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The silkworm Bombyx mori is an important economic insect for producing silk, the “queen of fabrics”. The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read genomes for 545 representatives. We construct a high-resolution pan-genome dataset representing almost the entire genomic content in the silkworm. We find that the silkworm population harbors a high density of genomic variants and identify 7308 new genes, 4260 (22%) core genes, and 3,432,266 non-redundant structure variations (SVs). We reveal hundreds of genes and SVs that may contribute to the artificial selection (domestication and breeding) of silkworm. Further, we focus on four genes responsible, respectively, for two economic (silk yield and silk fineness) and two ecologically adaptive traits (egg diapause and aposematic coloration). Taken together, our population-scale genomic resources will promote functional genomics studies and breeding improvement for silkworm.

Neural stem/progenitor cell (NSPC)-based spinal cord injury (SCI) therapy is expected to bridge the lesion site by transplanting exogenous NSPCs for replacement of lost cells. The transplanted NSPCs produce a microenvironment conducive to neuronal regeneration, and ultimately, functional recovery. Although both human fetal brain- and spinal cord- derived NSPCs (hbNSPCs and hscNSPCs, respectively) have been used for SCI repair, it remains unclear whether hscNSPCs are a more appropriate stem cell source for transplantation than hbNSPCs. Therefore, in this study, we transplanted hbNSPCs or hscNSPCs into rats with complete transection SCI to monitor their differences in SCI treatment. An aligned collagen sponge scaffold (ACSS) was used here for cell retention. Aligned biomaterial scaffolds provide a support platform and favorable morphology for cell growth and differentiation, and guide axial axonal extension. The ACSS fabricated by our group has been previously reported to improve spinal cord repair by promoting neuronal regeneration and remyelination. Compared with the hbNSPC-ACSS, the hscNSPC-ACSS effectively promoted long-term cell survival and neuronal differentiation and improved the SCI microenvironment by reducing inflammation and glial scar formation. Furthermore, the transplanted hscNSPC-ACSS improved recovery of locomotor functions. Therefore, hscNSPCs appear to be a superior cell source to hbNSPCs for SCI cell therapy with greater potential clinical applications.

Numerous studies have indicated that microgravity induces various changes in the cellular functions of neural stem cells (NSCs), and the use of microgravity to culture tissue engineered seed cells for the treatment of nervous system diseases has drawn increasing attention. The goal of this study was to verify the efficacy of collagen sponge-based 3-dimensional (3D) NSCs cultured in a rotary cell culture system (RCCS) in treating spinal cord injury (SCI). The Basso-Beattie-Bresnahan score, inclined plane test, and electrophysiology results all indicated that 3D cultured NSCs cultured in a RCCS had better therapeutic effects than those cultured in a traditional cell culture environment, suggesting that the microgravity provided by the RCCS could enhance the therapeutic effect of 3D cultured NSCs. Our study indicates the feasibility of combining the RCCS with collagen sponge-based 3D cell culture for producing tissue engineered seed cells for the treatment of SCI. This novel and effective method shows promise for application in cell-based therapy for SCI in the future.

Background With the emergence of CRISPR/Cas9 technology, multiple gene editing procedures became available for the silkworm. Although binary transgene-based methods have been widely used to generate mutants, delivery of the CRISPR/Cas9 system via DNA-free ribonucleoproteins offers several advantages. However, the T7 promoter that is widely used in the ribonucleoprotein-based method for production of sgRNAs in vitro requires a 5′ GG motif for efficient initiation. The resulting transcripts bear a 5′ GG motif, which significantly constrains the number of targetable sites in the silkworm genome. Results In this study, we used the T7 promoter to add two supernumerary G residues to the 5′ end of conventional (perfectly matched) 20-nucleotide sgRNA targeting sequences. We then asked if sgRNAs with this structure can generate mutations even if the genomic target does not contain corresponding GG residues. As expected, 5′ GG mismatches depress the mutagenic activity of sgRNAs, and a single 5′ G mismatch has a relatively minor effect. However, tests involving six sgRNAs targeting two genes show that the mismatches do not eliminate mutagenesis in vivo, and the efficiencies remain at useable levels. One sgRNA with a 5′ GG mismatch at its target performed mutagenesis more efficiently than a conventional sgRNA with 5′ matched GG residues at a second target within the same gene. Mutations generated by sgRNAs with 5′ GG mismatches are also heritable. We successfully obtained null mutants with detectable phenotypes from sib-mated mosaics after one generation. Conclusions In summary, our method improves the utility and flexibility of the ribonucleoprotein-based CRISPR/Cas9 system in silkworm.

Stem cell-based therapy has been considered as a potential treatment to restore spinal cord injury (SCI) through reconstructing neural networks and providing a favorable microenvironment for neuronal survival, differentiation, and axonal outgrowth. Biomaterial scaffolds can promote cell attachment and survival, neuronal differentiation, and axonal outgrowth; therefore, they were used to combine with stem cells for implantation in SCI treatment. In addition, a longitudinal scaffold can guide regenerated axons with orientated growth and axial extension. Both human umbilical cord-derived mesenchymal stem cells (hMSCs) and human fetal spinal cord-derived neural stem cells (hNSCs) have been applied in clinical trials worldwide. To our knowledge, a parallel comparison of the therapeutic effects of hMSC and hNSC implantations has not been conducted. Hence, in this study, we grafted hMSCs or hNSCs seeded on longitudinal collagen sponge scaffolds into rats with completely transected SCI to examine differences in SCI repair. Both hMSCs and hNSCs had equivalent effects on reducing glial scar formation around the lesion gap. More neuronal class III β-tubulin-positive neurons and neurofilament-positive nerve fibers were found in the lesion cavity after hNSC implantation. In addition, hNSCs had better capabilities to improve motor function, attenuate inflammation, and promote cell survival than hMSCs. These encouraging results provide a clinical basis for future stem cell-based SCI therapies.

Many insects spin cocoons to protect the pupae from unfavorable environments and predators. After emerging from the pupa, the moths must escape from the sealed cocoons. Previous works identified cocoonase as the active enzyme loosening the cocoon to form an escape-hatch. Here, using bioinformatics tools, we show that cocoonase is specific to Lepidoptera and that it probably existed before the occurrence of lepidopteran insects spinning cocoons. Despite differences in cocooning behavior, we further show that cocoonase evolved by purification selection in Lepidoptera and that the selection is more intense in lepidopteran insects spinning sealed cocoons. Experimentally, we applied gene editing techniques to the silkworm Bombyx mori, which spins a dense and sealed cocoon, as a model of lepidopteran insects spinning sealed cocoons. We knocked out cocoonase using the CRISPR/Cas9 system. The adults of homozygous knock-out mutants were completely formed and viable but stayed trapped and died naturally in the cocoon. This is the first experimental and phenotypic evidence that cocoonase is the determining factor for breaking the cocoon. This work led to a novel silkworm strain yielding permanently intact cocoons and provides a new strategy for controlling the pests that form cocoons., Author summary Spinning and cocooning are the instincts of many insects, providing a shelter to the residing pupae to resist adverse factors. After the metamorphosis of pupa into adult, the adult must break open the cocoon to emerge, which is called decocooning. We have bioinformatically identified that cocoonase is specific to Lepidoptera, and demonstrated that it is the determining factor for breaking the sealed cocoon experimentally for the first time. This work led to a novel silkworm strain yielding permanently intact cocoons and provides a new strategy for controlling the pests that form cocoons and for breeding.

Severe microenvironmental changes after spinal cord injury (SCI) present serious challenges in neural regeneration and tissue repair. Gelatin (GL)- and hyaluronic acid (HA)-based hydrogels are attractive scaffolds because they are major components of the extracellular matrix and can provide a favorable adjustable microenvironment for neurogenesis and motor function recovery. In this study, three-dimensional hybrid GL/HA hydrogel scaffolds were prepared and optimized. The hybrid hydrogels could undergo in situ gelation and fit the defects perfectly via visible light-induced crosslinking in the complete SCI rats. We found that the transplantation of the hybrid hydrogel scaffold significantly reduced the inflammatory responses and suppressed glial scar formation in an HA concentration-dependent manner. Moreover, the hybrid hydrogel with GL/HA ratios less than 8/2 effectively promoted endogenous neural stem cell migration and neurogenesis, as well as improved neuron maturation and axonal regeneration. The results showed locomotor function improved 60 days after transplantation, thus suggesting that GL/HA hydrogels can be considered as a promising scaffold for complete SCI repair.

In this study, we upregulated insulin-like growth factor-1 (IGF1) expression specifically in skeletal muscle by engineering an enhancer into its non-coding regions and verified the expected phenotype in a mouse model. To select an appropriate site for introducing a skeletal muscle-specific myosin light chain (MLC) enhancer, three candidate sites that exhibited the least evolutionary conservation were chosen and validated in C2C12 single-cell colonies harbouring the MLC enhancer at each site. IGF1 was dramatically upregulated in only the site 2 single-cell colony series, and it exhibited functional activity leading to the formation of extra myotubes. Therefore, we chose site 2 to generate a genetically modified (GM) mouse model with the MLC enhancer incorporated by CRISPR/Cas9 technology. The GM mice exhibited dramatically elevated IGF1 levels, which stimulated downstream pathways in skeletal muscle. Female GM mice exhibited more conspicuous muscle hypertrophy than male GM mice. The GM mice possessed similar circulating IGF1 levels and tibia length as their WT littermates; they also did not exhibit heart abnormalities. Our findings demonstrate that genetically modifying a non-coding region is a feasible method to upregulate gene expression and obtain animals with desirable traits.

Porcine hepatocytes are a promising option for xenotransplantation in light of the critical shortage of orthotopic donor livers. Because primary hepatocytes have limited ability to proliferate in vitro, several immortalized hepatocyte lines have been established. However, these cells have typically been generated using a virus-dependent transfection methodology and express viral oncogenes that introduce potential risks in clinical applications. In our study, we established immortalized porcine neonatal hepatocytes by introduction of a plasmid-based hTERT gene expression system by electroporation, without the use of viral components. We detected stable expression of hTERT by RT-PCR and Western blot. The immortalized hepatocytes exhibit a high growth rate, but retain the normal morphology of freshly isolated primary hepatocytes. To date, these immortalized hepatocytes have been expanded for over 80 passages. In addition, no significant differences were detected in glycogen synthesis, secretion of serum albumin, or lipid accumulation between the primary hepatocytes and our immortalized hepatocytes. The cells also exhibit serum-dependent growth and have no capacity for anchorage-independent growth in vitro, demonstrating that they have not been transformed in vitro. Our immortalized porcine hepatocytes will be useful for elucidating the pathogenesis of liver disease and developing efficient treatments. Furthermore, these immortalized hepatocytes may provide a safer source of cells for application in xenotransplantation, compared with immortalized cells generated using viral components.

Porcine reproductive and respiratory syndrome (PRRS) is a highly contagious disease and the most economically important disease of the swine industry worldwide. Highly pathogenic-PRRS virus (HP-PRRSV) is a variant of PRRSV, which caused high morbidity and mortality. Scavenger receptor CD163, which contains nine scavenger receptor cysteine-rich (SRCR) domains, is a key entry mediator for PRRSV. A previous study demonstrated that SRCR domain 5 (SRCR5), encoded by exon 7, was essential for PRRSV infection in vitro. Here, we substituted exon 7 of porcine CD163 with the corresponding exon of human CD163-like 1 (hCD163L1) using a CRISPR/Cas9 system combined with a donor vector. In CD163Mut/Mut pigs, modifying CD163 gene had no adverse effects on hemoglobin-haptoglobin (Hb-Hp) complex clearance or erythroblast growth. In vitro infection experiments showed that the CD163 mutant strongly inhibited HP-PRRSV replication by inhibiting virus uncoating and genome release. Compared to wild-type (WT) pigs in vivo, HP-PRRSV-infected CD163Mut/Mut pigs showed a substantially decreased viral load in blood and relief from PRRSV-induced fever. While all WT pigs were dead, there of four CD163Mut/Mut pigs survived and recovered at the termination of the experiment. Our data demonstrated that modifying CD163 remarkably inhibited PRRSV replication and protected pigs from HP-PRRSV infection, thus establishing a good foundation for breeding PRRSV-resistant pigs via gene editing technology.

The community structure of colonised bacteria in the gastrointestinal tracts (GITs) of pre-weaned calves is affected by extrinsic factors, such as the genetics and diet of the calves; however, the dietary impact is not fully understood and warrants further research. Our study revealed that a total of 6, 5, 2 and 10 bacterial genera showed biologically significant differences in the GITs of pre-weaned calves fed four waste-milk diets: acidified waste milk, pasteurised waste milk, untreated bulk milk, and untreated waste milk, respectively. Specifically, generic biomarkers were observed in the rumen (e.g., Bifidobacterium, Parabacteroides, Fibrobacter, Clostridium, etc.), caecum (e.g., Faecalibacterium, Oxalobacter, Odoribacter, etc.) and colon (e.g., Megamonas, Comamonas, Stenotrophomonas, etc.) but not in the faeces. In addition, the predicted metabolic pathways showed that the expression of genes related to metabolic diseases was increased in the calves fed untreated waste milk, which indicated that untreated waste milk is not a suitable liquid diet for pre-weaned calves. This is the first study to demonstrate how different types of waste milk fed to pre-weaned calves affect the community structure of colonised bacteria, and the results may provide insights for the intentional adjustment of diets and gastrointestinal bacterial communities.