Genome-Wide Identification and Expression Profiles of Myosin Genes in the Pacific White Shrimp, Litopenaeus vannamei

As the main structural protein of muscle fiber, myosin is essential for multiple cellular processes or functions, especially for muscle composition and development. Although the shrimp possess a well-developed muscular system, the knowledge about the myosin family in shrimp is far from understood. In this study, we performed comprehensive analysis on the myosin genes in the genome of the Pacific white shrimp, Litopenaeus vannamei. A total of 29 myosin genes were identified, which were classified into 14 subfamilies. Among them, Myo2 subfamily was significantly expanded in the penaeid shrimp genome. Most of the Myo2 subfamily genes were primarily expressed in abdominal muscle, which suggested that Myo2 subfamily genes might be responsible for the well-developed muscular system of the penaeid shrimp. In situ hybridization detection showed that the slow-type muscle myosin gene was mainly localized in pleopod muscle and superficial ventral muscle of the shrimp. This study provides valuable insights into the evolutionary and functional characterization of myosin genes in shrimps, which provides clues for us to understand the well-developed muscular system of shrimp

Experimental and Field Investigations on the Impact-Resistance Mechanical Properties of Negative Poisson’s Ratio Bolt/Cable

AbstractDynamic impact tests of negative Poisson’s ratio (NPR) and rebar bolts under different impact wavelengths were carried out using a self-developed NPR bolt tensile impact test system. Additionally, a field anti-impact test using blasting was performed to simulate rockburst, and the field anti-impact characteristics of the NPR and conventional cable were compared and analysed. The experimental test results revealed that the peak impact force of the NPR and rebar bolts was inversely proportional to the wavelength. The NPR bolt underwent only constant resistance structural deformation, and the rod body did not break. The rebar bolt body fractured and necked. Under the same impact wavelength, the impact force and elongation of the two bolt types were proportional to the impact velocity. Compared with the greater peak impact force of the rebar bolt, the NPR bolt output structure deformation reduced the peak impact force. At the same impact velocity, as the wavelength increased, the impact force of the NPR bolt decreased rapidly, and the number of peaks also decreased. The impact force peak value of the rebar bolt was high, the impact force-time curve had multipeak characteristics, and no apparent rapid attenuation occurred. The field test results indicated that the NPR cable could produce slip deformation under the action of an explosion impact force to absorb the impact energy and that it had special mechanical properties to maintain a constant resistance. Under the same equivalent blasting impact energy, the conventional cable test section collapsed completely. The NPR cable test section was stable overall, verifying that the NPR cable had better impact-resistance mechanical properties than conventional cable. The research results provide a reliable basis for the effectiveness of NPR bolts/cables in preventing rockbursts

Wnt Signaling Pathway Linked to Intestinal Regeneration via Evolutionary Patterns and Gene Expression in the Sea Cucumber Apostichopus japonicus

Many echinoderms are regenerative species that exhibit exceptional regenerative capacity, and sea cucumber is a representative organism that could regenerate the whole intestine after evisceration. There are many signaling pathways participate in the regeneration process, but it is not clear which is essential for the intestinal regeneration. In this study, we performed genome-wide comprehensive analyses on these regeneration-related signaling pathways, and found the Wnt signaling pathway was one of the most conservative pathways among regenerative species. Additionally, among these signaling pathways, we found that the Wnt signaling pathway was the only one under positive selection in regenerative echinoderms, and the only one enriched by differentially expressed genes during the intestinal regeneration. Thus, it suggests both coding sequence and gene expression of the Wnt signaling pathway have been shaped by natural selection to provide the genetic architecture for intestinal regeneration. Wnt7, Fz7, and Dvl are the three positively selected genes and also happen to be three upstream genes in the Wnt signaling pathway. They are all significantly upregulated at the early stages of regeneration, which may contribute significantly to the early activation of Wnt signaling and the initiation of intestinal regeneration. Expression knockdown of Wnt7 and Dvl by RNA interference significantly inhibit intestinal extension, implying that they are essential for intestinal regeneration. As an important regeneration-related gene, the downstream gene c-Myc is also conserved and highly expressed during the whole regeneration stages, which may make the Wnt/c-Myc signaling to be an important way to promote intestinal regeneration. Therefore, it is reasonable to conclude that the Wnt signaling pathway is the chosen one to play an important role in intestinal regeneration of sea cucumbers, or even in the regeneration of other echinoderms

Roughage quality determines the production performance of post-weaned Hu sheep via altering ruminal fermentation, morphology, microbiota, and the global methylome landscape of the rumen wall

Roughage quality is a crucial factor influencing the growth performance and feeding cost of ruminants; however, a systematic investigation of the mechanisms underlying this is still lacking. In this study, we examined the growth performance, meat quality, ruminal fermentation parameters, rumen microbiome, and tissue methylomes of post-weaned Hu sheep fed low- or high-quality forage-based diets. Our results showed that sheep in the alfalfa hay (AG) and peanut vine (PG) groups exhibited better growth performance, slaughter performance, and meat quality than sheep in the wheat straw group (WG). The sheep in the AG possessed relatively higher contents of serum immunoglobins (IgA, IgG, and IgM) and lower contents of serum inflammation factors (TNF-α, IL-1β, IL-6, and IL-8) than those in the WG and the PG did. In addition, the levels of blood T lymphocytes (CD4+ and CD8+) and the CD4-to-CD8 ratio were significantly higher in the AG sheep than in the WG sheep and PG sheep. The concentration of ruminal NH3-N was highest in WG sheep, whereas the concentrations of individual and total short-chain fatty acids (SCFAs) were highest in the PG sheep. The length, width, and surface area of ruminal papillae were markedly different among the three groups, with the sheep in the PG being the most morphologically developed. The main ruminal microbes at the genus level include Prevotella 1, Rikenellaceae RC9 gut group, norank f F082, Ruminococcus 1, and Ruminococcus 2. The relative abundances of certain species are positively or negatively associated with fermentation parameters and growth index. For example, the fibrolytic bacteria Ruminococcaceae UGG-001 showed positive relationships with the concentration of SCFAs, except propionate. In addition, the relative abundances of fibrolytic bacteria (e.g., Ruminoccus 1) showed a negative relationship with starch-degrading bacteria (e.g., Prevotellaceae). The genome-wide DNA methylation analysis revealed that rumen tissues in the PG sheep and WG sheep occupied different global DNA methylomes. The genes with differentially methylated promoters were involved in known pathways (e.g., the FoxO signaling pathway) and the Gene Ontology (GO) terms (e.g., anatomical structure morphogenesis) pertaining to rumen development. Two candidate genes (ACADL and ENSOARG00020014533) with hyper- and hypo-methylated promoters were screened as potential regulators of rumen development. In conclusion, roughage quality determines sheep growth performance via directly influencing rumen fermentation and microbiome composition, and indirectly affecting rumen development at the epigenetic level

Penaeid shrimp genome provides insights into benthic adaptation and frequent molting

Crustacea, the subphylum of Arthropoda which dominates the aquatic environment, is of major importance in ecology and fisheries. Here we report the genome sequence of the Pacific white shrimp Litopenaeus vannamei, covering similar to 1.66 Gb (scaffold N50 605.56 Kb) with 25,596 protein-coding genes and a high proportion of simple sequence repeats (>23.93%). The expansion of genes related to vision and locomotion is probably central to its benthic adaptation. Frequent molting of the shrimp may be explained by an intensified ecdysone signal pathway through gene expansion and positive selection. As an important aquaculture organism, L. vannamei has been subjected to high selection pressure during the past 30 years of breeding, and this has had a considerable impact on its genome. Decoding the L. vannamei genome not only provides an insight into the genetic underpinnings of specific biological processes, but also provides valuable information for enhancing crustacean aquaculture

A BAC-Based Physical Map of Zhikong Scallop (Chlamys farreri Jones et Preston)

Zhikong scallop (Chlamys farreri) is one of the most economically important aquaculture species in China. Physical maps are crucial tools for genome sequencing, gene mapping and cloning, genetic improvement and selective breeding. In this study, we have developed a genome-wide, BAC-based physical map for the species. A total of 81,408 clones from two BAC libraries of the scallop were fingerprinted using an ABI 3130xl Genetic Analyzer and a fingerprinting kit developed in our laboratory. After data processing, 63,641 (∼5.8× genome coverage) fingerprints were validated and used in the physical map assembly. A total of 3,696 contigs were assembled for the physical map. Each contig contained an average of 10.0 clones, with an average physical size of 490 kb. The combined total physical size of all contigs was 1.81 Gb, equivalent to approximately 1.5 fold of the scallop haploid genome. A total of 10,587 BAC end sequences (BESs) and 167 markers were integrated into the physical map. We evaluated the physical map by overgo hybridization, BAC-FISH (fluorescence in situ hybridization), contig BAC pool screening and source BAC library screening. The results have provided evidence of the high reliability of the contig physical map. This is the first physical map in mollusc; therefore, it provides an important platform for advanced research of genomics and genetics, and mapping of genes and QTL of economical importance, thus facilitating the genetic improvement and selective breeding of the scallop and other marine molluscs

Response of Gut Microbiota to Dietary Fiber and Metabolic Interaction With SCFAs in Piglets

Dietary fiber (DF) is increasingly thought to regulate diversity of piglet gut microbiota to alleviate weaning stress in piglets. This study was conducted to investigate the effects of DF on growth performance of piglets and composition of their gut microbiota, as well as the interaction between gut microbiota and short-chain fatty acids (SCFAs) in piglets. A total of 840 piglets were allocated to three dietary treatments consisting of a control group (CG), an alfalfa meal group (AG), and a commodity concentrated fiber group (OG) in a 30-day feeding trial. Gut mucosa and feces samples were used to determine bacterial community diversity by 16S rRNA gene amplicon sequencing. Fiber treatment had a positive effect on growth performance and metabolism of SCFAs in piglets, in particular, compared with CG, the diarrhea rate was significantly decreased, and the content of propionic acid (PA) in the cecum was markedly increased in AG. The Shannon indices of the jejunum microbiota in AG were higher than CG. At the genus level, compared to CG, in the duodenum, the relative abundance of Paenibacillus in AG and OG was higher; in the jejunum, the relative abundances of Bacillus, Oceanobacillus, Paenibacillus, Lactococcus, Enterococcus, and Exiguobacterium were higher, whereas the relative abundance of Mycoplasma was lower in AG; in the cecum, there was also lower relative abundance of Helicobacter in AG and OG, and furthermore, the relative abundance of Faecalibacterium in OG was higher than in CG and AG. Spearman correlation analysis showed that Pseudobutyrivibrio was positively correlated with acetic acid, PA, and butyric acid (BA), while Bacteroides and Anaerotruncus were negatively correlated with PA and BA. In addition, microbiota analyses among different intestine segments showed distinct differences in microbiota between the proximal and distal intestines. Bacteria in the proximal segments were mainly Firmicutes, while bacteria in the distal segments were mainly Bacteroidetes and Firmicutes. Overall, these findings suggested that DF treatment could reduce the diarrhea rate of piglets and had beneficial effects on gut health, which might be attributed to the alteration in gut microbiota induced by DF and the interaction of the gut microbiota with SCFAs