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Background Nowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep. Accumulating evidence suggesting that post-transcriptional modification events of precursor-messenger RNA (pre-mRNA), including alternative splicing (AS) and alternative polyadenylation (APA), may regulate tail fat deposition in sheep. Differentially expressed transcripts (DETs) analysis is a way to identify candidate genes related to tail fat deposition. However, due to the technological limitation, post-transcriptional modification events in the tail fat of sheep and DETs between thin-tailed and fat-tailed sheep remains unclear. Methods In the present study, we applied pooled PacBio isoform sequencing (Iso-Seq) to generate transcriptomic data of tail fat tissue from six sheep (three thin-tailed sheep and three fat-tailed sheep). By comparing with reference genome, potential gene loci and novel transcripts were identified. Post-transcriptional modification events, including AS and APA, and lncRNA in sheep tail fat were uncovered using pooled Iso-Seq data. Combining Iso-Seq data with six RNA-sequencing (RNA-Seq) data, DETs between thin- and fat-tailed sheep were identified. Protein protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were implemented to investigate the potential functions of DETs. Results In the present study, we revealed the transcriptomic complexity of the tail fat of sheep, result in 9,001 potential novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs. Combining Iso-Seq data with RNA-Seq data, we identified hundreds of DETs between thin- and fat-tailed sheep. Among them, 21 differentially expressed lncRNAs, such as ENSOART00020036299, ENSOART00020033641, ENSOART00020024562, ENSOART00020003848 and 9.53.1 may regulate tail fat deposition. Many novel transcripts were identified as DETs, including 15.527.13 (DGAT2), 13.624.23 (ACSS2), 11.689.28 (ACLY), 11.689.18 (ACLY), 11.689.14 (ACLY), 11.660.12 (ACLY), 22.289.6 (SCD), 22.289.3 (SCD) and 22.289.14 (SCD). Most of the identified DETs have been enriched in GO and KEGG pathways related to extracellular matrix (ECM). Our result revealed the transcriptome complexity and identified many candidate transcripts in tail fat, which could enhance the understanding of molecular mechanisms behind tail fat deposition.

This paper reports the fabrication of a highly sensitive and reusable substrate for surface-enhanced Raman scattering (SERS) analysis. Core–shell metal–organic framework (MOF; HKUST-1)@Ag nanoparticles (NPs) are prepared on a screen-printed carbon electrode (SPCE) via in situ electrodeposition. The morphology and Ag coverage of core–shell structures can be easily controlled by electrodeposition potential and time without substrate motion. The HKUST-1(Cu)@Ag composites combine abundant SERS “hot spots” among the high-density Ag NPs and the excellent adsorption performance of the MOF, resulting in effective pre-concentration of analytes in close proximity to these “hot spots” and enhancement of SERS sensitivity. The optimized polyhedral HKUST-1@Ag structures exhibit high SERS activity for detecting 4-aminothiophenol at a concentration as low as 5 × 10−10 M. More importantly, the polyhedral HKUST-1@Ag composites provide high sensitivity for detection of polycyclic aromatic hydrocarbons (PAHs) while preserving the cyclability and selectivity required for reliable quantitative analysis. The method is effective over a wide range of PAH concentrations (0.5 nM to 0.5 M), with detection limits as low as hundreds of pM. This study offers a new method to tailor the structure of MOF-based SERS substrates for on-site screening or point-of-care applications.

Development of flexible surface-enhanced Raman spectroscopy (SERS) substrate with controllable "hot spots" has spurred increasing interest because of its unique structure and plasmonic properties. Here, charged poly(vinyl alcohol) microgels containing silver nanoparticles are developed by using microfluidic emulsification to produce a "smart" SERS sensor with charge screening and signals amplification. Importantly, this charged microgel enables the selective concentration of counter-charged molecules and induces the formation of assembled arrays at an immiscible liquid-liquid interface because of the electrostatic interaction. The SERS-active microgels arrays possess controllable structures and facilitate on-site determination of charged pesticides with an enhancement factor of 5.0 × 105. Such nanostructures present the ease of assembly, stability, and reproducibility which allow multiplex detection of analytes at aqueous and organic phases without any pretreatment of the complex matrix samples. The interfacial sensing platform for on-site SERS analysis of charged pesticides will open vast possibilities for a wide range of in-field applications.

Potassium inwardly-rectifying channel, subfamily J, member 12 (KCNJ12) gene is one promising candidate for economic traits because of its crucial roles in myoblast development. Here, a missense mutation (Cys>Arg), was firstly detected to locate in exon 3 of KCNJ12 from three Chinese cattle breeds by DNA-pool sequencing. Then, we performed the association analysis of this SNP with stature in three Chinese cattle populations (n = 820). Significantly positive correlation was revealed by reduced animal general linear model and the genotype of CC is the most excellent genotype in three breeds. Further, we measured the expression profiling of the KCNJ12 gene in various cattle tissues and primary bovine skeletal muscle cells. Ubiquitous expression with high abundance in muscle was observed. Further, in primary bovine skeletal muscle cells, the KCNJ12 mRNA expression was gradually up-regulated in differentiation medium (DM) compared with that in growth medium (GM), suggesting that KCNJ12 gene is involved in bovine myocyte differentiation. Conclusively, KCNJ12 gene is a functional candidate gene which can be used as molecular marker for beef cattle breeding.

Potassium inwardly-rectifying channel, subfamily J, member 12 (KCNJ12) gene is one promising candidate for economic traits because of its crucial roles in myoblast development. Here, a missense mutation (Cys>Arg), was firstly detected to locate in exon 3 of KCNJ12 from three Chinese cattle breeds by DNA-pool sequencing. Then, we performed the association analysis of this SNP with stature in three Chinese cattle populations (n = 820). Significantly positive correlation was revealed by reduced animal general linear model and the genotype of CC is the most excellent genotype in three breeds. Further, we measured the expression profiling of the KCNJ12 gene in various cattle tissues and primary bovine skeletal muscle cells. Ubiquitous expression with high abundance in muscle was observed. Further, in primary bovine skeletal muscle cells, the KCNJ12 mRNA expression was gradually up-regulated in differentiation medium (DM) compared with that in growth medium (GM), suggesting that KCNJ12 gene is involved in bovine myocyte differentiation. Conclusively, KCNJ12 gene is a functional candidate gene which can be used as molecular marker for beef cattle breeding.