Baolin Zhang

Comparative analysis of primate genomes within a phylogenetic context is essential for understanding the evolution of human genetic architecture and primate diversity. We present such a study of 50 primate species spanning 38 genera and 14 families, including 27 genomes first reported here, with many from previously less well represented groups, the New World monkeys and the Strepsirrhini. Our analyses reveal heterogeneous rates of genomic rearrangement and gene evolution across primate lineages. Thousands of genes under positive selection in different lineages play roles in the nervous, skeletal, and digestive systems and may have contributed to primate innovations and adaptations. Our study reveals that many key genomic innovations occurred in the Simiiformes ancestral node and may have had an impact on the adaptive radiation of the Simiiformes and human evolution.

Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that the fascicularis group originated from an ancient hybridization between the sinica and silenus groups ~3.45 to 3.56 million years ago. The X chromosomes and low-recombination regions exhibited equal contributions from each parental lineage, suggesting that they were less affected by subsequent backcrossing and hence could have played an important role in maintaining hybrid integrity. We identified many reproduction-associated genes that could have contributed to the development of the mixed sexual phenotypes characteristic of the fascicularis group. The phylogeny within the silenus group was also resolved, and functional experimentation confirmed that all extant Western silenus species are susceptible to HIV-1 infection. Our study provides novel insights into macaque evolution and reveals a hybrid speciation event that has occurred only very rarely in primates.

Climate change has led to shifts in species distribution and become a crucial factor in the extinction of species. Increasing average temperatures, temperature extremes, and unpredictable weather events have all become a part of a perfect storm that is threatening ecosystems. Higher altitude habitats are disproportionately affected by climate change, and habitats for already threatened specialist species are shrinking. The Siberian ibex, Capra sibirica, is distributed across Central Asia and Southern Siberia and is the dominant ungulate in the Pamir plateau. To understand how climate change could affect the habitat of Siberian ibex in the Taxkorgan Nature Reserve (TNR), an ensemble species distribution model was built using 109 occurrence points from a four-year field survey. Fifteen environmental variables were used to simulate suitable habitat distribution under different climate change scenarios. Our results demonstrated that a stable, suitable habitat for Siberian ibex was mostly distributed in the northwest and northeast of the TNR. We found that climate change will further reduce the area of suitable habitat for this species. In the scenarios of RCP2.6 to 2070 and RCP8.5 to 2050, habitat loss would exceed 30%. In addition, suitable habitats for Siberian ibex will shift to higher latitudes under climate change. As a result, timely prediction of the distribution of endangered animals is conducive to the conservation of the biodiversity of mountain ecosystems, particularly in arid areas.

Guenons (tribe Cercopithecini) are the most widely distributed nonhuman primate in the tropical forest belt of Africa and show considerable phenotypic, taxonomic, and ecological diversity. However, genomic information for most species within this group is still lacking. Here, we present a high-quality de novo genome (total 2.90 Gb, contig N50 equal to 22.7 Mb) of the mona monkey (Cercopithecus mona), together with genome resequencing data of 13 individuals sampled across Nigeria. Our results showed differentiation between populations from East and West of the Niger River ∼84 ka and potential ancient introgression in the East population from other mona group species. The PTPRK, FRAS1, BNC2, and EDN3 genes related to pigmentation displayed signals of introgression in the East population. Genomic scans suggest that immunity genes such as AKT3 and IL13 (possibly involved in simian immunodeficiency virus defense), and G6PD, a gene involved in malaria resistance, are under positive natural selection. Our study gives insights into differentiation, natural selection, and introgression in guenons.

Many therapeutic monoclonal antibodies (mAbs) are clinically administered through intravenous infusion after mixing with a diluent, e.g., saline, 5% dextrose. Such a clinical setting increases the likelihood of interactions among mAb molecules, diluent, and plasma components, which may adversely affect product safety and efficacy. Avastin® (bevacizumab) and Herceptin® (trastuzumab), but not Remicade® (infliximab), were shown to undergo rapid aggregation upon dilution into 5% dextrose when mixed with human plasma in vitro; however, the biochemical pathways leading to the aggregation were not clearly defined. Here, we show that dextrose-mediated aggregation of Avastin or Herceptin in plasma involves isoelectric precipitation of complement proteins. Using mass spectrometry, we found that dextrose-induced insoluble aggregates were composed of mAb itself and multiple abundant plasma proteins, namely complement proteins C3, C4, factor H, fibronectin, and apolipoprotein. These plasma proteins, which are characterized by an isoelectronic point of 5.5–6.7, lost solubility at the resulting pH in the mixture with formulated Avastin (pH 6.2) and Herceptin (pH 6.0). Notably, switching formulation buffers for Avastin (pH 6.2) and Remicade (pH 7.2) reversed their aggregation profiles. Avastin formed little, if any, insoluble aggregates in dextrose-plasma upon raising the buffer pH to 7.2 or above. Furthermore, dextrose induced pH-dependent precipitation of plasma proteins, with massive insoluble aggregates being detected at pH 6.5–6.8. These data show that isoelectric precipitation of complement proteins is a prerequisite of dextrose-induced aggregation of mAb in human plasma. This finding highlights the importance of assessing the compatibility of a therapeutic mAb with diluent and human plasma during product development.

High-quality GdBa₂Cu₃O_7-δ (GdBCO) films with thicknesses of 0.14-1.62 μm were deposited on (100)-oriented LaAlO₃ substrates by photo-assisted metal-organic chemical vapor deposition technique. Evaluation of film microstructure and strain-relaxation phenomenon in the growing films and their effects on the crystallographic and superconducting properties of the GdBCO films have been investigated. A single-crystal-like cross-sectional morphology with dense and crack-free surface and no grain boundary visible was observed. The c-axis lattice parameters of the GdBCO films grown with different thicknesses were used to determine the out-of-plane strain. The result shows that the strain could be gradually relieved as film thickness increases. Highly biaxially textured GdBCO films have been obtained. For a 0.31-μm GdBCO film sample, the full-widths at half-maximum were 0.08° and 0.47° for out-of-plane and in-plane orientations, respectively. Such low values were similar to that of single-crystal GdBCO. The highest critical current density (J_c) value is ~ 2.5MA/cm² (77 K and 0 T). As films were getting thicker, their J_c values decrease gradually. This is mainly attributed to a lack of pinning centers in the thicker films.