Heterogeneous genomic architecture of skeletal armour traits in sticklebacks.

Whether populations adapt to similar selection pressures using the same underlying genetic variants depends on population history and the distribution of standing genetic variation at the metapopulation level. Studies of sticklebacks provide a case in point: when colonising and adapting to freshwater habitats, three-spined sticklebacks (Gasterosteus aculeatus) with high gene flow tend to fix the same adaptive alleles in the same major loci, whereas nine-spined sticklebacks (Pungitius pungitius) with limited gene flow tend to utilize a more heterogeneous set of loci. In accordance with this, we report results of quantitative trait locus (QTL) analyses using a backcross design showing that lateral plate number variation in the western European nine-spined sticklebacks mapped to three moderate-effect QTL, contrary to the major-effect QTL in three-spined sticklebacks and different from the four QTL previously identified in the eastern European nine-spined sticklebacks. Furthermore, several QTL were identified associated with variation in lateral plate size, and three moderate-effect QTL with body size. Together, these findings indicate more heterogenous and polygenic genetic underpinnings of skeletal armour variation in nine-spined than three-spined sticklebacks, indicating limited genetic parallelism underlying armour trait evolution in the family Gasterostidae.

SLRfinder: A method to detect candidate sex-linked regions with linkage disequilibrium clustering.

Despite their critical roles in genetic sex determination, sex chromosomes remain unknown in many non-model organisms, especially those having recently evolved sex-linked regions (SLRs). These evolutionarily young and labile sex chromosomes are important for understanding early sex chromosome evolution but are difficult to identify due to the lack of Y/W degeneration and SLRs limited to small genomic regions. Here, we present SLRfinder, a method to identify candidate SLRs using linkage disequilibrium (LD) clustering, heterozygosity and genetic divergence. SLRfinder does not rely on specific sequencing methods or a specific type of reference genome (e.g., from the homomorphic sex). In addition, the input of SLRfinder does not require phenotypic sexes, which may be unknown from population sampling, but sex information can be incorporated and is necessary to validate candidate SLRs. We tested SLRfinder using various published datasets and compared it to the local principal component analysis (PCA) method and the depth-based method Sex Assignment Through Coverage (SATC). As expected, the local PCA method could not be used to identify unknown SLRs. SATC works better on conserved sex chromosomes, whereas SLRfinder outperforms SATC in analysing labile sex chromosomes, especially when SLRs harbour inversions. Power analyses showed that SLRfinder worked better when sampling more populations that share the same SLR. If analysing one population, a relatively larger sample size (around 50) is needed for sufficient statistical power to detect significant SLR candidates, although true SLRs are likely always top-ranked. SLRfinder provides a novel and complementary approach for identifying SLRs and uncovering additional sex chromosome diversity in nature.

Improved assembly of the Pungitius pungitius reference genome.

The nine-spined stickleback (Pungitius pungitius) has been increasingly used as a model system in studies of local adaptation and sex chromosome evolution but its current reference genome assembly is far from perfect, lacking distinct sex chromosomes. We generated an improved assembly of the nine-spined stickleback reference genome (98.3% BUSCO completeness) with the aid of linked-read mapping. While the new assembly (v8) was of similar size as the earlier version (v7), we were able to assign 4.4 times more contigs to the linkage groups and improve the contiguity of the genome. Moreover, the new assembly contains a ∼22.8 Mb Y-linked scaffold (LG22) consisting mainly of previously assigned X-contigs, putative Y-contigs, putative centromere contigs, and highly repetitive elements. The male individual showed an even mapping depth on LG12 (pseudo X chromosome) and LG22 (Y-linked scaffold) in the segregating sites, suggesting near-pure X and Y representation in the v8 assembly. A total of 26,803 genes were annotated, and about 33% of the assembly was found to consist of repetitive elements. The high proportion of repetitive elements in LG22 (53.10%) suggests it can be difficult to assemble the complete sequence of the species' Y chromosome. Nevertheless, the new assembly is a significant improvement over the previous version and should provide a valuable resource for genomic studies of stickleback fishes.

Matrix metalloproteinase-responsive collagen-oxidized hyaluronic acid injectable hydrogels for osteoarthritic therapy.

Drug delivery system and intra-articular injection have been clinically applied to prolong drug residence time and reduce side effects in the treatment of osteoarthrosis. Herein, injectable hydrogels with sustained-dexamethasone sodium phosphate (DSP) release behavior in response to matrix metalloproteinase (MMP) were developed for osteoarthritic therapy. Hyaluronic acid undergoes specific oxidation in the present of sodium periodate to prepare oxidized hyaluronic acid (OHA). Then the DSP-loaded collagen-based hydrogels (Col-OHA) were developed by the Schiff's base crosslinking between OHA and Type I collagen besides the self-assembly of collagen induced by OHA. The results indicate that the collagen self-assembly into collagen fibrils makes great contribution for shortening gelation time of Col-OHA hydrogels. Col-OHA hydrogels possess interconnected porous microstructure, good injectability, excellent self-healing performance, strong mechanical property, low swelling ability, good blood compatibility and no cytotoxicity. Significantly, Col-OHA hydrogels show highly sensitive and significantly substantially sustained release of DSP in response to MMP. DSP-loaded Col-OHA hydrogel possesses significant inhibition for the production of inflammatory cytokines in the joint synovium, which can effectively relieve the symptoms of osteoarthritis continuously. Col-OHA hydrogel has no obvious effect on liver and kidney functions. Overall, the Col-OHA hydrogels with excellent biocompatibility are the promising drug-loading system for the intra-articular injection therapy of osteoarthrosis.

Systematics of the New World bats Eptesicus and Histiotus suggest trans-marine dispersal followed by Neotropical cryptic diversification.

Biodiversity can be boosted by colonization of new habitats such as remote islands and separated continents. Molecular studies have suggested that recently evolved organisms probably colonized already separated continents by dispersal, either via land bridge connections or crossing the ocean. Here we test the on-land and trans-marine dispersal hypotheses by evaluating possibilities of colonization routes over the Bering land bridge and across the Atlantic Ocean in the cosmopolitan bat genus Eptesicus (Chiroptera, Vespertilionidae). Previous molecular studies have found New World Eptesicus more closely related to Histiotus, a Neotropical endemic lineage with enlarged ears, than to Old World Eptesicus. However, phylogenetic relationships within the New World group remained unresolved and their evolutionary history was unclear. Here we studied the systematics of New World Eptesicus and Histiotus using extensive taxonomic and geographic sampling, and genomic data from thousands of ultra-conserved elements (UCEs). We estimated phylogenetic trees using concatenation and multispecies coalescent. All analyses supported four major New World clades and a novel topology where E. fuscus and Histiotus are sister clades that together diverged from two sister clades of Neotropical Eptesicus. Intra-clade divergence suggested cryptic diversity that has been concealed by morphological features, especially in the Neotropics where taxonomic re-evaluations are warranted. Molecular dating estimated that Old World and New World clades diverged around 17 million years ago followed by radiation of major New World clades in the mid-Miocene, when climatic changes might have facilitated global dispersal and radiation events. Biogeographic ancestral reconstruction supported the Neotropical origin of the New World clades, suggesting a trans-Atlantic colonization route from North Africa to the northern Neotropics. We highlight that trans-marine dispersal may be more prevalent than currently acknowledged and may be an important first step to global biodiversification.

Mimicking the Composition and Structure of the Osteochondral Tissue to Fabricate a Heterogeneous Three-Layer Scaffold for the Repair of Osteochondral Defects.

Heterogeneous three-layer scaffolds were fabricated by mimicking the biochemical composition and structure of the hyaline cartilage, calcified cartilage, and subchondral bone of the osteochondral tissue for the repair of osteochondral defects. The hyaline cartilage layer was composed of collagen I (50.0 wt %) and sodium hyaluronate (50.0 wt %). The calcified cartilage layer and subchondral bone layer were composed of collagen I, sodium hyaluronate, and nanohydroxyapatite with different proportions. N-Hydroxysuccinimide/N-(3-dimethylaminopropyl)-N'-ethylcarbodiimide hydrochloride was used to mediate the crosslinking reaction of the amine groups of collagen with carboxyl groups of sodium hyaluronate. The hyaline cartilage layer and calcified cartilage layer were designed as dense structures, while the subchondral bone layer was designed as a relatively loose structure by adjusting the crosslinking degree. The scaffolds displayed a uniform and interconnected porous structure and possessed a high porosity over 85%, which were conducive to cellular adhesion and proliferation. The scaffolds could remain at 50-75% after 30 days of degradation owing to crosslinking, providing enough time for the regeneration of the osteochondral tissue. Especially, the hyaline cartilage layer and calcified cartilage layer preferred to induce the proliferation of chondrocytes, while the subchondral bone layer was more conducive to the proliferation of osteoblasts. In conclusion, the heterogeneous multilayer scaffolds could serve as implant materials for osteochondral reconstruction.

Nonrandom missing data can bias Principal Component Analysis inference of population genetic structure.

Population genetic studies in non-model systems increasingly use next-generation sequencing to obtain more loci, but such methods also generate more missing data that may affect downstream analyses. Here we focus on the principal component analysis (PCA) which has been widely used to explore and visualize population structure with mean-imputed missing data. We simulated data of different population models with various total missingness (1%, 10%, 20%) introduced either randomly or biased among individuals or populations. We found that individuals biased with missing data would be dragged away from their real population clusters to the origin of PCA plots, making them indistinguishable from true admixed individuals and potentially leading to misinterpreted population structure. We also generated empirical data of the big brown bat (Eptesicus fuscus) using restriction site-associated DNA sequencing (RADseq). We filtered three data sets with 19.12%, 9.87%, and 1.35% total missingness, all showing nonrandom missing data with biased individuals dragged towards the PCA origin, consistent with results from simulations. We highlight the importance of considering missing data effects on PCA in non-model systems where nonrandom missing data are common due to varying sample quality. To help detect missing data effects, we suggest to (1) plot PCA with a colour gradient showing per sample missingness, (2) interpret samples close to the PCA origin with extra caution, (3) explore filtering parameters with and without the missingness-biased samples, and (4) use complementary analyses (e.g., model-based methods) to cross-validate PCA results and help interpret population structure.

Major histocompatibility complex variation is similar in little brown bats before and after white-nose syndrome outbreak.

White-nose syndrome (WNS), caused by the fungal pathogen Pseudogymnoascus destructans (Pd), has driven alarming declines in North American hibernating bats, such as little brown bat (Myotis lucifugus). During hibernation, infected little brown bats are able to initiate anti-Pd immune responses, indicating pathogen-mediated selection on the major histocompatibility complex (MHC) genes. However, such immune responses may not be protective as they interrupt torpor, elevate energy costs, and potentially lead to higher mortality rates. To assess whether WNS drives selection on MHC genes, we compared the MHC DRB gene in little brown bats pre- (Wisconsin) and post- (Michigan, New York, Vermont, and Pennsylvania) WNS (detection spanning 2014-2015). We genotyped 131 individuals and found 45 nucleotide alleles (27 amino acid alleles) indicating a maximum of 3 loci (1-5 alleles per individual). We observed high allelic admixture and a lack of genetic differentiation both among sampling sites and between pre- and post-WNS populations, indicating no signal of selection on MHC genes. However, post-WNS populations exhibited decreased allelic richness, reflecting effects from bottleneck and drift following rapid population declines. We propose that mechanisms other than adaptive immunity are more likely driving current persistence of little brown bats in affected regions.

MIL-53(Fe) MOF-mediated catalytic chemiluminescence for sensitive detection of glucose.

Various analytical applications of metal-organic frameworks (MOFs) have been rapidly developed in the past few years. However, the employment of MOFs as catalysts in chemiluminescence (CL) analysis is rare. Here, for the first time, we found that MIL-53(Fe) MOFs could significantly enhance the CL of luminol in the presence of H2O2 in an alkaline medium. The CL intensity in the luminol-H2O2-MIL-53(Fe) system was about 20 times higher than that in the luminol-H2O2 system. Moreover, the XRD pattern of MIL-53(Fe) after CL reaction was almost the same as that of the original MIL-53(Fe), confirming the catalytic role of MIL-53(Fe) in the luminol-H2O2-MIL-53(Fe) system. The possible mechanism behind the enhancing phenomenon was discussed based on the results from the CL spectra, FL probe experiments, and active oxygen species measurements. By coupling with the glucose oxidase-based catalytic oxidation reaction, a sensitive and selective CL method was developed for the detection of glucose. There is a linear relationship between the logarithm of CL intensity and the logarithm of glucose concentration in the range from 0.1 to 10 µM, and a detection limit of 0.05 µM (S/N = 3) is obtained. The proposed method has been applied to the determination of glucose in human serum samples with satisfactory results. Graphical abstract MIL-53(Fe) MOFs are found to greatly enhance the chemiluminescence emission of the luminol-H2O2 system, and this finding resulted in a new chemiluminescence method for biosensing of glucose when coupled with the glucose oxidase.