Additional file 1 Table S1. The information of profile HMMs of F-box and Kelch domains in Pfam database. Table S2. The sequences and positions information of F-box domains in 44 StKFB members. Table S3. The sequences and positions information of Kelch motifs in 44 StKFB members. Table S4. The 20 conserved motifs in StKFB proteins identified by MEME software and motifs annotation analysis by InterProScan. Table S5. The orthologous KFB genes identified by comparison between potato and other plants. Table S6. Expression profiles of 44 StKFB genes in different potato tissues, in potato plants with different treatments and in tubers with different colors. The FPKM values of 44 StKFB genes in different potato tissues and in potato plants with different treatments were extracted from RNA-Seq Gene Expression Data: DM_RH_RNA-Seq_FPKM_expression_matrix_for_DM_v4.03_13dec2013_desc.xlsx, the excel file of FPKM values of all the representative transcripts across 40 DM and 16 RH libraries ( http://spuddb.uga.edu/pgsc_download.shtml ); the FPKM values in tubers with different colors was extracted from RNA-seq data in our lab deposited in the NCBI Sequence Read Archive under the Bioproject accession PRJNA729884. Table S7. Quality of transcriptome sequencing of potato tuber with three colors. Raw reads: Number of reads in raw data; Clean reads: Number of reads filtered from raw data; Raw bases: The number of bases in the raw data; Clean bases: The number of bases filtered from the raw data; Error rate: Error rate of data sequencing; Q20: Percentage of bases with a Phred value greater than 20; Q30: Percentage of bases with a Phred value greater than 30; GC content: The percentage of G and C in clean reads. Table S8. Sequence alignment results of reads mapped to the reference genome (DM v4.03/v4.04). Total reads: the number of clean reads used for mapping analysis; Total mapped: the number of reads that could be mapped to the reference genome; Multiple mapped: the number of reads mapped to multiple locations in the reference genome; Uniquely mapped: the number of reads mapped to single location in the reference genome; Read-1 and Read-2: the number of reads mapped to the reference genome in Read 1 and Read 2, respectively; Reads mapped to ‘+’ and Reads mapped to ‘-’: the number of reads mapped to the positive and negative strands of the reference genome, respectively; Non-splice reads: the number of reads with the entire segment mapped to exons; Splice reads: the number of segmented reads mapped on two different exons; Reads mapped in proper pairs:the number of reads paired mapped to the reference genome; Proper-paired reads map to different chrom: the number of paired reads mapped to different chromosomes in the reference genome. Table S9. All primers used in qRT-PCR. Table S10. The annotation of 44 StKFBs and their corresponding orthologous genes in Arabidopsis thaliana. The potato StKFB protein sequences were aligned with those of Arabidopsis thaliana using Blastp.
In this paper, a new algorithm to detect overexposed regions in images is presented. The algorithm uses non-linear support vector machines (nSVM) and characteristics of over-exposed image features to detect the over-exposed regions. These features include intensity and color, as well as novel features of intensity-chrominance and boundary neighborhood. Optimal parameters for the classifier are obtained by using training sets for different scenes. The experimental results show that the detected over-exposed regions are better in terms of more connectivity and integrity. In addition, it has less isolated over-exposed pixels compared to previous method that is based on solely intensity and color features, which are more susceptible to noise.
The study was designed to screen and identify differentially expressed gnes following 50 Hz extremely low frequency magnetic field (ELFMF) exposurre by mRNA differential display. Results Using 75 primer combinations, 11 of cDNA fragments were found differentially displayed responding to MF exposure, including: cDNA fragments only present in MF exposed cultures; cDNA fragments only absentin MF exposed cultures, and cDNA fragments present in both MF and control groups with greater different extent. The interesting fragments were then recovered from the dried gel, reamplified by PCR. Some of them were identitied by reverse Northern and Northern blot.
Abstract Rice endosperm plays a very important role in seedling germination and determines the qualities of rice grain. Although studies on specific gene categories in endosperm have been carried out, global view of gene expression at a transcription level in rice endosperm is still limited. To gain a better understanding of the global and tissue‐specific gene expression profiles in rice endosperm, a cDNA library from rice endosperm of immature seeds was sequenced. A cDNA array was constructed based on the tentative unique transcripts derived from expression sequence tag (EST) assembling results and then hybridized with cDNAs from five different tissues or organs including endosperm, embryo, leaf, stem and root of rice. Significant redundancy was found for genes encoding prolamin, glutelin, allergen, and starch synthesis proteins, accounting for ∼34% of the total ESTs obtained. The cDNA array revealed 87 significantly expressed genes in endosperm compared with the other four organs or tissues. These genes included 13 prolamin family proteins, 17 glutelin family proteins, 12 binding proteins, nine catalytic proteins and four ribosomal proteins, indicating a complicated biological processing in rice endosperm. In addition, Northern verification of 1,4‐alpha‐glucan branching enzyme detected two isoforms in rice endosperm, the larger one of which only existed in endosperm.
In the field of weak signal detection, the nonlinear stochastic resonance system has been proved as an efficient approach for its property of transferring the energy of noise to periodic signals, which can be used for a variety of oceanic fields such as underwater acoustic communication, passive sonar detection, seismic wave detection, and etc. In this paper, a circuit system of large parameter stochastic resonance is designed and implemented with frequency shift normalized scale transformation, aiming to realize an enhancement of weak periodic signals. The circuit system based on stochastic resonance deals with continuous signals and can effectively overcome the problems as divergence may appears in numerical simulations. The analog circuit stochastic resonance system. A hardware analog circuit system with DSP as the control core is designed to realize rapid stochastic resonance detection of the weak signal of the higher frequency underwater, raise the frequency range of the detectable signal. Analog circuit system results show that the system circuit can achieve higher frequency signal stochastic resonance so as to effectively improve the system output.
Tire indentation mark matching is an essential tool used for the investigation of criminal cases and traffic incidents. As such images are unique and uncommon, there is a lack of dedicated databases and relevant research on this topic. This paper presents a feature extraction algorithm effective for tire indentation mark image description. The main contributions include: (1) Line feature Weber local descriptor (LWLD) is proposed, which uses the Gabor orientations instead of the original gradient orientation. This feature can describe texture information of tire indentation mark image more efficiently. (2) An attention model is constructed to produce attention feature map of tire indentation mark image. This attention feature map is then fused with LWLD resulting in a feature with more powerful representation capability. Experimental results prove that the combined use of LWLD and attention model greatly enhances the performance of tire indentation mark image matching tasks.
Abstract Background: Kelch repeat F-box (KFB) proteins play vital roles in the regulation of multitudinous biochemical and physiological processes in plants, including growth and development, stress response and secondary metabolism. Multiple KFBs have been characterized in various plant species, but this family members have not been systematically identified and analyzed in potato. Results: Genome and transcriptome analyses of StKFB gene family were conducted to dissect the structure, evolution and function of the KFBs in Solanum tuberosum L. Totally, 44 StKFB members were identified and were classified into 5 groups according to their structural and phylogenetic features. The chromosomal localization analysis showed that the 44 StKFB genes were located on 12 chromosomes. Among these genes, two pairs of genes ( StKFB15 / 16 and StKFB40 / 41 ) were predicted to be tandemly duplicated genes, and one pair of genes ( StKFB15 / 29 ) was segmentally duplicated genes. The syntenic analysis showed that the KFBs in potato were closely related to the KFBs in tomato and pepper. Expression profiles of StKFBs in 13 different tissues and in potato plants with different treatments uncovered distinct spatial expression patterns of these genes and their potential roles in response to various stresses. Transcriptomic and qRT-PCR analyses of StKFBs deciphered that multiple StKFB genes were differentially expressed in three colored potato tubers. Genes that were highly expressed in yellow fleshed tubers (Jin-16) and were lowly expressed in the red- (Red Rose-2) or purple-fleshed (Xisen-8) tubers, such as StKFB07 , StKFB15 , StKFB23 , StKFB29 and StKFB44 , may negatively regulate anthocyanin biosynthesis. Conclusions: This study reports the structure, evolution and expression characteristics of the KFB family in potato. These findings set the stage for further study of functional mechanisms of StKFBs, and also provide candidate genes for potato genetic improvement.
Sweetpotato (Ipomoea batatas (L.) Lam.) is a genetically intricate hexaploid crop. The purple-fleshed variety, enriched with anthocyanin pigments, is an outstanding source for creating high-value functional products. Previous research on anthocyanin biosynthesis has primarily focused on the above-ground plant parts at the transcriptional level. However, the regulatory mechanisms underlying anthocyanin accumulation in underground tuberous roots of sweetpotato remain largely unexplored. This study aimed to elucidate the post-transcriptional and post-translational mechanisms of Ib-miR2111 and its target gene IbKFB in anthocyanin synthesis in sweetpotato. Genetic manipulation techniques were used to validate the function of Ib-miR2111 and IbKFB in anthocyanin biosynthesis in sweetpotato. To investigate how IbKFB works, a series of protein interaction assays, including yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), GST pull-down, co-immunoprecipitation (Co-IP), and ubiquitination, were conducted. Additionally, the impact of anthocyanin extracts from the genetically modified sweetpotato lines on inflammatory cells morphology, cytokine expression, and cell proliferation were evaluated using in vitro assays. Purple-fleshed sweetpotato (PFSP) lines exhibited elevated Ib-miR2111 expression compared to white-fleshed sweetpotato (WFSP), with an inverse expression pattern in IbKFB. Genetic manipulations, including overexpression, CRISPR/Cas9 knockouts, and targeted mutations, confirmed their critical roles in anthocyanin modulation. Furthermore, IbKFB's interactions and ubiquitination with phenylalanine ammonia-lyase 1 (IbPAL1) and glyceraldehyde-3-phosphate dehydrogenase 1 (IbGAPCp1) were elucidated, revealing intricate regulatory mechanisms. Enhanced anthocyanin content showed significant effects on inflammatory cell morphology, cytokine expression, and cell proliferation. This study provides new insights into the regulatory mechanisms of Ib-miR2111 and IbKFB in anthocyanin biosynthesis and suggests potential health benefits of anthocyanin-rich sweetpotatoes.
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