Phylogenomics Reveals High Levels of Incomplete Lineage Sorting at the Ancestral Nodes of the Macaque Radiation.

The genus Macaca includes 23 species assigned into 4 to 7 groups. It exhibits the largest geographic range and represents the most successful example of adaptive radiation of nonhuman primates. However, intrageneric phylogenetic relationships among species remain controversial and have not been resolved so far. In this study, we conducted a phylogenomic analysis on 16 newly generated and 8 published macaque genomes. We found strong evidence supporting the division of this genus into 7 species groups. Incomplete lineage sorting (ILS) was the primary factor contributing to the discordance observed among gene trees; however, we also found evidence of hybridization events, specifically between the ancestral arctoides/sinica and silenus/nigra lineages that resulted in the hybrid formation of the fascicularis/mulatta group. Combined with fossil data, our phylogenomic data were used to establish a scenario for macaque radiation. These findings provide insights into ILS and potential ancient introgression events that were involved in the radiation of macaques, which will lead to a better understanding of the rapid speciation occurring in nonhuman primates.

Direct observation of highly effective hydrogen isotope separation at active metal sites by in situ DRIFT spectroscopy.

In situ diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy was developed for the first time to observe the hydrogen isotope separation behavior at active CuI sites within CuI-MFU-4l, and clear evidence of the preferential adsorption of D2 over H2 was directly captured. More importantly, our results show direct spectral proof to clarify the chemical affinity quantum sieving mechanism of hydrogen isotope separation within porous adsorbents.

Research on the utilization of ultra-long carbon nanotubes in lithium-ion batteries based on an environment-friendly society.

To build an environment-friendly society, clean transportation systems, and renewable energy sources play essential roles. It is critical to improve the lifetime mileage of electric vehicles' batteries for reducing the cycle life cost and carbon footprint in green transportation. In this paper, a long-life lithium-ion battery is achieved by using ultra-long carbon nanotubes (UCNTs) as a conductive agent with relatively low content (up to 0.2% wt.%) in the electrode. Ultra-long CNT could realize longer conductive path crossing active material bulks in the electrode. Meanwhile, the low content of UCNTs can help to minimize conductive agent content in electrodes and obtain higher energy density. The film resistance and electrochemical impedance spectroscopy (EIS) confirmed that the use of UCNTs could markedly enhance electronic conductivity in the battery. The battery's life and life mileage can be prolonged by almost half due to the superior electronic conductivity of UCNTs. The life cycle cost and carbon footprint are also significantly reduced, which could markedly increase economic and environmental performance.

Advancing to 4.6 V Review and Prospect in Developing High-Energy-Density LiCoO2 Cathode for Lithium-Ion Batteries.

Layered LiCoO2 (LCO) is one of the most important cathodes for portable electronic products at present and in the foreseeable future. It becomes a continuous push to increase the cutoff voltage of LCO so that a higher capacity can be achieved, for example, a capacity of 220 mAh g-1 at 4.6 V compared to 175 mAh g-1 at 4.45 V, which is unfortunately accompanied by severe capacity degradation due to the much-aggravated side reactions and irreversible phase transitions. Accordingly, strict control on the LCO becomes essential to combat the inherent instability related to the high voltage challenge for their future applications. This review begins with a discussion on the relationship between the crystal structures and electrochemical properties of LCO as well as the failure mechanisms at 4.6 V. Then, recent advances in control strategies for 4.6 V LCO are summarized with focus on both bulk structure and surface properties. One closes this review by presenting the outlook for future efforts on LCO-based lithium ion batteries (LIBs). It is hoped that this work can draw a clear map on the research status of 4.6 V LCO, and also shed light on the future directions of materials design for high energy LIBs.

Using molybdenum carbiding to induce digestion of carbon in H2O2: A sustainable approach to eliminate radioactivity for hazardous graphite waste inherited from nuclear enterprise.

To properly manage nuclear wastes is critical to sustainable utilization of nuclear power and environment health. Here, we show an innovative carbiding strategy for sustainable management of radioactive graphite through digestion of carbon in H2O2. The combined action of intermolecular oxidation of graphite by MoO3 and molybdenum carbiding demonstrates success in gasifying graphite and sequestrating uranium for a simulated uranium-contaminated graphite waste. The carbiding process plays a triple role: (1) converting graphite into atomic carbon digestible in H2O2, (2) generating oxalic ligands in the presence of H2O2 to favor U-precipitation, and (3) delivering oxalic ligands to coordinate to MoVI-oxo anionic species to improve sample batching capacity. We demonstrate > 99% of uranium to be sequestrated for the simulated waste with graphite matrix completely gasifying while no detectable U-migration occurred during operation. This method has further been extended to removal of surface carbon layers for graphite monolith and thus can be used to decontaminate monolithic graphite waste with emission of a minimal amount of secondary waste. We believe this work not only provides a sustainable approach to tackle the managing issue of heavily metal contaminated graphite waste, but also indicates a promising methodology toward surface decontamination for irradiated graphite in general.

Graphene quantum dot electrochemiluminescence increase by bio-generated H2O2 and its application in direct biosensing.

In this study, a novel signal-increase electrochemiluminescence (ECL) biosensor has been developed for the detection of glucose based on graphene quantum dot/glucose oxidase (GQD/GOx) on Ti foil. The proposed GQD with excellent ECL ability is synthesized through a green one-step strategy by the electrochemical reduction of graphene oxide quantum dot. Upon the addition of glucose, GOx can catalytically oxidize glucose and the direct electron transfer between the redox centre of GOx and the modified electrode also has been realized, which results in the bio-generated H2O2 for ECL signal increase in GQD and realizes the direct ECL detection of glucose. The signal-increase ECL biosensor enables glucose detection with high sensitivity reaching 5 × 10-6 mol l-1 in a wide linear range from 5 × 10-6 to 1.5 × 10-3 mol l-1. Additionally, the fabrication process of such GQD-based ECL biosensor is also suitable to other biologically produced H2O2 system, suggesting the possible applications in the sensitive detection of other biologically important targets (e.g. small molecules, protein, DNA and so on).

Al-doping enables high stability of single-crystalline LiNi0.7Co0.1Mn0.2O2 lithium-ion cathodes at high voltage.

LiNi0.7Co0.1Mn0.2O2 (NCM) is a kind of promising cathode material for lithium ion batteries because of its high capacities. However, the further commercialization of this material has been seriously hindered by the unstable structure at a deep de-lithiation state. Herein, it is identified that this drawback can be diminished by Al-doping, which is inherently stable in the lattice framework to restrain the structural collapse of LiNi0.7Co0.1Mn0.2O2 at a high cut-off voltage (4.4 V). As expected, the Al-doped NCM (NCM-0.2Al) material obtains the highest reversible capacity and capacity retention (144.69 mA h g-1, 80.26%) after 90 cycles at 1C. The excellent performance demonstrates that Al-doping can effectively enhance the Li+-ion diffusion kinetic and structural stability of NCM, providing a feasible strategy for the further industrialization of Ni-rich materials.

Genomic Mechanisms of Physiological and Morphological Adaptations of Limestone Langurs to Karst Habitats.

Knowledge of the physiological and morphological evolution and adaptation of nonhuman primates is critical to understand hominin origins, physiological ecology, morphological evolution, and applications in biomedicine. Particularly, limestone langurs represent a direct example of adaptations to the challenges of exploiting a high calcium and harsh environment. Here, we report a de novo genome assembly (Tfra_2.0) of a male François's langur (Trachypithecus francoisi) with contig N50 of 16.3 Mb and resequencing data of 23 individuals representing five limestone and four forest langur species. Comparative genomics reveals evidence for functional evolution in genes and gene families related to calcium signaling in the limestone langur genome, probably as an adaptation to naturally occurring high calcium levels present in water and plant resources in karst habitats. The genomic and functional analyses suggest that a single point mutation (Lys1905Arg) in the α1c subunit of the L-type voltage-gated calcium channel Cav1.2 (CACNA1C) attenuates the inward calcium current into the cells in vitro. Population genomic analyses and RNA-sequencing indicate that EDNRB is less expressed in white tail hair follicles of the white-headed langur (T. leucocephalus) compared with the black-colored François's langur and hence might be responsible for species-specific differences in body coloration. Our findings contribute to a new understanding of gene-environment interactions and physiomorphological adaptative mechanisms in ecologically specialized primate taxa.

Population genomics of wild Chinese rhesus macaques reveals a dynamic demographic history and local adaptation, with implications for biomedical research.

Background: The rhesus macaque (RM, Macaca mulatta) is the most important nonhuman primate model in biomedical research. We present the first genomic survey of wild RMs, sequencing 81 geo-referenced individuals of five subspecies from 17 locations in China, a large fraction of the species' natural distribution. Results: Populations were structured into five genetic lineages on the mainland and Hainan Island, recapitulating current subspecies designations. These subspecies are estimated to have diverged 125.8 to 51.3 thousand years ago, but feature recent gene flow. Consistent with the expectation of a larger body size in colder climates and smaller body size in warmer climates (Bergman's rule), the northernmost RM lineage (M. m. tcheliensis), possessing the largest body size of all Chinese RMs, and the southernmost lineage (M. m. brevicaudus), with the smallest body size of all Chinese RMs, feature positively selected genes responsible for skeletal development. Further, two candidate selected genes (Fbp1, Fbp2) found in M. m. tcheliensis are involved in gluconeogenesis, potentially maintaining stable blood glucose levels during starvation when food resources are scarce in winter. The tropical subspecies M. m. brevicaudus showed positively selected genes related to cardiovascular function and response to temperature stimuli, potentially involved in tropical adaptation. We found 118 single-nucleotide polymorphisms matching human disease-causing variants with 82 being subspecies specific. Conclusions: These data provide a resource for selection of RMs in biomedical experiments. The demographic history of Chinese RMs and their history of local adaption offer new insights into their evolution and provide valuable baseline information for biomedical investigation.

Genetic diversity and natural selection in wild fruit flies revealed by whole-genome resequencing.

We characterized 26 wild fruit flies comparative population genomics from six different altitude and latitude locations by whole genome resequencing. Genetic diversity was relatively higher in Ganzi and Chongqing populations. We also found 13 genes showing selection signature between different altitude flies and variants related to hypoxia and temperature stimulus, were preferentially selected during the flies evolution. One of the most striking selective sweeps found in all high altitude flies occurred in the region harboring Hsp70Aa and Hsp70Ab on chromosome 3R. Interestingly, these two genes are involved in GO terms including response to hypoxia, unfolded protein, temperature stimulus, heat, oxygen levels. Mutation in HPH gene, a candidate gene in the hypoxia inducible factor pathway, might contributes to hypoxic high-altitude adaptation. Intriguingly, some of the selected genes, primarily utilized in humans, were involved in the response to hypoxia, which could imply a conserved molecular mechanisms underlying high-altitude adaptation between insects and humans.

Dietary specialization drives multiple independent losses and gains in the bitter taste gene repertoire of Laurasiatherian Mammals.

BACKGROUND: Bitter taste perception is essential for species with selective food intake, enabling them to avoid unpalatable or toxic items. Previous studies noted a marked variation in the number of TAS2R genes among various vertebrate species, but the underlying causes are not well understood. Laurasiatherian mammals have highly diversified dietary niche, showing repeated evolution of specialized feeding preferences in multiple lineages and offering a unique chance to investigate how various feeding niches are associated with copy number variation for bitter taste receptor genes. RESULTS: Here we investigated the evolutionary trajectories of TAS2Rs and their implications on bitter taste perception in whole-genome assemblies of 41 Laurasiatherian species. The number of intact TAS2Rs copies varied considerably, ranging from 0 to 52. As an extreme example of a narrow dietary niche, the Chinese pangolin possessed the lowest number of intact TAS2Rs (n = 2) among studied terrestrial vertebrates. Marine mammals (cetacea and pinnipedia), which swallow prey whole, presented a reduced copy number of TAS2Rs (n = 0-5). In contrast, independent insectivorous lineages, such as the shrew and insectivorous bats possessed a higher TAS2R diversity (n = 52 and n = 20-32, respectively), exceeding that in herbivores (n = 9-22) and omnivores (n = 18-22). CONCLUSIONS: Besides herbivores, insectivores in Laurasiatheria tend to have more functional TAS2Rs in comparison to carnivores and omnivores. Furthermore, animals swallowing food whole (cetacean, pinnipedia and pangolin) have lost most functional TAS2Rs. These findings provide the most comprehensive view of the bitter taste gene repertoire in Laurasiatherian mammals to date, casting new light on the relationship between losses and gains of TAS2Rs and dietary specialization in mammals.

Complete mitochondrial genome of the Macaca mulatta brevicaudus.

The complete mitochondrial sequence of the Macaca mulatta brevicaudus has been determined by mapping the raw data to previously published mitochondrial assemblies of the corresponding species. The total sequence length is 16,561 bp, consisting of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one D-loop control region. The base composition of the mtDNA genome is 31.77% A, 25.14% T, 30.33% C, and 12.76% G, with an AT content of 56.90%. The arrangement of genes in M. m. brevicaudus is identical to that of M. mulatta. All genes are encoded on the heavy strand with the exception of ND6 and eight tRNA genes. The mitochondrial genome of M. m. brevicaudus presented here will contribute to a better understanding of the population genetics, help to protect its genetic diversity and resolve phylogenetic relationships within the family.

Single-Molecule Force Spectroscopy of an Artificial DNA Duplex Comprising a Silver(I)-Mediated Base Pair.

Single-molecule force spectroscopy measurements of a DNA duplex comprising an artificial metal-mediated base pair are reported. The measurements reveal that DNA duplexes comprising one central imidazole:imidazole mispair rupture at lower forces than a related duplex with canonical base pairs only. In contrast, DNA duplexes with one central imidazole-Ag(+)-imidazole base pair (formed by the addition of Ag(+) to the aforementioned duplex with the mispair) rupture at higher forces. These measurements indicate for the first time that the increase in thermal stability of a nucleic acid duplex that is observed upon the formation of a metal-mediated base pair is accompanied by a concomitant mechanical stabilization. In fact, the mechanical stabilization even exceeds the thermal one. This result indicates that nucleic acids with metal-mediated base pairs should be ideal building blocks for rigid functionalized DNA nano-objects.

Controllable Supramolecular Polymerization through Host-Guest Interaction and Photochemistry.

A new method for controllable supramolecular polymerization based on ABBA type monomer and cucurbit[8]uril monomer through host-guest interaction and photochemistry is reported. The molecular weight and polydispersity of supramolecular polymers can be well controlled by tuning the molar ratio of these host and guest monomers or by tuning the isomer ratio of azobenzene groups in the guest monomers upon the competitive irradiation of lights. This research provides a general methodology for the control of supramolecular polymerization and the structure of supramolecular polymers.

Differentiated adaptive evolution, episodic relaxation of selective constraints, and pseudogenization of umami and sweet taste genes TAS1Rs in catarrhine primates.

BACKGROUND: Umami and sweet tastes are two important basic taste perceptions that allow animals to recognize diets with nutritious carbohydrates and proteins, respectively. Until recently, analyses of umami and sweet taste were performed on various domestic and wild animals. While most of these studies focused on the pseudogenization of taste genes, which occur mostly in carnivores and species with absolute feeding specialization, omnivores and herbivores were more or less neglected. Catarrhine primates are a group of herbivorous animals (feeding mostly on plants) with significant divergence in dietary preference, especially the specialized folivorous Colobinae. Here, we conducted the most comprehensive investigation to date of selection pressure on sweet and umami taste genes (TAS1Rs) in catarrhine primates to test whether specific adaptive evolution occurred during their diversification, in association with particular plant diets. RESULTS: We documented significant relaxation of selective constraints on sweet taste gene TAS1R2 in the ancestral branch of Colobinae, which might correlate with their unique ingestion and digestion of leaves. Additionally, we identified positive selection acting on Cercopithecidae lineages for the umami taste gene TAS1R1, on the Cercopithecinae and extant Colobinae and Hylobatidae lineages for TAS1R2, and on Macaca lineages for TAS1R3. Our research further identified several site mutations in Cercopithecidae, Colobinae and Pygathrix, which were detected by previous studies altering the sensitivity of receptors. The positively selected sites were located mostly on the extra-cellular region of TAS1Rs. Among these positively selected sites, two vital sites for TAS1R1 and four vital sites for TAS1R2 in extra-cellular region were identified as being responsible for the binding of certain sweet and umami taste molecules through molecular modelling and docking. CONCLUSIONS: Our results suggest that episodic and differentiated adaptive evolution of TAS1Rs pervasively occurred in catarrhine primates, most concentrated upon the extra-cellular region of TAS1Rs.

Antagonistic action of Bacillus subtilis strain SG6 on Fusarium graminearum.

Fusarium graminearum causes Fusarium head blight (FHB), a devastating disease that leads to extensive yield and quality loss of wheat and barley. Bacteria isolated from wheat kernels and plant anthers were screened for antagonistic activity against F. graminearum. Based on its in vitro effectiveness, strain SG6 was selected for characterization and identified as Bacillus subtilis. B. subtilis SG6 exhibited a high antifungal effect on the mycelium growth, sporulation and DON production of F. graminearum with the inhibition rate of 87.9%, 95.6% and 100%, respectively. In order to gain insight into biological control effect in situ, we applied B. subtilis SG6 at anthesis through the soft dough stage of kernel development in field test. It was revealed that B. subtilis SG6 significantly reduced disease incidence (DI), FHB index and DON (P ≤ 0.05). Further, ultrastructural examination shows that B. subtilis SG6 strain induced stripping of F. graminearum hyphal surface by destroying the cellular structure. When hypha cell wall was damaged, the organelles and cytoplasm inside cell would exude, leading to cell death. The antifungal activity of SG6 could be associated with the coproduction of chitinase, fengycins and surfactins.

Stretching single polymer chains of donor-acceptor foldamers: toward the quantitative study on the extent of folding.

Single-molecule force spectroscopy has proven to be an efficient tool for the quantitative characterization of flexible foldamers on the single-molecule level in this study. The extent of folding has been estimated quantitatively for the first time to the best of our knowledge, which is crucial for a better understanding of the "folding-process" on single-molecule level. Therefore, this study may provide a guidance to regulate folding for realizing rational control over the functions of bulk materials.

Cucurbit[8]uril-based supramolecular polymers: promoting supramolecular polymerization by metal-coordination.

Linear supramolecular polymers were obtained in aqueous solution by employing cucurbit[8]uril-based host-guest interaction as the driving force. Water-soluble monomers were prepared through direct metal-coordination. The rigid and bulky terpyridine-Fe linker can effectively enhance the monomer's solubility and suppress its cyclization, thereby promoting supramolecular polymerization.

Supramolecular polymerization at low monomer concentrations: enhancing intermolecular interactions and suppressing cyclization by rational molecular design.

We present the construction of long-chain water-soluble supramolecular polymers at low monomer concentrations. Naphthalene-based host-enhanced π-π interactions, which possess high binding constants, were used as the driving force of supramolecular polymerization. A monomer, DNDAB, with a rigid, bulky 1,4-diazabicyclo[2.2.2]octane-1,4-diium linker was designed. The design of the monomer structure strongly influenced the efficiency of the supramolecular polymerization. The rigid, bulky linker in DNDAB effectively eliminates cyclization, promoting the formation of long-chain supramolecular polymers at low monomer concentrations. In contrast, a reference monomer containing a flexible linker (DNPDN) only forms oligomers owing to cyclization.