Identification and profiling of microRNA between back and belly Skin in Rex rabbits (Oryctolagus cuniculus)

[EN] Skin is an important trait for Rex rabbits and skin development is influenced by many processes, including hair follicle cycling, keratinocyte differentiation and formation of coat colour and skin morphogenesis. We identified differentially expressed microRNAs (miRNAs) between the back and belly skin in Rex rabbits. In total, 211 miRNAs (90 upregulated miRNAs and 121 downregulated miRNAs) were identified with a |log2 (fold change)|>1 and P-value<0.05. Using target gene prediction for the miRNAs, differentially expressed predicted target genes were identified and the functional enrichment and signalling pathways of these target genes were processed to reveal their biological functions. A number of differentially expressed miRNAs were found to be involved in regulation of the cell cycle, skin epithelium differentiation, keratinocyte proliferation, hair follicle development and melanogenesis. In addition, target genes regulated by miRNAs play key roles in the activities of the Hedgehog signalling pathway, Wnt signalling pathway, Osteoclast differentiation and MAPK pathway, revealing mechanisms of skin development. Nine candidate miRNAs and 5 predicted target genes were selected for verification of their expression by quantitative reverse transcription polymerase chain reaction. A regulation network of miRNA and their target genes was constructed by analysing the GO enrichment and signalling pathways. Further studies should be carried out to validate the regulatory relationships between candidate miRNAs and their target genes.This study was supported by the Modern Agricultural Industrial System Special Funding (CARS-44-A-1), the Priority Academic Programme Development of Jiangsu Higher Education Institutions (2014-134) and the General Programme of Natural Science Foundation of the Higher Education Institutions of Jiangsu Province (16KJB230001).Zhao, B.; Chen, Y.; Mu, L.; Hu, S.; Wu, X. (2018). Identification and profiling of microRNA between back and belly Skin in Rex rabbits (Oryctolagus cuniculus). World Rabbit Science. 26(2):179-190. https://doi.org/10.4995/wrs.2018.7058SWORD179190262Adamidi C. 2008. Discovering microRNAs from deep sequencing data using miRDeep. Nature Biotechnol., 26: 407-415. https://doi.org/10.1038/nbt1394Adijanto J., Castorino J.J., Wang Z.X., Maminishkis A., Grunwald G.B., Philp N.J. 2012. 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Municipal sewage sludge compost promotes Mangifera persiciforma tree growth with no risk of heavy metal contamination of soil

Application of sewage sludge compost (SSC) as a fertilizer on landscaping provides a potential way for the effective disposal of sludge. However, the response of landscape trees to SSC application and the impacts of heavy metals from SSC on soil are poorly understood. We conducted a pot experiment to investigate the effects of SSC addition on Mangifera persiciforma growth and quantified its uptake of heavy metals from SSC by setting five treatments with mass ratios of SSC to lateritic soil as 0%:100% (CK), 15%:85% (S15), 30%:70% (S30), 60%:40% (S60), and 100%:0% (S100). As expected, the fertility and heavy metal concentrations (Cu, Zn, Pb and Cd) in substrate significantly increased with SSC addition. The best performance in terms of plant height, ground diameter, biomass and N, P, K uptake were found i n S30, implying a reasonable amount of SSC could benefit the growth of M. persiciforma. The concentrations of Cu, Pb and Cd in S30 were insignificantly different from CK after harvest, indicating that M. persiciforma reduced the risk of heavy metal contamination of soil arising from SSC application. This study suggests that a reasonable rate of SSC addition can enhance M. persiciforma growth without causing the contamination of landscaping soil by heavy metals

Systematic Analysis of Non-coding RNAs Involved in the Angora Rabbit (Oryctolagus cuniculus) Hair Follicle Cycle by RNA Sequencing

The hair follicle (HF) cycle is a complicated and dynamic process in mammals, associated with various signaling pathways and gene expression patterns. Non-coding RNAs (ncRNAs) are RNA molecules that are not translated into proteins but are involved in the regulation of various cellular and biological processes. This study explored the relationship between ncRNAs and the HF cycle by developing a synchronization model in Angora rabbits. Transcriptome analysis was performed to investigate ncRNAs and mRNAs associated with the various stages of the HF cycle. One hundred and eleven long non-coding RNAs (lncRNAs), 247 circular RNAs (circRNAs), 97 microRNAs (miRNAs), and 1,168 mRNAs were differentially expressed during the three HF growth stages. Quantitative real-time PCR was used to validate the ncRNA transcriptome analysis results. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses provided information on the possible roles of ncRNAs and mRNAs during the HF cycle. In addition, lncRNA–miRNA–mRNA and circRNA–miRNA–mRNA ceRNA networks were constructed to investigate the underlying relationships between ncRNAs and mRNAs. LNC_002919 and novel_circ_0026326 were found to act as ceRNAs and participated in the regulation of the HF cycle as miR-320-3p sponges. This research comprehensively identified candidate regulatory ncRNAs during the HF cycle by transcriptome analysis, highlighting the possible association between ncRNAs and the regulation of hair growth. This study provides a basis for systematic further research and new insights on the regulation of the HF cycle

Deubiquitination of MITF-M Regulates Melanocytes Proliferation and Apoptosis

Microphthalmia-associated transcription factor-M (MITF-M) is the key gene in the proliferation and differentiation of melanocytes, which undergoes an array of post-translation modifications. As shown in our previous study, deubiquitinase USP13 is directly involved in melanogenesis. However, it is still ambiguous that the effect of USP13-mediated MITF-M expression on melanocytes proliferation and apoptosis. Herein, we found that MITF-M overexpressing melanocytes showed high cell proliferation, reduced apoptosis, and increased melanin levels. Besides, melanin-related genes, TYR, DCT, GPNMB, and PMEL, were significantly up-regulated in MITF-M overexpressing melanocytes. Furthermore, Exogenous USP13 significantly upregulated the endogenous MITF-M protein level, downregulated USP13 significantly inhibited MITF-M protein levels, without altering MITF-M mRNA expression. In addition, USP13 upregulation mitigated the MITF-M degradation and significantly increased the half-life of MITF-M. Also, USP13 stabilized the exogenous MITF protein levels. In conclusion, the MITF-M level was regulated by USP13 deubiquitinase in melanocytes, affecting melanocytes proliferation and apoptosis. This study provides the theoretical basis for coat color transformation that could be useful in the development of the new breed in fur animals

Scaling from single-point sap velocity measurements to stand transpiration in a multispecies deciduous forest: Uncertainty sources, stand structure effect, and future scenarios

9 páginas.-- 5 figuras.-- 2 tablas.-- 58 referencias[EN] A major challenge in studies estimating stand water use in mixed-species forests is how to effectively scale data from individual trees to the stand. This is the case for forest ecosystems in the northeastern USA where differences in water use among species and across different size classes have not been extensively studied, despite their relevance for a wide range of ecosystem services. Our objectives were to assess the importance of different sources of variability on transpiration upscaling and explore the potential impacts of future shifts in species composition on the forest water budget. We measured sap velocity in five tree species (Fagus grandifolia Ehrh., Acer rubrum L., Acer saccharum Marsh., Betula alleghaniensis Britton, and Betula papyrifera Marsh.) in a mature stand and a young stand in New Hampshire, USA. Our results showed that the greatest potential source of error was radial variability and that tree size was more important than species in determining sap velocity. Total sapwood area was demonstrated to exert a strong controlling influence on transpiration, varying depending on tree size and species. We conclude that the effect of potential species shifts on transpiration will depend on the sap velocity, determined not only by radial variation and tree size, but also by the sapwood area distribution in the stand.[FR] Les études dont le but est d'estimer l'utilisation de l'eau a` l'échelle du peuplement dans les forêts mélangées font face a` un défi majeur : comment passer efficacement de l'échelle des arbres individuels a` l'échelle du peuplement. C'est le cas pour les écosystèmes forestiers dans le nord-est des États-Unis où les différences dans l'utilisation de l'eau entre les espèces et parmi les différentes catégories de taille n'ont pas fait l'objet d'études approfondies malgré leur pertinence pour une vaste gamme de services de l'écosystème. Nos objectifs consistaient a` évaluer l'importance des différentes sources de variation sur l'extrapolation de la transpiration et a` explorer les impacts potentiels des changements futurs dans la composition en espèces sur le bilan hydrique de la forêt. Nous avons mesuré la vitesse de la sève chez cinq espèces d'arbre (Fagus grandifolia Ehrh., Acer rubrum L., Acer saccharum Marsh., Betula alleghaniensis Britton et Betula papyrifera Marsh.) dans un peuplement mature et dans un jeune peuplement au New Hampshire (É.-U.). Nos résultats ont montré que la plus grande source potentielle d'erreur était la variation radiale et que la vitesse de la sève était davantage déterminée par la taille des arbres que par l'espèce. La surface totale de bois d'aubier avait un effet très déterminant sur la transpiration qui variait selon la taille et l'espèce d'arbre. Nous concluons que l'effet des changements potentiels dans la composition en espèces sur la transpiration dépendra de la vitesse de la sève qui est principalement déterminée par la variation radiale et la taille des arbres mais aussi de la distribution de la surface de bois d'aubier dans le peuplement.This work was funded by the University of New Hampshire and the New Hampshire Agricultural Experiment Station. The Bartlett Experimental Forest is operated by the USDA Forest Service Northern Research Station. S. Mcgraw, P. Pellissier, C. Breton, S. Alvarado-Barrientos, R. Snyder, and Z. Aldag assisted in the field and in the lab. The 2011 stand inventory was led by S. Goswami. Tree heights were measured and compiled by C. Blodgett, T. Fahey, and L. Liu. A. Richardson shared meteorology and solar radiation data from the Bartlett Amerflux tower. The stands used in this experiment are maintained and monitored by the MELNHE project under the direction of R. Yanai and M. Fisk, with funding from NSF grants DEB 0235650 and DEB 0949324Peer reviewe

Physics-informed deep learning for fringe pattern analysis

Recently, deep learning has yielded transformative success across optics and photonics, especially in optical metrology. Deep neural networks (DNNs) with a fully convolutional architecture (e.g., U-Net and its derivatives) have been widely implemented in an end-to-end manner to accomplish various optical metrology tasks, such as fringe denoising, phase unwrapping, and fringe analysis. However, the task of training a DNN to accurately identify an image-to-image transform from massive input and output data pairs seems at best naïve, as the physical laws governing the image formation or other domain expertise pertaining to the measurement have not yet been fully exploited in current deep learning practice. To this end, we introduce a physics-informed deep learning method for fringe pattern analysis (PI-FPA) to overcome this limit by integrating a lightweight DNN with a learning-enhanced Fourier transform profilometry (LeFTP) module. By parameterizing conventional phase retrieval methods, the LeFTP module embeds the prior knowledge in the network structure and the loss function to directly provide reliable phase results for new types of samples, while circumventing the requirement of collecting a large amount of high-quality data in supervised learning methods. Guided by the initial phase from LeFTP, the phase recovery ability of the lightweight DNN is enhanced to further improve the phase accuracy at a low computational cost compared with existing end-to-end networks. Experimental results demonstrate that PI-FPA enables more accurate and computationally efficient single-shot phase retrieval, exhibiting its excellent generalization to various unseen objects during training. The proposed PI-FPA presents that challenging issues in optical metrology can be potentially overcome through the synergy of physics-priors-based traditional tools and data-driven learning approaches, opening new avenues to achieve fast and accurate single-shot 3D imaging

Diagnostic accuracy of a novel optical coherence tomography-based fractional flow reserve algorithm for assessment of coronary stenosis significance

Background: This study aimed to introduce a novel optical coherence tomography-derived fractional flow reserve (FFR) computational approach and assess the diagnostic performance of the algorithm for assessing physiological function. Methods: The fusion of coronary optical coherence tomography and angiography was used to generate a novel FFR algorithm (AccuFFRoct) to evaluate functional ischemia of coronary stenosis. In the current study, a total of 34 consecutive patients were included, and AccuFFRoct was used to calculate the FFR for these patients. With the wire-measured FFR as the reference standard, we evaluated the performance of our approach by accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Results: Per vessel accuracy, sensitivity, specificity, PPV, and NPV for AccuFFRoct in identifying hemodynamically significant coronary stenosis were 93.8%, 94.7%, 92.3%, 94.7%, and 92.3%, respectively, were found. Good correlation (Pearson’s correlation coefficient r = 0.80, p &lt; 0.001) between AccuFFRoct and FFR was observed. The Bland-Altman analysis showed a mean difference value of –0.037 (limits of agreement: –0.189 to 0.115). The area under the receiver-operating characteristic curve (AUC) of AccuFFRoct in identifying physiologically significant stenosis was 0.94, which was higher than the minimum lumen area (MLA, AUC = 0.91) and significantly higher than the diameter stenosis (%DS, AUC = 0.78). Conclusions: This clinical study shows the efficiency and accuracy of AccuFFRoct for clinical implementation when using invasive FFR measurement as a reference. It could provide important insights into coronary imaging superior to current methods based on the degree of coronary artery stenosis