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1. Environment-Dependent Heterosis and Transgressive Gene Expression in Reciprocal Hybrids between the Channel Catfish Ictalurus punctatus and the Blue Catfish Ictalurus furcatus

   https://doi.org/10.3390/biology11010117  

   Wang, Haolong ; Bruce, Timothy J. ; Su, Baofeng ; Li, Shangjia ; Dunham, Rex A. ; Wang, Xu ( January 2022 , Biology)

   The hybrid between female channel catfish (Ictalurus punctatus) and male blue catfish (Ictalurus furcatus) is superior in feed conversion, disease resistance, carcass yield, and harvestability compared to both parental species. However, heterosis and heterobeltiosis only occur in pond culture, and channel catfish grow much faster than the other genetic types in small culture units. This environment-dependent heterosis is intriguing, but the underlying genetic mechanisms are not well understood. In this study, phenotypic characterization and transcriptomic analyses were performed in the channel catfish, blue catfish, and their reciprocal F1s reared in tanks. The results showed that the channel catfish is superior in growth-related morphometrics, presumably due to significantly lower innate immune function, as investigated by reduced lysozyme activity and alternative complement activity. RNA-seq analysis revealed that genes involved in fatty acid metabolism/transport are significantly upregulated in channel catfish compared to blue catfish and hybrids, which also contributes to the growth phenotype. Interestingly, hybrids have a 40–80% elevation in blood glucose than the parental species, which can be explained by a phenomenon called transgressive expression (overexpression/underexpression in F1s than the parental species). A total of 1140 transgressive genes were identified in F1 hybrids, indicating that 8.5% of the transcriptome displayed transgressive expression. Transgressive genes upregulated in F1s are enriched for glycan degradation function, directly related to the increase in blood glucose level. This study is the first to explore molecular mechanisms of environment-dependent heterosis/heterobeltiosis in a vertebrate species and sheds light on the regulation and evolution of heterosis vs. hybrid incompatibility. 

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2. Chromosome-level assembly and annotation of the blue catfish Ictalurus furcatus , an aquaculture species for hybrid catfish reproduction, epigenetics, and heterosis studies

   https://doi.org/10.1093/gigascience/giac070  

   Wang, Haolong ; Su, Baofeng ; Butts, Ian A. E. ; Dunham, Rex A. ; Wang, Xu ( July 2022 , GigaScience)

   The blue catfish is of great value in aquaculture and recreational fisheries. The F1 hybrids of female channel catfish (Ictalurus punctatus) × male blue catfish (Ictalurusfurcatus) have been the primary driver of US catfish production in recent years because of superior growth, survival, and carcass yield. The channel–blue hybrid also provides an excellent model to investigate molecular mechanisms of environment-dependent heterosis. However, transcriptome and methylome studies suffered from low alignment rates to the channel catfish genome due to divergence, and the genome resources for blue catfish are not publicly available.

   The blue catfish genome assembly is 841.86 Mbp in length with excellent continuity (8.6 Mbp contig N50, 28.2 Mbp scaffold N50) and completeness (98.6% Eukaryota and 97.0% Actinopterygii BUSCO). A total of 30,971 protein-coding genes were predicted, of which 21,781 were supported by RNA sequencing evidence. Phylogenomic analyses revealed that it diverged from channel catfish approximately 9 million years ago with 15.7 million fixed nucleotide differences. The within-species single-nucleotide polymorphism (SNP) density is 0.32% between the most aquaculturally important blue catfish strains (D&B and Rio Grande). Gene family analysis discovered significant expansion of immune-related families in the blue catfish lineage, which may contribute to disease resistance in blue catfish.

   We reported the first high-quality, chromosome-level assembly of the blue catfish genome, which provides the necessary genomic tool kit for transcriptome and methylome analysis, SNP discovery and marker-assisted selection, gene editing and genome engineering, and reproductive enhancement of the blue catfish and hybrid catfish.

    

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3. Dynamic aqueous transformations of lithium cobalt oxide nanoparticle induce distinct oxidative stress responses of B. subtilis

   https://doi.org/10.1039/D0EN01151G  

   Gari, Metti K. ; Lemke, Paul ; Lu, Kelly H. ; Laudadio, Elizabeth D. ; Henke, Austin H. ; Green, Curtis M. ; Pho, Thomas ; Hoang, Khoi Nguyen ; Murphy, Catherine J. ; Hamers, Robert J. ; et al ( January 2021 , Environmental Science: Nano)

   null (Ed.)

   Lithium cobalt oxide (LiCoO 2 ), an example of nanoscale transition metal oxide and a widely commercialized cathode material in lithium ion batteries, has been shown to induce oxidative stress and generate intracellular reactive oxygen species (ROS) in model organisms. In this study, we aimed to understand the time-dependent roles of abiotic ROS generation and Co ions released in aqueous medium by LiCoO 2 NPs, and examined the induced biological responses in model bacterium, B. subtilis upon exposure. We found that the redox-active LiCoO 2 NPs produced abiotic ROS primarily through H 2 O 2 generation when freshly suspended. Subsequently, the freshly-suspended LiCoO 2 NPs induced additional DNA breakage, and changes in expression of oxidative stress genes in B. subtilis that could not be accounted for by the released Co ions alone. Notably, in 48 hour old LiCoO 2 suspensions, H 2 O 2 generation subsided while higher concentrations of Co ions were released. The biological responses in DNA damage and gene expression to the aged LiCoO 2 NPs recapitulated those induced by the released Co ions. Our results demonstrated oxidative stress mechanisms for bacteria exposed to LiCoO 2 NPs were mediated by the generation of distinct biotic and abiotic ROS species, which depended on the aqueous transformation state of the NPs. This study revealed the interdependent and dynamic nature of NP transformation and their biological consequences where the state of NPs resulted in distinct NP-specific mechanisms of oxidative injury. Our work highlights the need to capture the dynamic transformation of NPs that may activate the multiple routes of oxidative stress responses in cells. 

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4. Isolation of intact extracellular vesicles from cryopreserved samples

   https://doi.org/10.1371/journal.pone.0251290  

   Tessier, Shannon N. ; Bookstaver, Lauren D. ; Angpraseuth, Cindy ; Stannard, Cleo J. ; Marques, Beatriz ; Ho, Uyen K. ; Muzikansky, Alona ; Aldikacti, Berent ; Reátegui, Eduardo ; Rabe, Daniel C. ; et al ( May 2021 , PLOS ONE)

   Johnson, Colin (Ed.)

   Extracellular vesicles (EVs) have emerged as promising candidates in biomarker discovery and diagnostics. Protected by the lipid bilayer, the molecular content of EVs in diverse biofluids are protected from RNases and proteases in the surrounding environment that may rapidly degrade targets of interests. Nonetheless, cryopreservation of EV-containing samples to -80°C may expose the lipid bilayer to physical and biological stressors which may result in cryoinjury and contribute to changes in EV yield, function, or molecular cargo. In the present work, we systematically evaluate the effect of cryopreservation at -80°C for a relatively short duration of storage (up to 12 days) on plasma- and media-derived EV particle count and/or RNA yield/quality, as compared to paired fresh controls. On average, we found that the plasma-derived EV concentration of stored samples decreased to 23% of fresh samples. Further, this significant decrease in EV particle count was matched with a corresponding significant decrease in RNA yield whereby plasma-derived stored samples contained only 47–52% of the total RNA from fresh samples, depending on the extraction method used. Similarly, media-derived EVs showed a statistically significant decrease in RNA yield whereby stored samples were 58% of the total RNA from fresh samples. In contrast, we did not obtain clear evidence of decreased RNA quality through analysis of RNA traces. These results suggest that samples stored for up to 12 days can indeed produce high-quality RNA; however, we note that when directly comparing fresh versus cryopreserved samples without cryoprotective agents there are significant losses in total RNA. Finally, we demonstrate that the addition of the commonly used cryoprotectant agent, DMSO, alongside greater control of the rate of cooling/warming, can rescue EVs from damaging ice formation and improve RNA yield. 

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5. The Immp2l Mutation Causes Ovarian Aging Through ROS-Wnt/β-Catenin-Estrogen Pathway: Preventive Effect of Melatonin

   https://doi.org/10.1210/endocr/bqaa119  

   He, Qing ; Gu, Lifang ; Lin, Qingyin ; Ma, Yi ; Liu, Chunlian ; Pei, Xiuying ; Li, P Andy ; Yang, Yanzhou ( September 2020 , Endocrinology)

   Abstract Mitochondria play important roles in ovarian follicle development. Mitochondrial dysfunction, including mitochondrial gene deficiency, impairs ovarian development. Here, we explored the role and mechanism of mitochondrial inner membrane gene Immp2l in ovarian follicle growth and development. Our results revealed that female Immp2l-/- mice were infertile, whereas Immp2l+/- mice were normal. Body and ovarian weights were reduced in the female Immp2l-/- mice, ovarian follicle growth and development were stunted in the secondary follicle stage. Although a few ovarian follicles were ovulated, the oocytes were not fertilized because of mitochondrial dysfunction. Increased oxidative stress, decreased estrogen levels, and altered genes expression of Wnt/β-catenin and steroid hormone synthesis pathways were observed in 28-day-old Immp2l-/- mice. The Immp2l mutation accelerated ovarian aging process, as no ovarian follicles were detected by age 5 months in Immp2l-/- mice. All the aforementioned changes in the Immp2l-/- mice were reversed by administration of antioxidant melatonin to the Immp2l-/- mice. Furthermore, our in vitro study using Immp2l knockdown granulosa cells confirmed that the Immp2l downregulation induced granulosa cell aging by enhancing reactive oxygen species (ROS) levels, suppressing Wnt16, increasing β-catenin, and decreasing steroid hormone synthesis gene cyp19a1 and estrogen levels, accompanied by an increase in the aging phenotype of granulosa cells. Melatonin treatment delayed granulosa cell aging progression. Taken together, Immp2l causes ovarian aging through the ROS-Wnt/β-catenin-estrogen (cyp19a1) pathway, which can be reversed by melatonin treatment. 

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