Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants.

The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell-cell and microbiome-cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.

Genomic analyses of wild argali, domestic sheep, and their hybrids provide insights into chromosome evolution, phenotypic variation, and germplasm innovation.

Understanding the genetic mechanisms of phenotypic variation in hybrids between domestic animals and their wild relatives may aid germplasm innovation. Here, we report the high-quality genome assemblies of a male Pamir argali (O ammon polii, 2n = 56), a female Tibetan sheep (O aries, 2n = 54), and a male hybrid of Pamir argali and domestic sheep, and the high-throughput sequencing of 425 ovine animals, including the hybrids of argali and domestic sheep. We detected genomic synteny between Chromosome 2 of sheep and two acrocentric chromosomes of argali. We revealed consistent satellite repeats around the chromosome breakpoints, which could have resulted in chromosome fusion. We observed many more hybrids with karyotype 2n = 54 than with 2n = 55, which could be explained by the selfish centromeres, the possible decreased rate of normal/balanced sperm, and the increased incidence of early pregnancy loss in the aneuploid ewes or rams. We identified genes and variants associated with important morphological and production traits (e.g., body weight, cannon circumference, hip height, and tail length) that show significant variations. We revealed a strong selective signature at the mutation (c.334C > A, p.G112W) in TBXT and confirmed its association with tail length among sheep populations of wide geographic and genetic origins. We produced an intercross population of 110 F2 offspring with varied number of vertebrae and validated the causal mutation by whole-genome association analysis. We verified its function using CRISPR-Cas9 genome editing. Our results provide insights into chromosomal speciation and phenotypic evolution and a foundation of genetic variants for the breeding of sheep and other animals.

PD-1: A critical player and target for immune normalization.

Immune system imbalances contribute to the pathogenesis of several different diseases, and immunotherapy shows great therapeutic efficacy against tumours and infectious diseases with immune-mediated derivations. In recent years, molecules targeting the programmed cell death protein 1 (PD-1) immune checkpoint have attracted much attention, and related signalling pathways have been studied clearly. At present, several inhibitors and antibodies targeting PD-1 have been utilized as anti-tumour therapies. However, increasing evidence indicates that PD-1 blockade also has different degrees of adverse side effects, and these new explorations into the therapeutic safety of PD-1 inhibitors contribute to the emerging concept that immune normalization, rather than immune enhancement, is the ultimate goal of disease treatment. In this review, we summarize recent advancements in PD-1 research with regard to immune normalization and targeted therapy.

IBD sharing patterns as intra-breed admixture indicators in small ruminants.

In this study, we investigated how IBD patterns shared between individuals of the same breed could be informative of its admixture level, with the underlying assumption that the most admixed breeds, i.e. the least genetically isolated, should have a much more fragmented genome. We considered 111 goat breeds (i.e. 2501 individuals) and 156 sheep breeds (i.e. 3304 individuals) from Europe, Africa and Asia, for which beadchip SNP genotypes had been performed. We inferred the breed's level of admixture from: (i) the proportion of the genome shared by breed's members (i.e. "genetic integrity level" assessed from ADMIXTURE software analyses), and (ii) the "AV index" (calculated from Reynolds' genetic distances), used as a proxy for the "genetic distinctiveness". In both goat and sheep datasets, the statistical analyses (comparison of means, Spearman correlations, LM and GAM models) revealed that the most genetically isolated breeds, also showed IBD profiles made up of more shared IBD segments, which were also longer. These results pave the way for further research that could lead to the development of admixture indicators, based on the characterization of intra-breed shared IBD segments, particularly effective as they would be independent of the knowledge of the whole genetic landscape in which the breeds evolve. Finally, by highlighting the fragmentation experienced by the genomes subjected to crossbreeding carried out over the last few generations, the study reminds us of the need to preserve local breeds and the integrity of their adaptive architectures that have been shaped over the centuries.

Clinical characteristics of autoimmune encephalitis with co-existence of multiple anti-neuronal antibodies.

BACKGROUND: An increasing number of cases of autoimmune encephalitis (AE) with co-existing multiple anti-neuronal antibodies have been reported in recent years. However, the clinical significance of the concurrent presence of multiple anti-neuronal antibodies in patients with AE remains unclear. METHODS: We retrospectively enrolled AE patients with multiple anti-neuronal antibodies treated at our center between August 2019 and February 2022. We also reviewed cases reported in multiple literature databases. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guideline was followed on selection process. And then the clinical and laboratory data of these cases were collected for review and summary. RESULTS: A total of 83 AE cases with multiple antibodies (9 cases from our center and 74 cases from the literatures reviewed) were identified. In our center, nine patients presented with encephalitis symptoms, clinically characterized as disturbed consciousness, seizures, cognitive impairment, and psychiatric disorders. Of the 83 cases, 73 cases had co-existence of 2 types of antibodies, 8 cases had 3 types, and 2 cases had 4 types. Thirty-nine cases (39/83, 46.9%) were confirmed or suspected of also having a tumor, of which the most common was lung cancer (28/83, 33.7%). Partial or complete recovery was achieved in 57 cases (57/83, 68.6%), while 26 cases (26/83, 31.3%) died during treatment or follow-up. CONCLUSIONS: AE with co-existing multiple anti-neuronal antibodies is a specific subgroup, that is increasingly recognized in clinical practice. The co-existence of multiple anti-neuronal antibodies has a major impact on clinical features, disease progression, and prognosis.

Series of Viologen-Based Metal-Organic Polyhedra with Photo/Electrochromic Behavior for Inkless Printing and UV Detection.

The fabrication of molecular crystalline materials with fast, multistimuli-responsive behavior and the construction of the corresponding structure-activity relationship are of extraordinary significance for the development of smart materials. In this context, three multistimuli-responsive functional metal-organic polyhedra (MOP), {[Dy2(bcbp)3(NO3)1.5(H2O)7]·Cl4.2·(NO3)0.3·H2O}n (1), {[Dy2(bcbp)4(H2O)8]Cl6}n (2), and {[Eu2(bcbp)4(H2O)10]Cl6·H2O}n (3; bcbp = 1,1'-bis(4-carboxyphenyl)-4,4'-bipyridinium), were successfully prepared and characterized. All of the compounds exhibit rapid and reversible photochromic and electrochromic dual-responsive behaviors. Furthermore, benefiting from the well-defined crystal structure and different responsive behaviors, the photoinduced electron transfer (PIET) process and structure-activity relationship were explored. In addition, considering the excellent photochromic performance, function filter paper and smart organic glass were successfully prepared and used for ink-free printing and UV light detection.

The characterization and comorbidities of heterozygous Bardet-Biedl syndrome carriers.

Introduction: Bardet-Biedl syndrome (BBS) is a rare autosomal recessive disorder with clinical features of retinal dystrophy, obesity, postaxial polydactyly, renal anomalies, learning disabilities, hypogonadism, and genitourinary abnormalities. Nevertheless, previous studies on the phenotypic traits of BBS heterozygous carriers have generated inconclusive results. The aim of our study was to investigate the impact of BBS heterozygosity on carriers when compared to non-carriers within the Taiwanese population. Materials and Methods: This study follows a hospital-based case-control design. We employed the Taiwan Biobank version 2 (TWBv2) array to identify three specific loci associated with BBS (rs773862084, rs567573386, and rs199910690). In total, 716 patients were included in the case group, and they were compared to a control group of 2,864 patients who lacked BBS alleles. The control group was selected through gender and age matching at a ratio of 1:4. The association between BBS-related loci and comorbidity was assessed using logistic regression models. Results: We found that BBS heterozygous carriers exhibited a significant association with elevated BMI levels, especially the variant rs199910690 in MKS1 (p=0.0037). The prevalence of comorbidities in the carriers' group was not higher than that in the non-carriers' group. Besides, the average values of the biochemistry data showed no significant differences, except for creatinine level. Furthermore, we conducted a BMI-based analysis to identify specific risk factors for chronic kidney disease (CKD). Our findings revealed that individuals carrying the CA/AA genotype of the BBS2 rs773862084 variant or the CT/TT genotype of the MKS1 rs199910690 variant showed a reduced risk of developing CKD, irrespective of their BMI levels. When stratified by BMI level, obese males with the MKS1 rs199910690 variant and obese females with the BBS2 rs773862084 variant exhibited a negative association with CKD development. Conclusion: We found that aside from the association with overweight and obesity, heterozygous BBS mutations did not appear to increase the predisposition of individuals to comorbidities and metabolic diseases. To gain a more comprehensive understanding of the genetic susceptibility associated with Bardet-Biedl Syndrome (BBS), further research is warranted.

Inversion of heavy metal content in soil using hyperspectral characteristic bands-based machine learning method.

The global concern regarding the adverse effects of heavy metal pollution in soil has grown significantly. Accurate prediction of heavy metal content in soil is crucial for environmental protection. This study proposes an inversion analysis method for heavy metals (As, Cd, Cr, Cu, Ni, Pb) in soil based on hyperspectral and machine learning algorithms for 21 soil reference materials from multiple provinces in China. On this basis, an integrated learning model called Stacked RF (the base model is XGBoost, LightGBM, CatBoost, and the meta-model is RF) was established to perform soil heavy metal inversion. Specifically, three popular algorithms were initially employed to preprocess the spectral data, then Random Forest (RF) was used to select the best feature bands to reduce the impact of noise, finally Stacking and four basic machine learning algorithms were used to establish comparisons and analysis of inversion model. Compared with traditional machine learning methods, the stacking model showcases enhanced stability and superior accuracy. Research results indicate that machine learning algorithms, especially ensemble learning models, have better inversion effects on heavy metals in soil. Overall, the MF-RF-Stacking model performed best in the inversion of the six heavy metals. The research results will provide a new perspective on the ensemble learning model method for soil heavy metal content inversion using data of hyperspectral characteristic bands collected from soil reference materials.

Autophagic vacuolar myopathy involving the phenotype of spinocerebellar ataxia type 3.

Spinocerebellar ataxia type 3 (SCA3) is a form of autosomal dominant cerebellar ataxia with a wide range of clinical manifestations, including ataxia and pyramidal and extrapyramidal signs. A few SCA3 patients have been noticed to be predisposed to the development of inclusion body myositis. It is still unknown whether muscle can be primarily involved in the pathogenesis of SCA3. This study reported an SCA3 family in which the index patient initially presented with parkinsonism, sensory ataxia, and distal myopathy but the absence of cerebellar and pyramidal symptoms. The clinical and electrophysiological studies implied a possible combination of distal myopathy and sensory-motor neuropathy or neuronopathy. MRI muscle showed selective fat infiltration and absence of denervated edema-like changes, indicating the distal muscle weakness had a myopathic origin. Muscle pathology showed the myopathic involvement, besides neurogenic involvement, characterized by chronic myopathic changes with multiple autophagic vacuoles. Genetic screening revealed expanded CAG of 61 repeats in the ATXN3 gene, which showed co-segregation in the family. Besides the neurogenic origin, the myopathic origin may be partly attributed to the limb weakness of SCA3 patients, which expands the spectrum of the clinical manifestation of SCA3.

Variational Bayesian Algorithms for Maneuvering Target Tracking with Nonlinear Measurements in Sensor Networks.

The variational Bayesian method solves nonlinear estimation problems by iteratively computing the integral of the marginal density. Many researchers have demonstrated the fact its performance depends on the linear approximation in the computation of the variational density in the iteration and the degree of nonlinearity of the underlying scenario. In this paper, two methods for computing the variational density, namely, the natural gradient method and the simultaneous perturbation stochastic method, are used to implement a variational Bayesian Kalman filter for maneuvering target tracking using Doppler measurements. The latter are collected from a set of sensors subject to single-hop network constraints. We propose a distributed fusion variational Bayesian Kalman filter for a networked maneuvering target tracking scenario and both of the evidence lower bound and the posterior Cramér-Rao lower bound of the proposed methods are presented. The simulation results are compared with centralized fusion in terms of posterior Cramér-Rao lower bounds, root-mean-squared errors and the 3σ bound.

Historical Introgression from Wild Relatives Enhanced Climatic Adaptation and Resistance to Pneumonia in Sheep.

How animals, particularly livestock, adapt to various climates and environments over short evolutionary time is of fundamental biological interest. Further, understanding the genetic mechanisms of adaptation in indigenous livestock populations is important for designing appropriate breeding programs to cope with the impacts of changing climate. Here, we conducted a comprehensive genomic analysis of diversity, interspecies introgression, and climate-mediated selective signatures in a global sample of sheep and their wild relatives. By examining 600K and 50K genome-wide single nucleotide polymorphism data from 3,447 samples representing 111 domestic sheep populations and 403 samples from all their seven wild relatives (argali, Asiatic mouflon, European mouflon, urial, snow sheep, bighorn, and thinhorn sheep), coupled with 88 whole-genome sequences, we detected clear signals of common introgression from wild relatives into sympatric domestic populations, thereby increasing their genomic diversities. The introgressions provided beneficial genetic variants in native populations, which were significantly associated with local climatic adaptation. We observed common introgression signals of alleles in olfactory-related genes (e.g., ADCY3 and TRPV1) and the PADI gene family including in particular PADI2, which is associated with antibacterial innate immunity. Further analyses of whole-genome sequences showed that the introgressed alleles in a specific region of PADI2 (chr2: 248,302,667-248,306,614) correlate with resistance to pneumonia. We conclude that wild introgression enhanced climatic adaptation and resistance to pneumonia in sheep. This has enabled them to adapt to varying climatic and environmental conditions after domestication.

Donor-Acceptor Hybrid Heterostructures: An Emerging Class of Photoactive Materials with Inorganic and Organic Semiconductive Components.

Just as the heterojunctions in physics, donor-acceptor (D-A) heterostructures are an emerging class of photoactive materials fabricated from two semiconductive components at the molecular level. Among them, D-A hybrid heterostructures from organic and inorganic semiconductive components have attracted extensive attention in the past decades due to their combined advantages of high stability for the inorganic semiconductors and modifiability for the organic semiconductors, which are particularly beneficial to efficiently achieve photoinduced charge separation and transfer upon irradiations. In this review, by analogy with the heterojunctions in physics, a definition of the D-A heterostructures and their general design and synthetic strategies are given. Meanwhile, the D-A hybrid heterostructures are focused on and their recent advances in potential applications of photochromism, photomodulated luminescence, and photocatalysis summarized.

A Three-Component Donor-Acceptor Hybrid Framework with Low-Power X-ray-Induced Photochromism.

Donor-acceptor (D-A) hybrid frameworks with visual X-ray photochromism at room temperature are fascinating because of their promising applications as X-ray detectors. Herein, a 3-fold interpenetrated D-A hybrid framework, [Eu(bcbp)1.5(DMF)(H2O)2][Co(CN)6]·4H2O·CH3OH (1), has been obtained by incorporating electron-rich Co(CN)63- into the electron-deficient europium viologen framework, which interestingly exhibits ultraviolet and low-power X-ray dual photochromism with a remarkable color change from brown to green. Experimental and theoretical studies revealed that the X-ray photochromic behavior of hybrid 1 could be attributed to its D-A hybrid structural feature increasing the extent of photoinduced electron transfer and thus photogenerated radical species upon X-ray irradiation. Meanwhile, due to the introduction of emissive lanthanide cations in the D-A system, hybrid 1 exhibits photomodulated luminescence properties.

Photochromic Polyoxometalate/Perylenediimide Donor-Acceptor Hybrid Crystals with Interesting Luminescent Properties.

The self-assembly of electron-deficient protonated N, N'-dipyridyltetrachloroperylenediimide (4Cl-DPPDI) and electron-rich polyoxometalate acids HnXM12O40 (POMs; X = P or Si; M = W or Mo) resulted in four isomorphous donor-acceptor hybrid crystals 1-4 with segregated POM anions and one-dimensional racemic hydrogen-bonded 4Cl-DPPDI networks as electron-donor and -acceptor components, respectively. Because of the compact contacts between the POM anions and 4Cl-DPPDI tectons induced by anion-π interactions, besides enhanced photochromism, these four unique isostructural hybrids exhibited unusual room-temperature phosphorescence (RTP) emissions. More interestingly, owing to the facial compact contacts of two racemic 4Cl-DPPDI tectons induced by lone pair-π-assisted π-π interactions, they also showed unprecedented photon upconversion by triplet-triplet annihilation (TTA).

Dupilumab-induced Acute Generalized Exanthematous Pustulosis in a 17-year-old Female Chinese Patient with Atopic Dermatitis.

is missing (Short communication).

DPD Simulation on the Transformation and Stability of O/W and W/O Microemulsions.

The dissipative particle dynamics simulation method is adopted to investigate the microemulsion systems prepared with surfactant (H1T1), oil (O) and water (W), which are expressed by coarse-grained models. Two topologies of O/W and W/O microemulsions are simulated with various oil and water ratios. Inverse W/O microemulsion transform to O/W microemulsion by decreasing the ratio of oil-water from 3:1 to 1:3. The stability of O/W and W/O microemulsion is controlled by shear rate, inorganic salt and the temperature, and the corresponding results are analyzed by the translucent three-dimensional structure, the mean interfacial tension and end-to-end distance of H1T1. The results show that W/O microemulsion is more stable than O/W microemulsion to resist higher inorganic salt concentration, shear rate and temperature. This investigation provides a powerful tool to predict the structure and the stability of various microemulsion systems, which is of great importance to developing new multifunctional microemulsions for multiple applications.

Ancient hybridization patterns between bighorn and thinhorn sheep.

Whole-genome sequencing has advanced the study of species evolution, including the detection of genealogical discordant events such as ancient hybridization and incomplete lineage sorting (ILS). The evolutionary history of bighorn (Ovis canadensis) and thinhorn (Ovis dalli) sheep present an ideal system to investigate evolutionary discordance due to their recent and rapid radiation and putative secondary contact between bighorn and thinhorn sheep subspecies, specifically the dark pelage Stone sheep (O. dalli stonei) and predominately white Dall sheep (O. dalli dalli), during the last ice age. Here, we used multiple genomes of bighorn and thinhorn sheep, together with snow (O. nivicola) and the domestic sheep (O. aries) as outgroups, to assess their phylogenomic history, potential introgression patterns and their adaptive consequences. Among the Pachyceriforms (snow, bighorn and thinhorn sheep) a consistent monophyletic species tree was retrieved; however, many genealogical discordance patterns were observed. Alternative phylogenies frequently placed Stone and bighorn as sister clades. This relationship occurred more often and was less divergent than that between Dall and bighorn. We also observed many blocks containing introgression signal between Stone and bighorn genomes in which coat colour genes were present. Introgression signals observed between Dall and bighorn were more random and less frequent, and therefore probably due to ILS or intermediary secondary contact. These results strongly suggest that Stone sheep originated from a complex series of events, characterized by multiple, ancient periods of secondary contact with bighorn sheep.

Photochromic and Room Temperature Phosphorescent Donor-Acceptor Hybrid Crystals Regulated by Core-Substituted Naphthalenediimides.

Donor-acceptor (D-A) hybrid crystals are an emerging kind of crystalline hybrid material composed of semiconductive inorganic donors and organic acceptors. Except for the intrinsic photochromism, recently we have reported that the anion-π polyoxometalate (POM)/naphthalenediimide (NDI) hybrid crystals could produce an interesting room temperature phosphorescence (RTP) quantum yield up to 7.2%. Herein, we extended into core-substituted NDIs and anticipated the regulation of their photochromic and RTP properties. Thus, two hybrid crystals, namely (H4BDMPy-Br2NDI)·(NMP)4·(HPW12O40) (1) and (H4BDMPy-I2NDI)·(HPW12O40) (2) (H2BDMPy-Br2NDI: N,N'-bis(3,5-dimethylpyrazolyl)-2,6-dibromo-1,4,5,8-naphthalenediimide and H2BDMPy-I2NDI: N,N'-bis(3,5-dimethylpyrazolyl)-2,6-diiodide-1,4,5,8-naphthalenediimide), have been synthesized from phosphotungstic anions (PW12O403-) and Br or I core-substituted NDIs. Compared to the core-unsubstituted analogues (H4BDMPy-NDI)·(NMP)4·(HPW12O40) (3), 2 with photosensitive iodine substituents is more sensitive to light, which can become discolored under natural light. As a result of the heavy-atom effect, hybrid 1 exhibits remarkable RTP with the quantum yield up to 10.2% and a lifetime of 1.14 ms.

Donor-Acceptor Conjugated Heptazine Polymers with Highly Efficient Photocatalytic Degradations towards Tetracyclines.

Photocatalysis is an efficient and green technology in the environmental protection. Due to the high charge separation and transfer, donor-acceptor (D-A) conjugated polymers attract much attention for their photocatalytic degradations towards organic pollutants. Herein, the authors reported three novel D-A conjugated polymers, named as HPBP, HPTP, and HPF, with heptazine moieties as electron acceptors, while biphenyl, terphenyl, or fluorene moieties as electron donors, respectively, which indeed exhibit a highly efficient photocatalytic degradation towards tetracyclines upon the visible-light irradiation. Among them, the photocatalytic performance of HPF is especially noticeable with the degradation rate up to 87% within 30 min, almost 11 times in comparison to those of pristine g-C3 N4 , which is mainly attributed to its high crystallinity and conjugation. For their photocatalytic mechanism, the •O2 - radical anions are regarded as the active species.

The Genome Landscape of Tibetan Sheep Reveals Adaptive Introgression from Argali and the History of Early Human Settlements on the Qinghai-Tibetan Plateau.

Tibetan sheep are the most common and widespread domesticated animals on the Qinghai-Tibetan Plateau (QTP) and have played an essential role in the permanent human occupation of this high-altitude region. However, the precise timing, route, and process of sheep pastoralism in the QTP region remain poorly established, and little is known about the underlying genomic changes that occurred during the process. Here, we investigate the genomic variation in Tibetan sheep using whole-genome sequences, single nucleotide polymorphism arrays, mitochondrial DNA, and Y-chromosomal variants in 986 samples throughout their distribution range. We detect strong signatures of selection in genes involved in the hypoxia and ultraviolet signaling pathways (e.g., HIF-1 pathway and HBB and MITF genes) and in genes associated with morphological traits such as horn size and shape (e.g., RXFP2). We identify clear signals of argali (Ovis ammon) introgression into sympatric Tibetan sheep, covering 5.23-5.79% of their genomes. The introgressed genomic regions are enriched in genes related to oxygen transportation system, sensory perception, and morphological phenotypes, in particular the genes HBB and RXFP2 with strong signs of adaptive introgression. The spatial distribution of genomic diversity and demographic reconstruction of the history of Tibetan sheep show a stepwise pattern of colonization with their initial spread onto the QTP from its northeastern part ∼3,100 years ago, followed by further southwest expansion to the central QTP ∼1,300 years ago. Together with archeological evidence, the date and route reveal the history of human expansions on the QTP by the Tang-Bo Ancient Road during the late Holocene. Our findings contribute to a depth understanding of early pastoralism and the local adaptation of Tibetan sheep as well as the late-Holocene human occupation of the QTP.