Identification of the Key microRNAs and miRNA-mRNA Interaction Networks during the Ovarian Development of Hens

It is well-known that multiple functional miRNAs are found in mammals’ ovaries, which are linked not only to ovarian development, but also to maturation and apoptosis. However, there is still a lack of knowledge regarding the role of miRNAs in the hen ovary. In the present study, we analyzed the miRNA sequencing libraries of ovaries at the four different developmental stages of hens (15, 20, 30, and 68 W) and a total of 677 known miRNAs and 61 novel miRNAs were identified. In total, 209 of them were differently expressed miRNAs (DE miRNAs) obtained from comparisons of the four stages, including 84 upregulated and 125 downregulated DE miRNAs. Furthermore, the five key DE miRNAs gga-miR-2954, gga-miR-6634-5p, gga-miR-449b-5p, gga-miR-449c-3p, and gga-miR449c-5p were screened using an analysis of the miRNA-mRNA interaction network and functional enrichment annotated in seven significantly enriched pathways, such as endocytosis, lysine degradation, the biosynthesis of amino acids, and the MAPK signaling pathway, which may primarily participate in cell differentiation and proliferation, steroid hormone biosynthesis, and angiogenesis by targeting the related genes. For instance, gga-miR-449 family members were predicted to target 15 genes, including TGFB1, TPM1, TPM3, and CAMKB2, which were reported to regulate follicular growth, selection, and the ovulatory cycle. Taken together, our results illustrate the ovarian miRNA profiles of the four classic developmental stages of hens and highlight the significant role of miRNAs in ovarian development and functions. However, in-depth research needs to be carried out to validate the potential functional miRNAs found in this study.

SARS-CoV-2 Quasispecies Mediate Rapid Virus Evolution and Adaptation

ABSTRACTThe pandemic spread of SARS-CoV-2 and the resulting global healthcare emergency warrants a better understanding of its biology. The potential of SARS-CoV-2 evolution to create novel dangerous variants remains underexplored. Thus, we passaged SARS-CoV-2 in defined conditions and determined its genomic adaptation dynamics. We demonstrate the presence of remarkably stable SARS-CoV-2 quasispecies. We further show that the quasispecies nature of the virus population ensured rapid adaptation of the spike PRRARS motif upon passaging in Vero cells. On the other hand, SARS-CoV-2 replication in TMPRSS2 expressing cells led to a reverse mutation at the same site. We observed the emergence of novel mutations in envelope protein upon virus culture in Calu-3 and Caco-2 cells. Finally, we show that the heparan sulfate-binding motif (PRRARS) of the SARS-CoV-2 S protein acted as a determinant of negative growth selection. Overall, our research has far-reaching implications for development of antiviral strategies, suggesting viral quasispecies may facilitate rapid emergence of escape mutants under selection pressure, such as the treatment with antivirals against SARS-CoV-2.

Vegetative morphophysiological responses of four rice cultivars to drought stress

Miftahudin, Putri RE, Chikmawati T. 2020. Vegetative morphophysiological responses of four rice cultivars to drought stress. Biodiversitas 21: 3727-3734. Each rice genotype develops certain morphophysiological responses to drought stress. The study aimed to analyze the morphophysiological responses of vegetative aspect of four rice cultivars to drought stress. A 10% Polyethylene glycol-6000 was added to a Yoshida nutrient solution medium as a drought stress stimulant for four rice cultivars, i.e., IR64, Hawara Bunar, Situbagendit, and Inpago 10. Fourteen-days-old rice seedlings were grown on the media with and without drought stress treatment for 9 days, and morphophysiological characters of vegetative aspects were observed. Drought stress inhibited the shoot growth of cv. Hawara Bunar, but increased shoot growth of cv. Inpago 10. The physiological responses in the form of leaf relative water content, proline, malondialdehyde (MDA), and total chlorophyll contents in cv. Hawara Bunar was inversely proportional to those of cv. IR64 showed an inferior response to drought stress. The rice cv. Hawara Bunar might develop better response mechanisms to drought than that of cv. IR64. The physiological responses of cvs. Situbagendit and Inpago 10 were in between the other two cultivars. We conclude that the variation of morphophysiological responses to drought stress among rice cultivars is an indicator of tolerance capability to drought that could be used as early-growth selection criteria in rice breeding programs for drought tolerance.

Pairing two growth-based, high-throughput selections to fine tune conformational dynamics in oxygenase engineering

ABSTRACTCyclohexanone monooxygenases (CHMO) consume molecular oxygen and NADPH to catalyze the valuable oxidation of cyclic ketones. However, CHMO usage is restricted by poor thermostability and stringent specificity for NADPH. Efforts to engineer CHMO have been limited by the sensitivity of the enzyme to perturbations in conformational dynamics and long-range interactions that cannot be predicted. We demonstrate a pair of aerobic, high-throughput growth selection platforms in Escherichia coli for oxygenase evolution, based on NADPH or NADH redox balance. We utilize the NADPH-dependent selection in the directed evolution of thermostable CHMO and discover the variant CHMO GV (A245G-A288V) with a 2.7-fold improvement in residual activity compared to the wild type after 40 °C incubation. Addition of a previously reported mutation resulted in A245G-A288V-T415C which has further improved thermostability at 45 °C. We apply the NADH-dependent selection to alter the cofactor specificity of CHMO to accept NADH, a less expensive cofactor than NADPH. We identified the variant CHMO DTNP (S208D-K326T-K349N-L143P) with a 21-fold cofactor specificity switch from NADPH to NADH compared to the wild type. Molecular modeling indicates that CHMO GV experiences more favorable residue packing and backbone torsions, and CHMO DTNP activity is driven by cooperative fine-tuning of cofactor contacts. Our introduced tools for oxygenase evolution enable the rapid engineering of properties critical to industrial scalability.

The influence of larval growth rate on juvenile recruitment in Lake Erie walleye (Sander vitreus)

Growth-selective mortality as larvae can influence recruitment in marine fishes. Its importance in freshwater fishes, however, remains speculative. We quantified growth trajectories within annual cohorts (2011–2013) of Lake Erie walleye (Sander vitreus) and their relationship with recruitment. We hypothesized that selection against slow or fast growth would be associated with high mortality and poor recruitment, whereas weak or nonexistent growth-selective mortality co-occurring with fast growth would be associated with good recruitment. We used otoliths to reconstruct growth rates during the first 15 days of life from larvae collected during spring and juvenile recruits (survivors) collected during late summer. We documented growth-selective mortality during 2011 and 2013, which exhibited poor recruitment as expected. During 2012, growth selection was absent, but growth was slow when compared to historical averages, resulting in poor recruitment. Growth was also considered slow in 2011 and 2013, due to multiple interacting conditions. Our study indicates that the relationship among larval growth, mortality, and future recruitment is complex, highlighting the need for continued research into how larval processes affect recruitment dynamics in freshwater fishes.

Water Deficit Tolerance of Some Pepper Inbred Lines

Water deficit is one of the main limiting factors affecting plant growth. Selection in water-limited environments can result in populations or species with improved response to drought. Water deficit decreases yield and quality, therefore, it is important to identify genotypes that are tolerant to deficit irrigation conditions. In this study, the water-deficit tolerance of 59 pepper-inbred lines was determined. Experiments were conducted in a growth chamber and under field conditions (Şanlıurfa) with a control (100% full-irrigation) and water-deficit treatment (50% irrigation). Fruit weight, fruit length and number of fruits were recorded. Pepper lines 1900, 896 A-W, 74, 760, 1560-W, 912 A-W, 405-A, 953-W, 226, 1105-W and 441 were identified as the most tolerant to water deficit conditions. Present findings revealed that these pepper lines could be used to develop cultivars that have satisfactory yield under water deficit conditions.

25 Evolution of the commercial sow

Swine production has dramatically changed in the past 30 to 40 years. The small producer that raised pigs with minimal investment when the economics were desirable (“part-timers”) has been replaced by full-time swine producers with massive capital investments. As this revolution in production practices has occurred, the optimal animal has evolved. Today’s market hog is leaner and weighs 20% more, yet goes to market at a similar age and consumes a similar quantity of feed. While these changes are impressive, they are dwarfed by the changes in the modern commercial sow, which births 30% more piglets and has 10% more litters/year. Today’s commercial sow is a culmination of research efforts in reproductive physiology, nutrition, facility design and animal management synergistically combined with modern genetic selection theory. She is a first-generation cross between a Landrace and a Yorkshire/Large White parent from lines that have been selected for superior reproductive performance and lean tissue growth. Selection has emphasized prolificacy, milk production and return to estrus in a lean, fast growing animal. While her current performance figures are impressive, there is still room to improve. She will continue to evolve to fit future production needs and environments to supply the world with nutritious pork products.USDA is an equal opportunity provider and employer.