Zhiyu Liu

Bio: Zhiyu Liu is an academic researcher from Marine Institute of Memorial University of Newfoundland. The author has contributed to research in topics: Medicine & Biology. The author has an hindex of 2, co-authored 2 publications receiving 25 citations.

Overexpression of acetyl-CoA carboxylase increases fatty acid production in the green alga Chlamydomonas reinhardtii.

Abstract: Chlamydomonas reinhardtii is a photosynthetic unicellular model algae with multiple biotechnological advantages, and its fatty acids can be used to produce biofuels. Numerous studies suggest that acetyl-coA carboxylase (ACCa) catalyzes the first committed and rate-limiting step of fatty acid biosynthesis, thereby playing a central role in oil accumulation. Here, we cloned and overexpressed ACCa in C. reinhardtii to directly evaluate its effect on fatty acid synthesis. GC–MS analysis found that the unsaturated FAs contents of the CW15-24 and CW15-85 strains were 55.45% and 56.15%, which were significantly enriched compared to the wild type CW15 (48.39%). Under the optimized conditions, the content of lipid by overexpressed the ACCa gene in the mutant CW15-85 (0.46 g/l) was 1.16-fold greater than control through optimization of N and P sources. Altogether, our data clearly demonstrate that ACCa overexpression in C. reinhardtii can directly increase the synthesis of fatty acids.

Chromosome genome assembly and annotation of the yellowbelly pufferfish with PacBio and Hi-C sequencing data.

Abstract: Pufferfish are ideal models for vertebrate chromosome evolution studies. The yellowbelly pufferfish, Takifugu flavidus, is an important marine fish species in the aquaculture industry and ecology of East Asia. The chromosome assembly of the species could facilitate the study of chromosome evolution and functional gene mapping. To this end, 44, 27 and 50 Gb reads were generated for genome assembly using Illumina, PacBio and Hi-C sequencing technologies, respectively. More than 13 Gb full-length transcripts were sequenced on the PacBio platform. A 366 Mb genome was obtained with the contig of 4.4 Mb and scaffold N50 length of 15.7 Mb. 266 contigs were reliably assembled into 22 chromosomes, representing 95.9% of the total genome. A total of 29,416 protein-coding genes were predicted and 28,071 genes were functionally annotated. More than 97.7% of the BUSCO genes were successfully detected in the genome. The genome resource in this work will be used for the conservation and population genetics of the yellowbelly pufferfish, as well as in vertebrate chromosome evolution studies. Machine-accessible metadata file describing the reported data: https://doi.org/10.6084/m9.figshare.10008740

Antibiotic Chlortetracycline Causes Transgenerational Immunosuppression via NF-κB

Abstract: The extensive and increasing global use of antibiotics results in the ubiquitous presence of antibiotics in the environment, which has made them “pseudo persistent organic contaminants.” Despite numerous studies showing wide adverse effects of antibiotics on organisms, the chronic environmental risk of their exposure is unknown, and the molecular and cellular mechanisms of antibiotic toxicity remain unclear. Here, we systematically quantified transgenerational immune disturbances after chronic parental exposure to environmental levels of a common antibiotic, chlortetracycline (CTC), using zebrafish as a model. CTC strongly reduced the antibacterial activities of fish offspring by transgenerational immunosuppression. Both innate and adaptive immunities of the offspring were suppressed, showing significant perturbation of macrophages and neutrophils, expression of immune-related genes, and other immune functions. Moreover, these CTC-induced immune effects were either prevented or alleviated by the supplementation with PDTC, an antagonist of nuclear factor-κB (NF-κB), uncovering a seminal role of NF-κB in CTC immunotoxicity. Our results provide the evidence in fish that CTC at environmentally relevant concentrations can be transmitted over multiple generations and weaken the immune defense of offspring, raising concerns on the population hazards and ecological risk of antibiotics in the natural environment.

Regulatory effects of differential dietary energy levels on spermatogenesis and sperm motility of yellow-feathered breeder cocks

Abstract: The semen quality of breeder cocks profoundly impacted the numbers of matched layer hens and the economic benefits of the poultry industry. Adequacy and balance of poultry nutrition, especially the energy provision, critically modulated the reproductive potential of breeder cocks, however, the underlying mechanism was still unclear. For the purpose of this study, a total of 90 yellow-feathered 13-week-old roosters with the same age in days and similar body weight (1,437 ± 44.3 g) were selected and randomly divided into the low energy diet (LE), the moderate energy diet (ME), and the high energy diet (HE) treatments. The phenotypic parameters related to reproduction include semen quality, fertility, and hatchability, and the testis morphological parameters, including seminiferous epithelium length (SEL), seminiferous tubule perimeter (STP), seminiferous tubule area (STA), and Johnsen score, were measured to investigate the regulatory effects of different energy diets on reproductive performances. Furthermore, spermatogenesis and sperm motility-related genes, which included the sry-related high mobility group box (SOX) gene family and sperm-associated antigen (SPAG) gene family, and mitochondria apoptosis-related genes, such as Cyt-C, Bcl-2, and Bax, were measured to determine the underlying mechanism of energy on the reproductive performances. The The results showed that the gonadosomatic index and sperm motility in the ME treatment significantly increased compared with the LE treatment. Chickens in the ME treatment showed a preferable performance of testis development, especially a significant increment of SEL and Johnsen Score, compared with the LE and HE treatments. Finally, spermatogenesis-related genes, which included SPAG6, SPAG16, SOX5, SOX6, and SOX13, and apoptosis-related genes of mitochondria, such as the Cyt-C and Bcl-2, were significantly upregulated in the ME treatment. This study concluded that proper energy provision stimulated regular energy metabolism for spermatogenesis and sperm capacitation, which finally increased semen quality and reproductive performances of breeder cocks.

Telomere-to-telomere assembly of a fish Y chromosome reveals the origin of a young sex chromosome pair.

Abstract: The origin of sex chromosomes requires the establishment of recombination suppression between the proto-sex chromosomes. In many fish species, the sex chromosome pair is homomorphic with a recent origin, providing species for studying how and why recombination suppression evolved in the initial stages of sex chromosome differentiation, but this requires accurate sequence assembly of the X and Y (or Z and W) chromosomes, which may be difficult if they are recently diverged. Here we produce a haplotype-resolved genome assembly of zig-zag eel (Mastacembelus armatus), an aquaculture fish, at the chromosomal scale. The diploid assembly is nearly gap-free, and in most chromosomes, we resolve the centromeric and subtelomeric heterochromatic sequences. In particular, the Y chromosome, including its highly repetitive short arm, has zero gaps. Using resequencing data, we identify a ~7 Mb fully sex-linked region (SLR), spanning the sex chromosome centromere and almost entirely embedded in the pericentromeric heterochromatin. The SLRs on the X and Y chromosomes are almost identical in sequence and gene content, but both are repetitive and heterochromatic, consistent with zero or low recombination. We further identify an HMG-domain containing gene HMGN6 in the SLR as a candidate sex-determining gene that is expressed at the onset of testis development. Our study supports the idea that preexisting regions of low recombination, such as pericentromeric regions, can give rise to SLR in the absence of structural variations between the proto-sex chromosomes.