Emx2 underlies the development and evolution of marsupial gliding membranes.

Phenotypic variation among species is a product of evolutionary changes to developmental programs1,2. However, how these changes generate novel morphological traits remains largely unclear. Here we studied the genomic and developmental basis of the mammalian gliding membrane, or patagium-an adaptative trait that has repeatedly evolved in different lineages, including in closely related marsupial species. Through comparative genomic analysis of 15 marsupial genomes, both from gliding and non-gliding species, we find that the Emx2 locus experienced lineage-specific patterns of accelerated cis-regulatory evolution in gliding species. By combining epigenomics, transcriptomics and in-pouch marsupial transgenics, we show that Emx2 is a critical upstream regulator of patagium development. Moreover, we identify different cis-regulatory elements that may be responsible for driving increased Emx2 expression levels in gliding species. Lastly, using mouse functional experiments, we find evidence that Emx2 expression patterns in gliders may have been modified from a pre-existing program found in all mammals. Together, our results suggest that patagia repeatedly originated through a process of convergent genomic evolution, whereby regulation of Emx2 was altered by distinct cis-regulatory elements in independently evolved species. Thus, different regulatory elements targeting the same key developmental gene may constitute an effective strategy by which natural selection has harnessed regulatory evolution in marsupial genomes to generate phenotypic novelty.

Increased enhancer-promoter interactions during developmental enhancer activation in mammals.

Remote enhancers are thought to interact with their target promoters via physical proximity, yet the importance of this proximity for enhancer function remains unclear. Here we investigate the three-dimensional (3D) conformation of enhancers during mammalian development by generating high-resolution tissue-resolved contact maps for nearly a thousand enhancers with characterized in vivo activities in ten murine embryonic tissues. Sixty-one percent of developmental enhancers bypass their neighboring genes, which are often marked by promoter CpG methylation. The majority of enhancers display tissue-specific 3D conformations, and both enhancer-promoter and enhancer-enhancer interactions are moderately but consistently increased upon enhancer activation in vivo. Less than 14% of enhancer-promoter interactions form stably across tissues; however, these invariant interactions form in the absence of the enhancer and are likely mediated by adjacent CTCF binding. Our results highlight the general importance of enhancer-promoter physical proximity for developmental gene activation in mammals.

Response of soil erodibility of permanent gully heads to revegetation along a vegetation zone gradient in the loess-table and gully region of the Chinese Loess Plateau.

Revegetation has been proven to significantly affect soil erodibility of gully heads, and climate conditions are expected to affect soil erodibility by determining the vegetation characteristic. However, there are crucial scientific/knowledge gaps regarding the change in the response of soil erodibility of gully heads to revegetation along a vegetation zone gradient. Therefore, we selected the gully heads with different restoration years along a vegetation zone gradient encompassing the steppe zone (SZ), forest-steppe zone (FSZ), and forest zone (FZ) on the Chinese Loess Plateau to clarify the variation in soil erodibility of gully head and its response to soil and vegetation properties from SZ to FZ. Furtherly, we systematically and comprehensively reveal driving factors of changes in soil erodibility in three vegetation zones. Results showed that: (1) Vegetation and soil properties were affected positively by revegetation and differed significantly in three vegetation zones. (2) Soil erodibility of gully heads in SZ was significantly higher than in FSZ and FZ, by 3.3 % and 6.7 % on average, respectively, and it showed a significantly different decrease with restoration years in three vegetation zones. (3) Standardized major axis analysis proved that the sensitivity of response soil erodibility to vegetation characteristics and soil characteristics presented a significant difference as the revegetation proceeded. Vegetation roots were the primary driver in SZ, but soil organic matter content dominated the change in soil erodibility in FSZ and FZ. (4) Structural equation modeling indicated that climate conditions played an indirect role in regulating soil erodibility of gully heads by mediating vegetation characteristics. This study offers essential insights for assessing the ecological functions of revegetation in the gully heads of the Chinese Loess Plateau under different climatic scenarios.

Revegetation-induced changes in vegetation diversity improve soil properties of gully heads.

Revegetation is among the most efficient methods to improve gully headcut erosion. However, the influencing mechanism of revegetation on the soil properties of the gully head (GHSP) is still unclear. Thus, this study hypothesized that the variations in the GHSP were influenced by vegetation diversity during nature revegetation, and the influence pathways were mainly root traits, aboveground dry biomass (ADB), and vegetation coverage (VC). We studied six grassland communities of the gully head with different natural revegetation ages. The findings showed that the GHSP were improved during 22-year revegetation. The interaction effect of vegetation diversity, roots, aboveground dry biomass, and vegetation coverage on the GHSP was 43 %. In addition, vegetation diversity significantly explained >70.3 % of the changes in the root traits, ADB, and VC of the gully head (P < 0.05). Therefore, we combined vegetation diversity, roots, ADB, and VC to establish the path model to explain the GHSP changes, and the goodness of fit of the model was 82.3 %. The results showed that the model explained 96.1 % of the variation in the GHSP, and the vegetation diversity of the gully head affected the GHSP through roots, ADB, and VC. Therefore, during nature revegetation, vegetation diversity dominates the improvement of the GHSP, which has important significance for designing an optimal vegetation restoration strategy to control gully erosion.

Vegetation restoration restricts rill development on dump slopes in coalfields.

Severe rill erosion on dump slopes poses a great threat to the ecological environment in mining areas. Vegetation restoration is an effective measure for controlling soil erosion on dump slopes. However, few studies have identified the long-term influence of vegetation restoration on rill development on dump slopes. Therefore, we investigated the rill development characteristics of dump slopes with three typical restoration models (CK: natural restoration; ED: Elymus dahuricus; and AO: Artemisia ordosica) and three recovery time (1 y, 3 y and 5 y). The results showed that vegetation adequately controlled rill erosion on dump slopes. ED and AO could effectively control the development of rills with widths >15 cm and depths of 10-20 cm. ED vegetation restoration inhibited the development rill morphology and network better than AO. The rill erosion modulus of the ED slope and AO slope decreased by 76.29%-90.77% and 46.66%-61.49%, respectively, compared with that of natural restoration slopes with recovery time of 1 y, 3 y, and 5 y. ED controlled rill erosion better than AO, but this effect gradually weakened with recovery time. Vegetation coverage contributed 34.99% of the total variation in rill morphology and was the main factor affecting the development of rills on dump slopes. Furthermore, vegetation coverage had a more important role in controlling rill development than did the root system on dump slopes. This study provides valuable information for optimizing vegetation construction for soil loss control on dump slopes.

Heterogenous hydrogel mimicking the osteochondral ECM applied to tissue regeneration.

Inspired by the intricate extracellular matrix (ECM) of natural cartilage and subchondral bone, a heterogenous bilayer hydrogel scaffold is fabricated. Gelatin methacrylate (GelMA) and acryloyl glucosamine (AGA) serve as the main components in the upper layer, mimicking the chondral ECM. Meanwhile, vinylphosphonic acid (VPA) as a non-collagen protein analogue is incorporated into the bottom layer to induce the in situ biomineralization of calcium phosphate. The two heterogenous layers are effectively sutured together by the inter-diffusion between the upper and bottom layer hydrogels, together with chelation between the calcium ions and alginate added to separate layers. The interfacial bonding between the two different layers was thoroughly investigated via rheological measurements. The incorporation of AGA promotes chondrocytes to produce collagen type II and glycosaminoglycans and upregulates the expression of chondrogenesis-related genes. In addition, the minerals induced by VPA facilitate the osteogenesis of bone marrow mesenchymal stem cells (BMSCs). In vivo evaluation confirms the biocompatibility of the scaffold with minor inflammation and confirms the best repair ability of the bilayer hydrogel. This cell-free, cost-effective and efficient hydrogel shows great potential for osteochondral repair and inspires the design of other tissue-engineering scaffolds.

Revegetation induced change in soil erodibility as influenced by slope situation on the Loess Plateau.

Soil erodibility is an indispensable parameter for predicting soil erosion and evaluating the benefits of soil and water conservation. Slope situation can alter revegetation and its effects on soil properties and root traits, and thus may affect soil erodibility. However, whether slope situation will change the effect of revegetation on soil erodibility through improving soil properties and root traits has rarely been evaluated. Therefore, this study was conducted to detect the response of soil erodibility to slope situations (loess-tableland, hill-slope and gully-slope) in a typical watershed of the Loess Plateau. Five soil erodibility parameters (saturated soil hydraulic conductivity, SHC; mean weight diameter of aggregates, MWD; clay ratio, CR; soil disintegration rate, SDR; soil erodibility factor, K) and a comprehensive soil erodibility index (CSEI) are selected to clarify the study targets. The results revealed that soil properties, root traits, soil erodibility parameters and CSEI were affected by slope situation significantly. Soil and root can explain 79.7%, 79.1% and 69.8% of total variance in soil erodibility of loess-tableland, hill-slope and gully-slope, respectively. Slope situation influenced soil erodibility by changing the effects of revegetation on soil properties and root traits. Evidently, the slope situation greatly changed the relations between CSEI and soil and root parameters, whereafter a model considering slope situation (slope steepness), sand, organic matter content and root surface area density was reliable to estimate soil erodibility (CSEI). Our study suggested that the Armeniaca sibirica, the combination of Bothriochloa ischcemum and Robinia pseudoacacia and the combination of Armeniaca sibirica and Lespedeza bicolor can be used as the optimal selection for mitigating soil erodibility of loess-tableland, hill-slope and gully-slope, respectively. This study is of great significance in optimizing the spatial layout of soil and water conservation measures for different slope situations of the Loess Plateau.

Sulfated alginate based complex for sustained calcitonin delivery and enhanced osteogenesis.

Direct administration of salmon calcitonin (sCT) by subcutaneous or intramuscular injection is limited by its low efficiency. Drug delivery systems with sustained delivery properties and high bioactivity are urgently needed. For clinical applications an economical and effective carrier is required, which has been a challenge until now. In this study, a simple alginate/alginate sulfate-sCT (Alg/AlgS-sCT) complex was successfully constructed for sustained release of sCT. The negatively charged sulfate groups facilitate bonding with sCT, which avoids the burst release of sCT and extends the release time up to 15 d (it is only 2 d for pure sCT). More importantly, the bioactivity of the released sCT is not affected during such a long release time, suggesting a conformation similar to that of native sCT.In vitroanalysis implies that the complex is biocompatible. Moreover, the combination of AlgS and sCT synergistically improves the osteogenic ability of MC3T3 cells, which show higher alkaline phosphatase levels and intracellular and extracellular calcium ion concentrations. The concentration of intracellular calcium ions is 5.26-fold higher than in the control group after 10 d of incubation. This simple yet effective system has potential applications in clinical trials and may inspire the design of other protein delivery systems.

[Erosion morphology and the characteristics of runoff and sediment yielding in platform-slope system of opencast coal mine]. / 露天矿排土场平台-边坡系统侵蚀形态及径流产沙特征.

In the open pit, runoff from the platform is large discharge and rapid afflux, which often results in serious gully erosion of dump slope. The study of erosion process under catchment conditions of the platform-slope system is still backward. In this study, field scouring experiments were conducted to investigate runoff characteristics and sediment yield processes of the platform-slope system under different flow discharges (48, 60, 72 and 84 L·min-1). Our results showed that rill erosion dominated the platform-slope system under the flow discharge of 48 L·min-1, and gully was formed under 60-84 L·min-1. The flow velocity of the platform and the slope showed an abrupting-fluctuating-stable trend with the duration of discharge. The flow velocity of the platform was smaller than that of the slope, with the magnitude of reduction at 8.3%-67.1%. The highest flow velocity appeared on the up-slop/down-slope, being 18.5%-44.6% higher than that of the middle-slope. In general, the sediment yield rate of the platform and the slope varied with the duration of discharge, with the sediment yield rate of the slope being 17.4 times as that of the platform. The ratio of gully width to depth showed substantial difference between the platform and slope. The platform generally had the largest ratio than the slope. For the slope, the largest ratio appeared on the middle-slop/down-slope, being 1.36-1.93 times as that of the up-slope. The morphology of rill and gully along the platform to down-slope presented in the form of "wide and shallow-narrow and deep-wide and shallow". Rill erosion mainly concentrated in the platform and the middle slope under the flow discharge of 48 L·min-1, contributed 29.9% and 26.8% of the total erosion volume, respectively. When the flow discharge increased to 60-84 L·min-1, the largest average across-section areas (1083.25-1737.86 cm2) formed on the up-slope accounted for 36.1%-44.7% of the total erosion volume. Our results provided evidence for modelling soil and water erosion of the platform-slope system in opencast coal mine.

Programmed antibacterial and mineralization therapy for dental caries based on zinc-substituted hydroxyapatite/ alendronate-grafted polyacrylic acid hybrid material.

The domination of cariogenic bacteria in dental plaque biofilms is the primary cause of dental caries. In view of this, for the purpose of an effective treatment of dental caries, it is of great importance to inhibit the activity of acidogenic bacteria and promote the remineralization of damaged teeth simultaneously. However, the expensive antibacterial agents and poor mineralization ability of materials limit the practical applications. Biomineralization regulated by non-collagenous proteins (NCPs) gives hints to combine the remineralization ability of NCPs with accessible antibacterial property effectively. In this work, we propose a programmed antibacterial and remineralization strategy for the therapy of dental caries based on zinc-substituted hydroxyapatite/ alendronate-grafted polyacrylic acid hybrid nanoneedles (ZHA@ALN-PAA). This hybrid material dissolves in the acidic caries environment and regulate the pH to nearly neutral (6.5). Abundant calcium/ phosphate ions are supplemented and the ALN-PAA embedded in it has also been released, which assists the biomineralization on tooth defect. It has been revealed that the inhibition ratio of ZHA@ALN-PAA against Streptococcus mutans is the highest (11.25 folds that of HA), which originates from the highest zinc ions released (132.9 mg/L). Besides, the interspace of etched enamel is fully filled with regenerated nanorods and the surface microhardness (SMH) is significantly improved (3.68 folds that of etched enamel) after only 3 days of mineralization in vitro. This strategy developed here is simple and cost-effective, which can be referred to design the effective anti-caries materials applied for clinic treatment and daily oral care.

The Origin of Additive Genetic Variance Driven by Positive Selection.

Fisher's fundamental theorem of natural selection predicts no additive variance of fitness in a natural population. Consistently, studies in a variety of wild populations show virtually no narrow-sense heritability (h2) for traits important to fitness. However, counterexamples are occasionally reported, calling for a deeper understanding on the evolution of additive variance. In this study, we propose adaptive divergence followed by population admixture as a source of the additive genetic variance of evolutionarily important traits. We experimentally tested the hypothesis by examining a panel of ∼1,000 yeast segregants produced by a hybrid of two yeast strains that experienced adaptive divergence. We measured >400 yeast cell morphological traits and found a strong positive correlation between h2 and evolutionary importance. Because adaptive divergence followed by population admixture could happen constantly, particularly in species with wide geographic distribution and strong migratory capacity (e.g., humans), the finding reconciles the observation of abundant additive variances in evolutionarily important traits with Fisher's fundamental theorem of natural selection. Importantly, the revealed role of positive selection in promoting rather than depleting additive variance suggests a simple explanation for why additive genetic variance can be dominant in a population despite the ubiquitous between-gene epistasis observed in functional assays.

Wood-Derived Hybrid Scaffold with Highly Anisotropic Features on Mechanics and Liquid Transport toward Cell Migration and Alignment.

Fantastic structures in nature have inspired much incredible research. Wood, a typical model of anisotropy and hierarchy, has been widely investigated for its mechanical properties and water extraction abilities, although applications in biological areas remain challenging. Delignified wood composite with in situ deposited hydroxyapatite (HAp) and infiltrated polycaprolactone (PCL) is hereby fabricated in an attempt to mimic natural bone. The inherent structure and properties of wood are carefully preserved during the fabrication, showing anisotropic mechanical properties in the radial direction (420 MPa) and longitudinal direction (20 MPa). In addition, it also performs directional liquid transport, effectively inducing the migration and alignment of cells to simulate the uniform seeding behavior of various cells in natural bone. Moreover, the synergistic effect of blended HAp and PCL largely promotes cell proliferation and osteogenic differentiation, providing a promising candidate for bone regeneration materials.

Defining endogenous barcoding sites for CRISPR/Cas9-based cell lineage tracing in zebrafish.

There is a growing interest in developing experimental methods for tracking the developmental cell lineages of a complex organism. The recently developed CRISPR/Cas9-based barcoding method is, although highly promising, difficult to scale up because it relies on exogenous barcoding sequences that are engineered into the genome. In this study, we characterized 78 high-quality endogenous sites in the zebrafish genome that can be used as CRISPR/Cas9-based barcoding sites. The 78 sites are all highly expressed in most of the cell types according to single-cell RNA sequencing (scRNA-seq) data. Hence, the barcoding information of the 78 endogenous sites is recovered by the available scRNA-seq platforms, enabling simultaneous characterization of cell type and cell lineage information.

Promotion of the osteogenic activity of an antibacterial polyaniline coating by electrical stimulation.

Electrical stimulation (ES) exhibits a positive role in promoting the cell activity of osteoblasts. Conducting polymers have the advantages of biocompatibility, good environmental stability and easy synthesis, which have been widely used as charge carriers for electrical stimulation; moreover, considering clinical applications, biomaterial-related infection is an important issue that needs to be solved. Thus, conducting polymers with both antibacterial and osteogenic properties are highly demanded for effect repair. However, it remains a challenge to combine these two characteristics efficiently in a simple way. Herein, an Ag-loaded poly(amide-amine) dendrimer was prepared by a simple chemical reduction procedure, which acted as a dopant for the polymerization of polyaniline (PANI) on biomedical titanium (Ti) sheets. The obtained PANI coating showed outstanding antibacterial properties against Gram-negative (E. coli) and Gram-positive (S. aureus) microbes with a 1000-fold increase when compared with that of pure Ti. In addition, note that the polymer coating together with ES facilitated the proliferation and differentiation of MC3T3. The alkaline phosphatase (ALP) activity and intracellular calcium content of the cells showed a 19.09% and 24.02% increase, respectively, when compared with the case of electrically stimulated Ti after 12 days. Moreover, the existence of PAMAM facilitated mineralization. The strategy developed herein is simple and can be easily manipulated, which shows potential applications in the coating of implants for hard tissue repair.

Bioinspired enamel-like oriented minerals on general surfaces: towards improved mechanical properties.

As the hardest tissue in human body, enamel has attracted significant research interest in recent years. It has been acknowledged that the highly oriented arrangement of hydroxyapatite (HAp) crystallites of the enamel plays a crucial role owing to its excellent mechanical properties. So far, the preparation of enamel-like HAp crystallites on general substrates using mild conditions remains a challenge. Here, inspired by natural enamel, we developed a biomimetic, anodic alumina oxide (AAO)-assisted, double-layered gel system to fabricate well-oriented HAp crystals on universal surfaces. The one-directional ion flow was elaborately modulated for mineralization based on the synergistic effect of the double-layered gel and the AAO membrane, leading to highly oriented HAp crystallites. In addition, the introduction of polydopamine as a nucleating agent makes this method applicable for a wide range of substrates. The as-prepared minerals show a well-aligned enamel-like structure, exhibiting an elastic modulus of 52 GPa and nanohardness of 0.73 GPa, which are close to those of natural enamel. We envision that the strategy has potential applications for tooth repair and will provide guidelines for the mineralization of other inorganic minerals.

Bacterial Whole Cell Typing by Mass Spectra Pattern Matching with Bootstrapping Assessment.

Bacterial typing is of great importance in clinical diagnosis, environmental monitoring, food safety analysis, and biological research. Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is now widely used to analyze bacterial samples. Identification of bacteria at the species level can be realized by matching the mass spectra of samples against a library of mass spectra of known bacteria. Nevertheless, in order to reasonably type bacteria, identification accuracy should be further improved. Herein, we propose a new framework to the identification and assessment for MALDI-MS based bacterial analysis. Our approach combines new measures for spectra similarity and a novel bootstrapping assessment. We tested our approach on a general data set containing the mass spectra of 1741 strains of bacteria and another challenging data set containing 250 strains, including 40 strains in the Bacillus cereus group that were previously claimed to be impossible to resolve by MALDI-MS. With the bootstrapping assessment, we achieved much more reliable predictions at both the genus and species level, and enabled to resolve the Bacillus cereus group. To the best of the authors' knowledge, our method is the first to provide a statistical assessment to MALDI-MS based bacterial typing that could lead to more reliable bacterial typing.

From molecules to macrostructures: recent development of bioinspired hard tissue repair.

Enamel, dentin and bone are calcified hard tissues in the human body that play significant roles in food mastication and movement support. Generally, hard tissues lack the ability of self-repair, except for the regeneration ability of bone for small-scale defects. Fabrication of man-made repair materials is therefore highly demanded. In this review, following a bioinspired strategy, we describe the composition and multiscale structures of different hard tissues, and highlight the key points for the reconstruction of hard tissues. Finally, bioinspired tissue repair techniques ranging from molecule-induced mineralization, to microscale assembly to macroscaffold fabrication are summarised.

Sensitive and fast identification of bacteria in blood samples by immunoaffinity mass spectrometry for quick BSI diagnosis.

Bloodstream infections rank among the most serious causes of morbidity and mortality in hospitalized patients, partly due to the long period (up to one week) required for clinical diagnosis. In this work, we have developed a sensitive method to quickly and accurately identify bacteria in human blood samples by combining optimized matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MS) and efficient immunoaffinity enrichment/separation. A library of bacteria reference mass spectra at different cell numbers was firstly built. Due to a reduced sample spot size, the reference spectra could be obtained from as few as 10 to 102 intact bacterial cells. Bacteria in human blood samples were then extracted using antibodies-modified magnetic beads for MS fingerprinting. By comparing the sample spectra with the reference spectra based on a cosine correlation, bacteria with concentrations as low as 500 cells per mL in blood serum and 8000 cells per mL in whole blood were identified. The proposed method was further applied to positive clinical blood cultures (BCs) provided by a local hospital, where Escherichia coli and Staphylococcus aureus were identified. Because of the method's high sensitivity, the BC time required for diagnosis can be greatly reduced. As a proof of concept, whole blood spiked with a low initial concentration (102 or 103 cells per mL) of bacteria was cultured in commercial BC bottles and analysed by the developed method after different BC times. Bacteria were successfully identified after 4 hours of BC. Therefore, an entire diagnostic process could be accurately accomplished within half a day using the newly developed method, which could facilitate the timely determination of appropriate anti-bacterial therapy and decrease the risk of mortality from bloodstream infections.

A continuous cell line, SYSU-OfHe-C, from hemocytes of Ostrinia furnacalis possesses immune ability depending on the presence of larval plasma.

A continuous cell line, SYSU-OfHe-C, from larval hemocytes of corn borer, Ostrinia furnacalis was established. With increasing passages, the cells grew increasingly faster, and approximately 45% of the cells were in division at passage 55. The culture was mainly composed of two types of cells, granulocytes and plasmatocytes, which showed different division and proliferation behaviors, but possessed similar phagocytic ability. Its spreading ability was significantly weaker than that of hemocytes from naïve larva; however, it could be promoted by larval plasma. Furthermore, its encapsulation ability was also promoted by larval plasma to form multilayer capsules on Sephadex A-25 beads. Finally, the expression of several immune-related genes was verified after provocation by microbes or Sephadex beads. These results indicated that the cell line possessed immune ability depending on the presence of plasma of naïve larvae and are beneficial to studies of insect cellular systems.