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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Oblivious Transfer from Rerandomizable PKE

The relationship between oblivious transfer (OT) and public-key encryption (PKE) has been studied by Gertner et al. (FOCS 2000). They showed that OT can be constructed from special types of PKE, i.e., PKE with oblivious sampleability of public keys or ciphertexts. In this work, we give new black-box constructions of OT from PKE without any oblivious sampleability. Instead, we require that the PKE scheme is rerandomizable, meaning that one can use the public key to rerandomize a ciphertext into a fresh ciphertext. We give two different OT protocols with different efficiency features based on rerandomizable PKE. For $1$-out-of-$n$ OT, in our first OT protocol, the sender has sublinear (in $n$) cost, and in our second OT protocol, the cost of the receiver is independent of $n$. As a comparison, in the PKE-based OT protocols of Gertner et al., both the sender and receiver have linear cost

The transcription factor CREB is involved in sorafenib-inhibited renal cancer cell proliferation, migration and invasion

Our previous reports showed that the cyclic-AMP-response element-binding protein (CREB) served as a proto-oncogene in the process of tumorigenesis and mediated the growth and metastatic activity of renal cancer cells. Our study, therefore, explored the role of CREB in sorafenib-inhibited cell proliferation, migration and invasion. Renal cancer cells were cultured in medium containing sorafenib for 12, 24, 48 and 72 h. The MTT assay was used to study the cytotoxic effects of sorafenib. Cell invasion and migration were assayed in wound healing and transwell experiments, respectively. Protein expression levels were evaluated by western blotting. The results show that sorafenib treatment decreased cell viability in a dose- and time-dependent manner. Sorafenib inhibited cell migration and invasion and decreased the expression of MMP-2 and MMP-9. Moreover, addition of the recombinant plasmid pCI-neo/CREB (PN) reversed the sorafenib-induced inhibition of cell proliferation, migration and invasion. These results show that CREB is associated with the sorafenib-induced inhibition of proliferation, migration and invasion

Revisiting the Multisite Phosphorylation That Produces the M-Phase Supershift of Key Mitotic Regulators

The term M-phase supershift denotes the phosphorylation-dependent substantial increase in the apparent molecular weight of numerous proteins of varied biological functions during M-phase induction. Although the M-phase supershift of multiple key mitotic regulators has been attributed to the multisite phosphorylation catalyzed by the Cdk1/cyclin B/Cks complex, this view is challenged by multiple lines of paradoxical observations. To solve this problem, we reconstituted the M-phase supershift of Xenopus Cdc25C, Myt1, Wee1A, APC3, and Greatwall in Xenopus egg extracts and characterized the supershift-producing phosphorylations. Our results demonstrate that their M-phase supershifts are each due to simultaneous phosphorylation of a considerable portion of S/T/Y residues in a long intrinsically disordered region that is enriched in both S/T residues and S/TP motifs. Although the major mitotic kinases in Xenopus egg extracts, Cdk1, MAPK, Plx1, and RSK2, are able to phosphorylate the five mitotic regulators, they are neither sufficient nor required to produce the M-phase supershift. Accordingly, inhibition of the four major mitotic kinase activities in Xenopus oocytes did not inhibit the M-phase supershift in okadaic acid-induced oocyte maturation. These findings indicate that the M-phase supershift is produced by a previously unrecognized category of mitotic phosphorylation that likely plays important roles in M-phase induction

Intrinsic Electronic Structure and Nodeless Superconducting Gap of YBa2Cu3O7−δ\mathrm{YBa_{2} Cu_{3} O_{7-\delta} } Observed by Spatially-Resolved Laser-Based Angle Resolved Photoemission Spectroscopy

The spatially-resolved laser-based high resolution ARPES measurements have been performed on the optimally-doped $\mathrm{YBa_{2} Cu_{3} O_{7-\delta} }$ (Y123) superconductor. For the first time, we found the region from the cleaved surface that reveals clear bulk electronic properties. The intrinsic Fermi surface and band structures of Y123 are observed. The Fermi surface-dependent and momentum-dependent superconducting gap is determined which is nodeless and consistent with the d+is gap form

Encode and Permute that Database! Single-Server Private Information Retrieval with Constant Online Time, Communication, and Client-Side Storage

Private Information Retrieval (PIR) facilitates the retrieval of database entries by a client from a remote server without revealing which specific entry is being queried. The preprocessing model has emerged as a significant technique for constructing efficient PIR systems, allowing parties to execute a one-time, query-independent offline phase, and then a fast online retrieval phase. In particular, Corrigan-Gibbs and Kogan (EUROCRYPT 2020) presented a new framework for constructing PIR with sublinear online time. Nevertheless, their protocol is deemed impractical in the single-server setting due to the heavy use of Fully Homomorphic Encryption (FHE). More recently, two state-of-the-art (SOTA) single-server PIR protocols (Zhou et al., S&P 2024 and Mughees-Ren, ePrint 2023) have eliminated FHE, at the price of linear offline communication. However, the client-side storage is still relatively large ($\tilde{O}(\sqrt{n})$), which poses challenges to practical deployment, especially when the client has limited computation and storage capabilities. To address such limitation, we propose a novel PIR protocol Pai, which only requires constant online time, communication, and client-side storage. The price we pay is only a $1$ - $5\times$ increase in offline communication, which would be acceptable since it is a one-time cost.Building upon our Pai, we also present a Symmetric KPIR (KSPIR) PaiKSPIR and a Chargeable KSPIR (CKSPIR) PaiCKSPIR. These two variants of PIR offer enhanced functionalities while maintaining computational complexities similar to the original Pai. In addition to providing rigorous theoretical proofs of correctness and privacy for Pai, we have undertaken comprehensive protocol implementations and conducted extensive experiments to validate their high efficiency. Our empirical findings demonstrate that our protocols achieve notably higher online efficiency than SOTA protocols, e.g., Pai exhibits $8.8$ - $91.8\times$ better online communication cost and $2.5$ - $8.8\times$ better online time. Given the superior online time and storage, our protocol is well-suited for practical deployment

Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA.

Intronic splicing enhancers and silencers (ISEs and ISSs) are two groups of splicing-regulatory elements (SREs) that play critical roles in determining splice-site selection, particularly for alternatively spliced introns or exons. SREs are often short motifs; their mutation or dysregulation of their cognate proteins frequently causes aberrant splicing and results in disease. To date, however, knowledge about SRE sequences and how they regulate splicing remains limited. Here, using an SMN2 minigene, we generated a complete pentamer-sequence library that comprises all possible combinations of 5 nucleotides in intron 7, at a fixed site downstream of the 5' splice site. We systematically analyzed the effects of all 1023 mutant pentamers on exon 7 splicing, in comparison to the wild-type minigene, in HEK293 cells. Our data show that the majority of pentamers significantly affect exon 7 splicing: 584 of them are stimulatory and 230 are inhibitory. To identify actual SREs, we utilized a motif set enrichment analysis (MSEA), from which we identified groups of stimulatory and inhibitory SRE motifs. We experimentally validated several strong SREs in SMN1/2 and other minigene settings. Our results provide a valuable resource for understanding how short RNA sequences regulate splicing. Many novel SREs can be explored further to elucidate their mechanism of action

Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution

Seahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses’ worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring “bony spines” adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.Fil: Chunyan, Li. Southern Marine Science and Engineering Guangdong Laboratory; China. Pilot National Laboratory for Marine Science and Technology; China. Chinese Academy of Sciences; República de ChinaFil: Olave, Melisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina. University of Konstanz; AlemaniaFil: Hou, Yali. Chinese Academy of Sciences; República de ChinaFil: Geng, Qi. Chinese Academy of Sciences; República de China. Southern Marine Science and Engineering Guangdong Laboratory; ChinaFil: Schneider, Ralf. University Of Konstanz; Alemania. Helmholtz Centre for Ocean Research Kie; AlemaniaFil: Zeixa, Gao. Huazhong Agricultural University; ChinaFil: Xiaolong, Tu. Allwegene Technologies ; ChinaFil: Xin, Wang. Chinese Academy of Sciences; República de ChinaFil: Furong, Qi. China National Center for Bioinformation; China. University of Chinese Academy of Sciences; ChinaFil: Nater, Alexander. University of Konstanz; AlemaniaFil: Kautt, Andreas F.. University of Konstanz; Alemania. Harvard University; Estados UnidosFil: Wan, Shiming. Chinese Academy of Sciences; República de ChinaFil: Yanhong, Zhang. Chinese Academy of Sciences; República de ChinaFil: Yali, Liu. Chinese Academy of Sciences; República de ChinaFil: Huixian, Zhang. Chinese Academy of Sciences; República de ChinaFil: Bo, Zhang. Chinese Academy of Sciences; República de ChinaFil: Hao, Zhang. Chinese Academy of Sciences; República de ChinaFil: Meng, Qu ,. Chinese Academy of Sciences; República de ChinaFil: Shuaishuai, Liu. Chinese Academy of Sciences; República de ChinaFil: Zeyu, Chen. Chinese Academy of Sciences; República de China. University of Chinese Academy of Sciences; ChinaFil: Zhong, Jia. Chinese Academy of Sciences; República de ChinaFil: Zhang, He. BGI-Shenzhen; ChinaFil: Meng, Lingfeng. BGI-Shenzhen; ChinaFil: Wang, Kai. Ludong University; ChinaFil: Yin, Jianping. Chinese Academy of Sciences; República de ChinaFil: Huang, Liangmin. Chinese Academy of Sciences; República de China. University of Chinese Academy of Sciences; ChinaFil: Venkatesh, Byrappa. Institute of Molecular and Cell Biology; SingapurFil: Meyer, Axel. University of Konstanz; AlemaniaFil: Lu, Xuemei. Chinese Academy of Sciences; República de ChinaFil: Lin, Qiang. Chinese Academy of Sciences; República de China. Southern Marine Science and Engineering Guangdong Laboratory; China. Pilot National Laboratory for Marine Science and Technology; China. University of Chinese Academy of Sciences; Chin

Understanding and exploring the diversity of soil microorganisms in tea (Camellia sinensis) gardens: toward sustainable tea production

Leaves of Camellia sinensis plants are used to produce tea, one of the most consumed beverages worldwide, containing a wide variety of bioactive compounds that help to promote human health. Tea cultivation is economically important, and its sustainable production can have significant consequences in providing agricultural opportunities and lowering extreme poverty. Soil parameters are well known to affect the quality of the resultant leaves and consequently, the understanding of the diversity and functions of soil microorganisms in tea gardens will provide insight to harnessing soil microbial communities to improve tea yield and quality. Current analyses indicate that tea garden soils possess a rich composition of diverse microorganisms (bacteria and fungi) of which the bacterial Proteobacteria, Actinobacteria, Acidobacteria, Firmicutes and Chloroflexi and fungal Ascomycota, Basidiomycota, Glomeromycota are the prominent groups. When optimized, these microbes’ function in keeping garden soil ecosystems balanced by acting on nutrient cycling processes, biofertilizers, biocontrol of pests and pathogens, and bioremediation of persistent organic chemicals. Here, we summarize research on the activities of (tea garden) soil microorganisms as biofertilizers, biological control agents and as bioremediators to improve soil health and consequently, tea yield and quality, focusing mainly on bacterial and fungal members. Recent advances in molecular techniques that characterize the diverse microorganisms in tea gardens are examined. In terms of viruses there is a paucity of information regarding any beneficial functions of soil viruses in tea gardens, although in some instances insect pathogenic viruses have been used to control tea pests. The potential of soil microorganisms is reported here, as well as recent techniques used to study microbial diversity and their genetic manipulation, aimed at improving the yield and quality of tea plants for sustainable production