Deploying synthetic coevolution and machine learning to engineer protein-protein interactions.

Fine-tuning of protein-protein interactions occurs naturally through coevolution, but this process is difficult to recapitulate in the laboratory. We describe a platform for synthetic protein-protein coevolution that can isolate matched pairs of interacting muteins from complex libraries. This large dataset of coevolved complexes drove a systems-level analysis of molecular recognition between Z domain-affibody pairs spanning a wide range of structures, affinities, cross-reactivities, and orthogonalities, and captured a broad spectrum of coevolutionary networks. Furthermore, we harnessed pretrained protein language models to expand, in silico, the amino acid diversity of our coevolution screen, predicting remodeled interfaces beyond the reach of the experimental library. The integration of these approaches provides a means of simulating protein coevolution and generating protein complexes with diverse molecular recognition properties for biotechnology and synthetic biology.

Compartmentally scavenging hepatic oxidants through AMPK/SIRT3-PGC1α axis improves mitochondrial biogenesis and glucose catabolism.

Early treatment can prevent the occurrence of diabetes; however, there are few pharmacological treatment strategies to date. The liver is a major metabolic organ, and hepatic glucose homeostasis is dysregulated in type 1 and type 2 diabetes mellitus. However, the potential of specifically targeting the liver to prevent diabetes has not been fully exploited. In this study, we found that compartmentally inhibiting hepatic oxidants by nano-MitoPBN, a liver mitochondrial-targeting ROS scavenger, could effectively prevent diabetes. Our results demonstrated that nano-MitoPBN reversed the downregulation of PGC-1α and the enhanced gluconeogenesis in the livers of diabetic mice. PGC-1α, through an AMPK- and SIRT3-mediated mechanism, promoted mitochondrial biogenesis, increased the number of mitochondria, and enhanced the rate of aerobic oxidation, leading to decreased glucose levels in the blood by increasing glucose uptake and catabolism in the liver. Moreover, the increase in PGC-1α activity did not promote the activation of gluconeogenesis. Our study demonstrated that by regulating the redox balance of liver mitochondria in the early stage of diabetes, PGC-1α could selectively inhibit gluconeogenesis in the liver and promote hepatic mitochondrial function, which accelerated the catabolism of hepatic glucose and reduced blood glucose. Thus, glucose tolerance can be normalized through only three weeks of intervention. Our results showed that nano-MitoPBN could effectively prevent diabetes in a short period of time, highlighting the effectiveness and importance of early intervention for diabetes and suggesting the potential advantages of hepatic mitochondrial targeting oxidants nano-inhibitors in the prevention and early treatment of diabetes.

Effects of redox interference on the pancreatic mitochondria and the abnormal blood glucose.

Reactive oxygen species (ROS) has been implicated as a contributor to both the onset and the progression of diabetes, however how does redox state affect diabetes has not been fully understood. Here we study the role of redox interference on pancreatic mitochondria and the progression of diabetes. We applied streptozotocin (STZ) to establish diabetes mellitus (DM) model in rats, applied FeSO4 to produce oxidative stress (OS) and Ganoderma lucidum polysaccharides as antioxidant intervention (AO). Our results showed that in OS and DM group, oxidative stress caused the imbalance of redox state, resulting in higher lipid peroxidation level and lower antioxidant level, while AO treatment group reduced blood glucose by repairing the redox balance. The insulin level has the order of Normal Control (NC)

Temporal quantification of mating system parameters in a coastal Douglas-fir seed orchard under manipulated pollination environment.

Seed orchards main function is delivering breeding programs' gains in the form of genetically improved seedlings. They are unique experimental populations, perfectly suited for studying various pollination environments (natural or otherwise), affecting their mating system parameters. Here, under different pollination environment (natural and intrusive (pollen augmentation and/or bloom-delay)), the mating system of a second generation, wind-pollinated, coastal Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) seed orchard was evaluated over four years. Using DNA microsatellite markers and bulk seed samples, we conducted pedigree reconstruction to assign each seed's male and female parents, followed by determining the extent of pollen contamination (external gene flow), selfing rate, and, parental gametic contribution for each year. Overall, external pollen contamination rates ranged between 10 and 28%, selfing rate varied between 12 and 17%, and 80% of the seed crops were produced by 37-64% of the orchard's parents. Pollination environment and seed crop size substantially influenced the observed results, particularly for small crops as pollen contamination was high in natural (28%) vs. intrusive pollination (10%). Generally, irrespective of the crop size, seed produced under natural pollination had higher pollen contamination, confirming the role of pollination environment manipulation in improving seed crops' genetic quality.

Organ-On-A-Chip Platforms: A Convergence of Advanced Materials, Cells, and Microscale Technologies.

Significant advances in biomaterials, stem cell biology, and microscale technologies have enabled the fabrication of biologically relevant tissues and organs. Such tissues and organs, referred to as organ-on-a-chip (OOC) platforms, have emerged as a powerful tool in tissue analysis and disease modeling for biological and pharmacological applications. A variety of biomaterials are used in tissue fabrication providing multiple biological, structural, and mechanical cues in the regulation of cell behavior and tissue morphogenesis. Cells derived from humans enable the fabrication of personalized OOC platforms. Microscale technologies are specifically helpful in providing physiological microenvironments for tissues and organs. In this review, biomaterials, cells, and microscale technologies are described as essential components to construct OOC platforms. The latest developments in OOC platforms (e.g., liver, skeletal muscle, cardiac, cancer, lung, skin, bone, and brain) are then discussed as functional tools in simulating human physiology and metabolism. Future perspectives and major challenges in the development of OOC platforms toward accelerating clinical studies of drug discovery are finally highlighted.

Changes in protein expression in rat bronchoalveolar lavage fluid after exposure to zinc oxide nanoparticles: an iTRAQ proteomic approach.

RATIONALE: Zinc oxide nanoparticles (ZnO NPs) are widely used in consumer products and various biomedical fields. As a result, humans are frequently exposed to these NPs. However, there is a lack of information about the proteins that are expressed in the airway in response to exposure to ZnO NPs. METHODS: Bronchoalveolar lavage fluid (BALF) from Sprague-Dawley (SD) rats that had been exposed to high-dose 35 nm ZnO NPs (N = 6) and filtered air (N = 4) was collected and then labeled with isobaric tags for relative and absolute quantitation (iTRAQ). The differentially expressed proteins were identified by two-dimensional liquid chromatography/tandem mass spectrometry (2D-LC/MS/MS) and further classified by Gene Ontology (GO) annotation. RESULTS: A total of 46 proteins displayed significant changes after exposure. GO annotation of these differentially expressed proteins indicated that exposure to ZnO NPs mainly affected immune and inflammatory processes. Furthermore, S100A8 and S100A9, candidate markers of idiopathic pulmonary fibrosis and lung cancer, were significantly up-regulated (2.78- and 2.87-fold, respectively) following exposure. CONCLUSIONS: Our data are consistent with recent study results that exposure to ZnO NPs induces lung inflammation. These data contribute to a better understanding of how exposure to ZnO NPs leads to lung damage through the functional classification of these proteins.

Populus trichocarpa cell wall chemistry and ultrastructure trait variation, genetic control and genetic correlations.

The increasing ecological and economical importance of Populus species and hybrids has stimulated research into the investigation of the natural variation of the species and the estimation of the extent of genetic control over its wood quality traits for traditional forestry activities as well as the emerging bioenergy sector. A realized kinship matrix based on informative, high-density, biallelic single nucleotide polymorphism (SNP) genetic markers was constructed to estimate trait variance components, heritabilities, and genetic and phenotypic correlations. Seventeen traits related to wood chemistry and ultrastructure were examined in 334 9-yr-old Populus trichocarpa grown in a common-garden plot representing populations spanning the latitudinal range 44° to 58.6°. In these individuals, 9342 SNPs that conformed to Hardy-Weinberg expectations were employed to assess the genomic pair-wise kinship to estimate narrow-sense heritabilities and genetic correlations among traits. The range-wide phenotypic variation in all traits was substantial and several trait heritabilities were > 0.6. In total, 61 significant genetic and phenotypic correlations and a network of highly interrelated traits were identified. The high trait variation, the evidence for moderate to high heritabilities and the identification of advantageous trait combinations of industrially important characteristics should aid in providing the foundation for the enhancement of poplar tree breeding strategies for modern industrial use.

Female reproductive success variation in a Pseudotsuga menziesii seed orchard as revealed by pedigree reconstruction from a bulk seed collection.

The impact of female reproductive success on the mating system, gene flow, and genetic diversity of the filial generation was studied using a random sample of 801 bulk seed from a 49-clone Pseudotsuga menziesii seed orchard. We used microsatellite DNA fingerprinting and pedigree reconstruction to assign each seed's maternal and paternal parents and directly estimated clonal reproductive success, selfing rate, and the proportion of seed sired by outside pollen sources. Unlike most family array mating system and gene flow studies conducted on natural and experimental populations, which used an equal number of seeds per maternal genotype and thus generating unbiased inferences only on male reproductive success, the random sample we used was a representative of the entire seed crop; therefore, provided a unique opportunity to draw unbiased inferences on both female and male reproductive success variation. Selfing rate and the number of seed sired by outside pollen sources were found to be a function of female fertility variation. This variation also substantially and negatively affected female effective population size. Additionally, the results provided convincing evidence that the use of clone size as a proxy to fertility is questionable and requires further consideration.