediate phases using long chain polymers, which leads to the formation of a polymer-perovskite composite cross-linker. The cross-linker functions to bridge the perovskite grains, minimizing grain-to-grain electrical decoupling and yielding excellent environmental stability against moisture, light, and heat, which has not been attainable with small molecule defect passivating agents. Consequently, all photovoltaic parameters are significantly enhanced in the solar cells and the devices also show excellent stability

Angleâ Insensitive and CMOSâ Compatible Subwavelength Color Printing

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/134900/1/adom201600287_am.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134900/2/adom201600287.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/134900/3/adom201600287-sup-0001-S1.pd

Volumetric photoacoustic endoscopy of upper gastrointestinal tract: ultrasonic transducer technology development

We have successfully implemented a focused ultrasonic transducer for photoacoustic endoscopy. The photoacoustic endoscopic probe's ultrasound transducer determines the lateral resolution of the system. By using a focused ultrasonic transducer, we significantly improved the endoscope's spatial resolution and signal-to-noise ratio. This paper describes the technical details of the ultrasonic transducer incorporated into the photoacoustic endoscopic probe and the experimental results from which the transducer's resolution is quantified and the image improvement is validated

Deep-Learning-Based Algorithm for the Removal of Electromagnetic Interference Noise in Photoacoustic Endoscopic Image Processing

Despite all the expectations for photoacoustic endoscopy (PAE), there are still several technical issues that must be resolved before the technique can be successfully translated into clinics. Among these, electromagnetic interference (EMI) noise, in addition to the limited signal-to-noise ratio (SNR), have hindered the rapid development of related technologies. Unlike endoscopic ultrasound, in which the SNR can be increased by simply applying a higher pulsing voltage, there is a fundamental limitation in leveraging the SNR of PAE signals because they are mostly determined by the optical pulse energy applied, which must be within the safety limits. Moreover, a typical PAE hardware situation requires a wide separation between the ultrasonic sensor and the amplifier, meaning that it is not easy to build an ideal PAE system that would be unaffected by EMI noise. With the intention of expediting the progress of related research, in this study, we investigated the feasibility of deep-learning-based EMI noise removal involved in PAE image processing. In particular, we selected four fully convolutional neural network architectures, U-Net, Segnet, FCN-16s, and FCN-8s, and observed that a modified U-Net architecture outperformed the other architectures in the EMI noise removal. Classical filter methods were also compared to confirm the superiority of the deep-learning-based approach. Still, it was by the U-Net architecture that we were able to successfully produce a denoised 3D vasculature map that could even depict the mesh-like capillary networks distributed in the wall of a rat colorectum. As the development of a low-cost laser diode or LED-based photoacoustic tomography (PAT) system is now emerging as one of the important topics in PAT, we expect that the presented AI strategy for the removal of EMI noise could be broadly applicable to many areas of PAT, in which the ability to apply a hardware-based prevention method is limited and thus EMI noise appears more prominently due to poor SNR

Tapered catheter-based transurethral photoacoustic and ultrasonic endoscopy of the urinary system

Early diagnosis is critical for treating bladder cancer, as this cancer is very aggressive and lethal if detected too late. To address this important clinical issue, a photoacoustic tomography (PAT)-based transabdominal imaging approach was suggested in previous reports, in which its in vivo feasibility was also demonstrated based on a small animal model. However, successful translation of this approach to real clinical settings would be challenging because the human bladder is located at a depth that far exceeds the typical penetration depth of PAT (???3 cm for in vivo cases). In this study, we developed a tapered catheter-based, transurethral photoacoustic and ultrasonic endoscopic probe with a 2.8 mm outer diameter to investigate whether the well-known benefits of PAT can be harnessed to resolve unmet urological issues, including early diagnosis of bladder cancer. To demonstrate the in vivo imaging capability of the proposed imaging probe, we performed a rabbit model-based urinary system imaging experiment and acquired a 3D microvasculature map distributed in the wall of the urinary system, which is a first in PAT, to the best of our knowledge. We believe that the results strongly support the use of this transurethral imaging approach as a feasible strategy for addressing urological diagnosis issues

Protective Immunity Against Challenge Infection with Trichinella spiralis in the Rat

Protective immunity and immune response were studied in rats after primarily infection with Trichinella spiralis. The parameters measured include serum antibody isotype responses, mesenteric lymph node (MLN) cell and spleen cell proliferation responses in vitro, and the levels of interferon (IFN)-γ, interleukin (IL)-2, IL-4 and IL-10 as markers of the T-helper (Th) subset. Protective immunity was assessed by the degree of expulsion of adult worms from the rat intestine. Protective immunity against adult worms after challenge infection was 99.80%. Although IFN-γ, IL-2, IL-4 and IL-10 in both the MLNs and spleen were detected, IFN-γ and IL-2 levels were higher in the spleen than in the MLNs, and IL-4 and an increased amount of IL-10 was released in the MLNs as compared to the spleen. The levels of the specific immunoglobulins (Ig) G, IgM, IgG1 and IgG2a on week 6 after primary infection, and on day 7 after challenge infection, were higher as compared to levels in uninfected rats that only received a challenge infection (P ? 0.001), whereas the antibody level of IgG1 was significantly elevated from that of IgG2a (P ? 0.001). These results demonstrate that Th1 type responses predominated. In addition, as Th2 type cytokines were also produced, it is proposed that the protective immunity by primary infection was also related to the Th1 type responses