Integration of multi-omics data reveals cis-regulatory variants that are associated with phenotypic differentiation of eastern from western pigs.

BACKGROUND: The genetic mechanisms that underlie phenotypic differentiation in breeding animals have important implications in evolutionary biology and agriculture. However, the contribution of cis-regulatory variants to pig phenotypes is poorly understood. Therefore, our aim was to elucidate the molecular mechanisms by which non-coding variants cause phenotypic differences in pigs by combining evolutionary biology analyses and functional genomics. RESULTS: We obtained a high-resolution phased chromosome-scale reference genome with a contig N50 of 18.03 Mb for the Luchuan pig breed (a representative eastern breed) and profiled potential selective sweeps in eastern and western pigs by resequencing the genomes of 234 pigs. Multi-tissue transcriptome and chromatin accessibility analyses of these regions suggest that tissue-specific selection pressure is mediated by promoters and distal cis-regulatory elements. Promoter variants that are associated with increased expression of the lysozyme (LYZ) gene in the small intestine might enhance the immunity of the gastrointestinal tract and roughage tolerance in pigs. In skeletal muscle, an enhancer-modulating single-nucleotide polymorphism that is associated with up-regulation of the expression of the troponin C1, slow skeletal and cardiac type (TNNC1) gene might increase the proportion of slow muscle fibers and affect meat quality. CONCLUSIONS: Our work sheds light on the molecular mechanisms by which non-coding variants shape phenotypic differences in pigs and provides valuable resources and novel perspectives to dissect the role of gene regulatory evolution in animal domestication and breeding.

Application of Bio-Impedance Analysis to Estimate the Condition of Yellowtail (Seriola quinqueradiata) Muscle at Different Storage Temperatures.

Changes in impedance at 2 kHz, adenosine triphosphate (ATP) content, and muscle contraction were evaluated in yellowtail during 0 (ice), 5, 10, 15, and 20°C storage. Histological changes during ice storage were also measured. At any temperature, although impedance increased with both rigor mortis and ATP consumption during early storage, it began to decrease rapidly when ATP was almost depleted. Moreover, temporarily increasing impedance had a strong relationship with ATP content; decreasing impedance had a significant correlation with storage temperature after ATP depletion. Furthermore, impedance increased with narrowing of intercellular spaces when sarcolemma was intact and decreased with expansion of intercellular spaces when sarcolemma was leaky. Meanwhile, changes of sarcolemma and intercellular spaces were accompanied by ATP change. Thus, ATP is one significant physiological factor for impedance change, and temperature greatly influenced impedance after depletion of ATP. Results suggest that impedance analysis can be used as a convenient and nondestructive method to diagnose condition of tissue at different storage temperatures. Bioelectromagnetics. 2019;40:488-497. © 2019 Bioelectromagnetics Society.

Protease Hydrolysates of Filefish (Thamnaconus modestus) Byproducts Effectively Inhibit Foodborne Pathogens.

In this study, novel antimicrobial peptides had been derived by enzymatic hydrolysis of filefish (Thamnaconus modestus) byproduct (HFBP). Different proteases, (papain [P], trypsin [T], neutrase [N], pepsin [PE], and the mixture I [PN] and mixture II [PT]) and different hydrolysis time (60, 120, 180, and 240 min), have been used to generate peptides with different lengths and amino acid sequences. The antimicrobial properties of HFBPs were tested, against Gram-positive and Gram-negative strains, using disc diffusion method. HFBP prepared after 120 min of the enzymatic hydrolysis by trypsin (HFBP-T) exhibited greatest antibacterial activities. Bacillus cereus 10451 (BC) and Salmonella enteritidis 10982 (SE) strains were most sensitive to HFBP-T with an inhibitory zone of 24.68 and 29.67 mm diameter and minimum inhibitory concentration of 1.25 and 2.5 mg/mL, respectively. Moreover, the antimicrobial activities of tested HFBPs increased significantly at low pH and temperature. The amino acid analysis showed that HFBP-T protein hydrolysate is high in an amino acid of proline, which probably contributes to the antimicrobial activity. The results obtained from scanning electron microscopy suggested that HFBPs might kill bacteria by acting on the cell wall of bacteria. Conclusively, the HFBP derived from filefish byproduct with biological activates is an interesting alternative to the use of waste from the fishing industry as natural antimicrobials in food stuff.

N-aminomorpholine-functionalized bromine-doped carbon dots for hypochlorous acid detection in foods and imaging in live cells.

Hypochlorous acid (HClO) is used in food preservation. However, excessive HClO can deteriorate nutritional composition of food, compromise its quality, and potentially induce various diseases. Consequently, the development of multifunctional fluorescent probes for the sensitive and selective detection of HClO is highly anticipated for food safety. In this work, we designed a nanoprobe using N-aminomorpholine (AM)-functionalized bromine-doped carbon dots (Br-CDs-AM) for sensing HClO. This nanoprobe exhibits pH stability, strong resistance to photobleaching, superior long-term photostability (12 weeks), high sensitivity (19.3 nM), and an ultrarapid response (8 s) for detecting HClO residues in food matrices with percentage recovery (96.5 %-108 %) and RSDs less than 5.34 %. In addition, extremely low cytotoxicity and outstanding biocompatibility enable the nanoprobe to be used primarily for lysosome tracking and rapidly visualizing HClO in live cells. Thus, this study provides a new pathway to design unconventional nanoprobes for food safety assessment and subcellular organelle-specific imaging HClO.

DNA Methylation Data Analysis Using Msuite.

DNA methylation is a widespread epigenetic modification responsible for many biological regulation pathways. The development of various powerful biochemical assays, including conventional bisulfite treatment-based and emerging bisulfite-free techniques, has promised high-resolution DNA methylome profiling and significantly propelled the DNA methylation research field. However, the analysis of large-scale data generated from such assays is still complex and challenging. In this paper, we present a step-by-step protocol for using Msuite for whole-spectrum DNA methylation data analysis, from quality control, read alignment, to methylation call and data visualization. The Msuite package and a testing dataset are freely available at https://github.com/hellosunking/Msuite.

Label-free based proteomics revealed the specific changes of muscle proteins in pike eel (Muraenesox cinereus) under cold stress.

Chemical- and liquid chromatography coupled with mass spectrometry (LC-MS) based proteomics strategies were executed to investigate the alterations of protein profiles in pike eel (Muraenesox cinereus) muscle during chilling (CPE) and frozen (FPE) storage. Chemical results indicated that springiness and myofibrillar protein (MP) content of muscle tissues decreased significantly during 6 days of chilled and 120 days of frozen storage. LC-MS-based proteomics analysis suggested that great alterations occurred in muscle proteins mainly induced by cold stress. The differentially abundant proteins (DAPs) with low abundances in CPE and FPE samples included the annexins, fibronectin, ribosomal proteins, T-complex proteins, tubulin beta chain, and histones, which were mostly associated with the membrane structural constituents, cytoskeleton, and binding functional proteins. Results of eukaryotic cluster of orthologous group (KOG) verified that these identified DAPs were mainly converged in the cytoskeleton function resulting from cold conditions, which in turn affected the physical structure and chemical performances of muscle tissues.

The Influence of Hypothermia Hibernation Combined with CO2 Anesthesia on Life and Storage Quality of Large Yellow Croaker (Pseudosciaena crocea).

We explore the feasibility of the long-term transportation of live large yellow croakers (Pseudosciaena crocea) using the combined method of CO2 anesthesia and hypothermia hibernation, and its effect on the quality of recovered fish stored at 4 °C. Fish treated with CO2 anesthesia at a 2 ppm/s aeration rate were cooled at 3 °C/h to hibernate survived for 36 h at 8 °C in seawater. This method resulted in better survival rates and time, and a lower operational time than hypothermia hibernation or CO2 anesthesia methods. The results of a blood analysis indicated that the stress experienced by the fish during hibernation was mitigated, but existent after recovery. The drip loss rate of the ordinary muscle of hibernated fish was significantly different from that of the control group at 4 °C, but there was no significant difference in the pH, lactic acid content, and color during early storage. Furthermore, hibernation did not affect springiness and chewiness. Thus, the combination of CO2 anesthesia and hibernation may improve the survival and operation efficiency of fish in long-term transportation. However, this method affects the quality of fish after long-term storage. Thus, hibernated fish should be consumed after appropriate domestication or immediately after recovery.

Msuite2: All-in-one DNA methylation data analysis toolkit with enhanced usability and performance.

DNA methylation is an important epigenetic regulator that plays crucial roles in various biological processes. Recent developments in experimental approaches and dramatic expansion of sequencing capacities have imposed new challenges in the analysis of large-scale, cross-species DNA methylation data. Hence, user-friendly toolkits with high usability and performance are in urgent need. In this work, we present Msuite2, an easy-to-use, all-in-one, and universal toolkit for DNA methylation data analysis and visualization with high flexibility, usability, and performance. Msuite2 is among the fastest tools in read alignment (in particular, it runs as much as 5x faster than its predecessor, Msuite1) with low computing resource usage. In addition, Msuite2 shows both balanced and high performance in terms of mapping efficiency and accuracy, demonstrating high potential to facilitate the investigation and application of large-scale DNA methylation analysis in various biomedical studies. Msuite2 is freely available at https://github.com/hellosunking/Msuite2/.

Characterization of the complete mitochondrial genome of Chrysochir aureus and phylogenetic studies of Sciaenidae.

The complete mitochondrial genome of Chrysochir aureus was sequenced. The full length of the mitochondrial genome was 16,501 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, a non-coding control region (CR) and one origin of replication on the light-strand (OL). The total nucleotide composition of mitochondrial DNA was 26.95% A, 29.99% C, 26.29% T, and 16.77% G. Twelve PCGs used the canonical ATG as their initiation codon, whereas COI gene started with an alternative start codon GTG. The mitochondrial genome of C. aureus described in this study could be a useful basis for management of this species and laid a foundation for further research involved with phylogenetic relationship within Sciaenidae.

Characterization of the complete mitochondrial genome of Hyphessobrycon herbertaxelrodi (Characiformes, Characidae) and phylogenetic studies of Characiformes.

In this study, the complete mitochondrial genome of Hyphessobrycon herbertaxelrodi is presented, and we also discussed its mitochondrial characteristics. The full length of the mitochondrial genome was 17,417 bp, including 13 protein coding genes (PCGs), 2 ribosomal RNAs (12S and 16S), 22 transfer RNA genes, 1 non-coding control region (D-loop), and 1 origin of replication on the light-strand. The total nucleotide composition of mitochondrial DNA was 29.76%A, 29.88%T, 25.35%C, 15.01%G, and AT was 59.64%. The phylogenetic tree suggested that H. herbertaxelrodi shared the most recent common ancestor with Astyanax giton, Grundulus bogotensis, Astyanax paranae, and Oligosarcus argenteus.

Characterization of the complete mitochondrial genome of Chinese Konosirus punctatus (Clupeiformes, Clupeidae) and phylogenetic studies of Clupeiformes.

The Dotted Gizzard Shad (Konosirus punctatus) was one of the most important commercial fish species in China, Japan and Korea. In this study, the complete mitochondrial genome of K. punctatus was presented. The full length of the mitochondrial genome was 16,705 bp, including 13 protein-coding genes (PCGs), two ribosomal RNAs, 22 transfer RNA genes, one non-coding control region (CR) and one origin of replication on the light-strand. The total nucleotide composition of mitochondrial DNA was 25.79%A, 25.09%T, 29.05%C, 20.08%G, and AT was 50.88%. The mitochondrial genome provides an important resource for solving taxonomic problems and studying molecular evolution.

The complete mitochondrial genome of ostorhinchus fleurieu (kurtiformes: Apogonidae) and phylogenetic studies of apogoninae.

The complete mitochondrial genome of Ostorhinchus fleurieu was first determined, which was 16,521 bp in length, containing 13 protein-coding genes, two rRNA genes, 22 tRNA genes, a putative control region and one origin of replication on the light-strand. The overall base composition included C(29.2%), A(26.7%), T(26.7%) and G(17.4%). Moreover, the 13 PCGs encoded 3800 amino acids in total, twelve of which used the initiation codon ATG except for COI started with GTG. Most of them ended with complete stop codon, whereas three protein-coding genes (COII, ND4 and Cytb) used incomplete stop codon and represented as T. The phylogenetic tree based on the Neighbour Joining method was constructed to provide relationship within Apogoninae, which could be a useful basis for management of this species.

Effect of blood deposition phenomenon on flesh quality of yellowtail (Seriola quinqueradiata) during storage.

We examined the influence of blood deposition on flesh quality of ordinary muscle in yellowtail. This study compared the flesh quality changes in upper and under-sides of yellowtails killed by two different methods: spinal-cord destruction (SCD) with blood removal and suffocation in air without blood removal (SA). The under-sides of the SA group showed the highest values for a*, cathepsin B and B + L activities, the lowest value in breaking strength and the greatest degradation of myosin heavy chain (MHC) among the four groups. However, the values of the SCD-upper group indicated the best flesh quality. In addition, the white blood cells presented the highest cathepsin B and B + L activities among the blood components. These results indicate that blood has the tendency to deposit downward in accordance with the direction of placement. This phenomenon influences the distribution of white blood cells which contain enzymes that accelerate the deterioration of flesh quality. The texture of fish muscle is an important part of the flesh quality. In captured fishery (purse-seine fishery and dragnet fishery), it is impossible to immediately and completely remove blood. Therefore, suffocation in air is the common method after the fish is caught. The commercial value of fish is decreased and the price varies greatly when these fish enter market circulation. In our study, we examined the influence of blood deposition on the flesh quality of yellowtail during storage. The degradation of structural proteins accelerated in the deposited blood which contain proteases. The movement and deposition of blood caused the difference of quality on both sides, which seriously affected the quality of fish during preservation. Our study has some theoretical guidance for muscle softening and give a better understanding of the adverse effect of blood during preservation.