Nitrated T cell epitope linked vaccine targeting CD47 elicits antitumor immune responses and acts synergistically with vaccine targeting PDL1.

Despite the clinical breakthrough made by immune checkpoint blockades (ICB) in cancer immunotherapy, immunosuppressed tumor microenvironment (TME) remains a major impediment in the efficacy of ICB immunotherapy. In this study, we constructed a Nitrated T cell epitope (NitraTh) linked vaccine targeting CD47, namely CD47-NitraTh. CD47-NitraTh could repress the progression of tumor by inducing tumor-specific immune response. Furthermore, combination vaccination with CD47-NitraTh and PDL1-NitraTh could reconstruct tumor associated macrophage, enhance macrophage-mediated phagocytosis for tumor cells, and promote the activation of tumor infiltrating T cells. Notably, by activating chemokine signaling pathway, NitraTh based vaccines reversed immunosuppressed TME, resulting in improved therapeutic outcome for tumor. With the advantage of reversing immunosuppressed TME, NitraTh based vaccine seems an optimal immunotherapy strategy for patients who are not sensitive to antibody based ICB.

Comparative Analysis of PRNP Gene Indel Polymorphism and Expression among Zhongdian Yellow Cattle, Zhongdian Yak, and Their Hybrids.

Bovine spongiform encephalopathy (BSE) is a fatal disease in cattle caused by misfolded prion proteins and linked to indel polymorphisms in the promoter and intron 1 of the PRNP gene. The aim of this study was to determine the allele, genotype, and haplotype frequencies of PRNP indel polymorphisms and to investigate the effect of PRNP gene expressions of 23 bp and 12 bp indels via polymerase chain reaction (PCR) in Zhongdian Yak (Bos-grunniens) (YK), Zhongdian Yellow cattle (Bos-taurus) (YC), and Zhongdian Yakow (Bos-primigenius taurus × Bos-grunniens) (PK). Resultant high allelic frequencies were found in 23- and 12+, while haplotype frequencies were very low in 23+/12 in YK, YC, and PK. PRNP expression was higher in the +-/-- diplotype of the PK and (mean ± SE) was 3.6578 ± 1.85964. Furthermore, two variable sites were investigated-a 23 bp indel polymorphism holding AP1 binding site and a 12 bp indel polymorphism holding SP1 binding site. Additionally, reporter gene assays revealed a link between two proposed transcription factors and lower expression levels of the +/+ allele compared with the -/- allele. The expression level of PRNP was shown to be dependent on two indel polymorphisms in the bovine PRNP promoter, which includes binding sites for RP58 and SP1 transcription factors. These findings raised the possibility that the PRNP genotype may contribute to the high variation in PRNP expression.

Pharmacovigilance for rare diseases: a bibliometrics and knowledge-map analysis based on web of science.

OBJECTIVES: The aims of this paper is to search and explore publications in the field of pharmacovigilance for rare diseases and to visualize general information, research hotspots, frontiers and future trends in the field using the bibliometric tool CiteSpace to provide evidence-based evidence for scholars. METHODS: We searched the Web of Science Core Collection (WoSCC) for studies related to pharmacovigilance for rare diseases, spanning January 1, 1997-October 25, 2022. CiteSpace software was utilized to discuss countries/regions, institutions, authors, journals, and keywords. RESULTS: After screening, a total of 599 valid publications were included in this study, with a significant upward trend in the number of publications. These studies were from 68 countries/regions with the United States and the United Kingdom making the largest contributions to the field. 4,806 research scholars from 493 institutions conducted studies on pharmacovigilance for rare diseases. Harvard University and University of California were the top two productive institutions in the research field. He Dian of the Affiliated Hospital of Guizhou Medical University and Peter G.M. Mol of the University of Groningen, The Netherlands, were the two most prolific researchers. The Cochrane Database of Systematic Reviews and the New England Journal of Medicine were the journals with the highest number of articles and co-citation frequency respectively. Clinical trial, therapy and adverse event were the top three most cited keywords. CONCLUSIONS: Based on keywords co-occurrence analysis, four research topics were identified: orphan drug clinical trials, postmarketing ADR surveillance for orphan drugs, rare diseases and orphan drug management, and diagnosis and treatment of rare diseases. Immune-related adverse reactions and benefit-risk assessment of enzyme replacement therapy were at the forefront of research in this field. Treatment outcomes, early diagnosis and natural history studies of rare diseases may become hotspots for future research.

Water turbidity dynamics using random forest in the Yangtze River Delta Region, China.

Turbidity is a water quality indicator that is essential for the sustainable development of aquatic ecosystems and the protection of biodiversity. The turbidity of different water surfaces and its response mechanisms to regional climatic factors and human activities in the Yangtze River Delta Region (YRDR), an important rapid economic development region in China, remain poorly understood. To enhance the knowledge of turbidity variations and dominant drivers of YRDR water surfaces, a complete long-term turbidity series was obtained using Landsat images from 1990 to 2020. The results show that the turbidity trend differed from -1.3 NTU/yr to 0.7 NTU/yr in different water surfaces. Turbidity decreased significantly in the mainstream of the Yangtze River (MYR), aquaculture ponds (AP) and other water bodies, whilst increasing significantly in the medium lakes (ML) and mainstream of the Qiantang River (MQR). Meanwhile, no significant changes in turbidity were observed in the great lakes (GL) and small lakes (SL). Rather than climatic factors, urbanisation and decreasing wastewater discharge were the dominant drivers of turbidity trends during the study period. In addition, ecological engineering in AP increased water transparency. The Three Gorges Dam also decreased turbidity in MYR. Increasing turbidity in the downstream of MQR was driven by increasing seasonal water surfaces and reclamation projects near Hangzhou Bay. GL faced no significant increase in turbidity due to the offset of afforestation to urbanisation-induced turbidity increase. These findings provide important information for government decision-making for subsequent aquatic environmental protection and restoration in the YRDR.

Three-dimensional genome structure and function.

Linear DNA undergoes a series of compression and folding events, forming various three-dimensional (3D) structural units in mammalian cells, including chromosomal territory, compartment, topologically associating domain, and chromatin loop. These structures play crucial roles in regulating gene expression, cell differentiation, and disease progression. Deciphering the principles underlying 3D genome folding and the molecular mechanisms governing cell fate determination remains a challenge. With advancements in high-throughput sequencing and imaging techniques, the hierarchical organization and functional roles of higher-order chromatin structures have been gradually illuminated. This review systematically discussed the structural hierarchy of the 3D genome, the effects and mechanisms of cis-regulatory elements interaction in the 3D genome for regulating spatiotemporally specific gene expression, the roles and mechanisms of dynamic changes in 3D chromatin conformation during embryonic development, and the pathological mechanisms of diseases such as congenital developmental abnormalities and cancer, which are attributed to alterations in 3D genome organization and aberrations in key structural proteins. Finally, prospects were made for the research about 3D genome structure, function, and genetic intervention, and the roles in disease development, prevention, and treatment, which may offer some clues for precise diagnosis and treatment of related diseases.

Visual Positioning of Nasal Swab Robot Based on Hierarchical Decision.

This study focuses on a robot vision localization method for coping with the operational task of automatic nasal swab sampling. The application is important in the detection and epidemic prevention of Corona Virus Disease 2019 (COVID-19) to alleviate the large-scale negative impact of individuals suffering from pneumonia owing to COVID-19. In this method, the idea of a hierarchical decision network is used to consider the strong infectious characteristics of the COVID-19, which is followed by processing the robot behavior constraint condition. The visual navigation and positioning method using a single-arm robot for sampling is also planned, which considers the operation characteristics of medical staff. In the decision network, the risk factor for potential contact infection caused by swab sampling operations is established to avoid the spread among personnel. A robot visual servo control with artificial intelligence characteristics is developed to achieve a stable and safe nasal swab sampling operation. Experiments demonstrate that the proposed method can achieve good vision positioning for the robots and provide technical support for managing new major public health situations.

PRNP gene polymorphism frequencies for comparing possible vulnerability to BSE in Chinese bovine population.

Among the numerous transmissible spongiform encephalopathies (TSEs), bovine spongiform encephalopathy (BSE) is the most well-known TSEs. It is a potential Creutzfeldt-Jakob (CJD) disease mutation that can be transferred through cattle to humans. In several animals, the prion protein gene (PRNP) is recognized to take active part in TSE vulnerability or tolerance. Previous studies have found indels polymorphism in PRNP gene promoter and intron1 region linked to BSE vulnerability. It's linked with 23 bp indels polymorphism in putative promoter and 12 bp indel in intron 1 of the PRNP gene. The aim of this study was to compare the allele, genotype and haplotype frequencies of PRNP indel polymorphisms in Zhongdian Yak (Bos grunniens) (YK), Zhongdian Yellow cattle (Bos taurus) (YC) and Zhongdian Yakow (Bos primigenius taurus × Bos grunniens) (PK) with worldwide reported healthy or affected BSE cattle, in order to assess their potential resistance to BSE. A comparison of Chinese bovine populations with healthy and BSE-affected German and Swiss cattle from globally was conducted, and result indicating significant difference (p < .001) between healthy and affected cattle. Additionally, as compared to prior studies with Chinese bovine population, the significant results were found. In this study, the allelic frequency D23 finding high deletion in all analyzed Chinese bovine species, and haplotype D12-D23 exhibited a less significant inclination toward susceptibility to BSE.

Analysis of Whole-Transcriptome RNA-Seq Data Reveals the Involvement of Alternative Splicing in the Drought Response of Glycyrrhiza uralensis.

Alternative splicing (AS) is a post-transcriptional regulatory mechanism that increases protein diversity. There is growing evidence that AS plays an important role in regulating plant stress responses. However, the mechanism by which AS coordinates with transcriptional regulation to regulate the drought response in Glycyrrhiza uralensis remains unclear. In this study, we performed a genome-wide analysis of AS events in G. uralensis at different time points under drought stress using a high-throughput RNA sequencing approach. We detected 2,479 and 2,764 AS events in the aerial parts (AP) and underground parts (UP), respectively, of drought-stressed G. uralensis. Of these, last exon AS and exon skipping were the main types of AS. Overall, 2,653 genes undergoing significant AS regulation were identified from the AP and UP of G. uralensis exposed to drought for 2, 6, 12, and 24 h. Gene Ontology analyses indicated that AS plays an important role in the regulation of nitrogen and protein metabolism in the drought response of G. uralensis. Notably, the spliceosomal pathway and basal transcription factor pathway were significantly enriched with differentially spliced genes under drought stress. Genes related to splicing regulators in the AP and UP of G. uralensis responded to drought stress and underwent AS under drought conditions. In summary, our data suggest that drought-responsive AS directly and indirectly regulates the drought response of G. uralensis. Further in-depth studies on the functions and mechanisms of AS during abiotic stresses will provide new strategies for improving plant stress resistance.

Role of several cytochrome P450s in the resistance and cross-resistance against imidacloprid and acetamiprid of Bemisia tabaci (Hemiptera: Aleyrodidae) MEAM1 cryptic species in Xinjiang, China.

Neonicotinoids are commonly used for the control of the whitefly Bemisia tabaci in cotton field. Laboratory test and field experiments have found that whitefly has a high risk of developing resistance and cross-resistance to the pesticide. Over expression of cytochrome P450 is one of the main mechanism that controls pesticide resistance in many insects. In this study we use MEAM1 whitefly, the dominant cryptic species of B. tabaci in Xinjiang cotton field, to investigate the possible resistance and cross-resistance mechanism controlled by cytochrome P450 enzymes. The P450 enzyme activity was higher in both selected strains of imidacloprid and acetamipird than that of susceptible strain. Synergism test showed that piperonyl butoxide (PBO) distinctly increased the control efficiency of imidacloprid and acetamiprid to the two resistance selected strains. Four out of 13 cytochrome genes, CYP4CS3, CYP6CX5, CYP6DW2 and CYP6CM1 were significantly up-regulated in the two selected strains based on real-time fluorescence quantitative PCR results. Other 3 genes, CYP6CX2, CYP6CX4 and CYP6DW3 were only highly expressed in the acetamiprid selected strain instead of the susceptible strain and imidacloprid selected strain. CYP6CM1 showed the highest expression level among all the 13 tested genes. No functional mutation of CYP6CM1 was found by sequence analysis. The possible role of these genes involving the resistance and cross-resistance of the whitefly MEAM1 cryptic species against neonicotinoids was discussed.

The in-plane crashworthiness of multi-layer regularly arranged circular honeycombs.

The in-plane crashworthiness of multi-layer regularly arranged circular honeycombs are investigated numerically at v = 1-250 m/s, with aim to disclose the influences of t/R ratio and crushing velocity, v. A novel evaluation methodology of crashworthiness and a new mechanical term, most appropriate strain, are put forward, which results in some new evaluation parameters. The theoretical analysis shows the most appropriate strain is a significant parameter for measuring the crashworthiness. Different deformation modes cause different change rules of these evaluation parameters. Under the quasi-static homogeneous mode and transition mode, the most appropriate strain is linear with the t/R ratio for a given v; the crushing force efficiency is approximately independent of t/R and sensitive to the v; the maximum energy absorption efficiency roughly decreases and then fluctuates. With the increase of v, the crushing force efficiency first becomes smaller sharply, and then fluctuates. Under dynamic mode, the maximum energy absorption efficiency is nearly constant for a given t/R ratio. Based on the finite element results, the empirical expressions of all evaluation parameters are given. The finite element calculated results of optimal specific energy absorption are consistent with those calculated by empirical expressions, which validates all empirical expressions.

Deletion/insertion polymorphisms of the prion protein gene (PRNP) in gayal (Bos frontalis).

Resistance to fatal disease bovine spongiformencephalopathy (BSE), due to misfolded prion protein in cattle, is associated with a 23-bp indel polymorphism in the putative promoter and a 12-bp indel in intron 1 of the PRNP gene. Gayal (Bos frontalis) is an important semiwild bovid species and of great conservation concern, but till today these indel polymorphisms have not been evaluated in gayals. Therefore, we collected 225 samples of gayals and evaluated the genetic indel polymorphism in the two regions of this PRNP gene. The results revealed high allelic frequencies of insertions at these indel sites: 0.909 and 0.667 for, respectively, the 23 bp and 12 bp indels, both also with significant genotype frequencies (χ2: 9.81; 23 bp and χ2: 43.56; 12 bp). At the same time, the haplotype data showed indel polymorphisms with extremely low deletion (0.01) in both regions of the PRNP gene. We compared these data with those reported for healthy and BSE-affected cattle (Bos taurus) breeds from two European countries, Germany and Switzerland, and significant difference (P <0.001) was observed between BSE-affected as well as the healthy cattle. Further, our data were also extensively compared with previous reports on BSE and highly significant (P<0.001) outcomes were observed. This result suggested negligible genetic susceptibility to BSE in gayals. To the best of our knowledge, this study is the first comprehensive deciphering information about the PRNP indel polymorphisms of 23 bp and 12 bp in gayals, a semiwild species of China.

Isolation and characterization of the major histocompatibility complex DQA1 and DQA2 genes in gayal (Bos frontalis).

The species origin of Yunnan gayal has been controversial since many years. However, few recent genetic studies have suggested that it has perhaps originated from the hybridization between male Bos frontalis and female B. taurus or B. indicus. Being an important semi-wild bovid species, this has also been listed under the red list of International Union of Conservation of Nature and Natural Resources. However, there is limited information available about the immunogenicity of this precarious species of Bos. Major histocompatibility complex (MHC) plays a pivotal role in immune response to infectious diseases in vertebrates. In the present study, we have investigated the structural and functional characteristics and possible duplication of the MHC-DQA genes in gayal (B. frontalis). Two full-length cDNA clones of the MHC-DQA genes were amplified and designated as Bofr-DQA1 (DQA*0101) and Bofr-DQA2 (DQA*2001) with GenBank accession numbers KT318732 and KT318733, respectively. A comparison between Bofr-DQA1, Bofr-DQA2 and to other MHC-DQA molecules from different animal species showed that nucleotide and encoded amino acid sequences of these two identifiedMHC-DQA genes have more similarity to alleles of specific DQA1 and DQA2 molecules from other Ruminantia species than to each other. The phylogenic investigation also demonstrated a large genetic distance between these two genes than to homologous from the other species. The large genetic distance between Bofr-DQA1 and Bofr-DQA2, and the presence of different bovine DQA putative motifs clarify that these sequences are nonallelic type. These results could suggest thatduplication of the DQA genes has also occurred in gayal. The findings of the present study have strengthened our understanding to MHC diversity in rare ruminants and mutation of immunological functions, selective and evolutionary forces that affect MHC variation within and between species.

Isolation and cDNA characteristics of MHC-DRA genes from gayal (Bos frontalis) and gaytle (Bos frontalis × Bos taurus).

The mammalian major histocompatibility complex (MHC) plays important roles in pathogen recognition and disease resistance. In the present study, the coding sequence and the 5'- and 3'-untranslated regions of MHC class II DR alpha chain (the DRA gene) from rare gayal and gaytle were cloned and analyzed to dissect structural and functional variations. The nucleotide and amino acid sequences for the DRA genes in gayal (Bofr-DRA) and gaytle (Bofr × BoLA-DRA) were almost identical to those for cattle and yak (99%). Compared to yak, two amino acids substitutions in the signal peptide (SP) domain for gayal were found within all Bos animals. Except for only one replacement in the amino acid within the α2 domain of the DRA protein in gayal, the additional residues were highly conserved across the species investigated. The 20 peptide-binding sites (PBS) of Bofr-DRA and Bofr × BoLA-DRA were essentially reserved in the α1 domain among all species investigated. The lesser degree of substitution in Bofr-DRA is concordant with the concept that the DRA gene is highly conserved among all mammals. The very high degree of conservativity of the DRA gene among ruminants, including gayal, suggests its recent evolutionary separation.

Whole-genome sequencing of six dog breeds from continuous altitudes reveals adaptation to high-altitude hypoxia.

The hypoxic environment imposes severe selective pressure on species living at high altitude. To understand the genetic bases of adaptation to high altitude in dogs, we performed whole-genome sequencing of 60 dogs including five breeds living at continuous altitudes along the Tibetan Plateau from 800 to 5100 m as well as one European breed. More than 150× sequencing coverage for each breed provides us with a comprehensive assessment of the genetic polymorphisms of the dogs, including Tibetan Mastiffs. Comparison of the breeds from different altitudes reveals strong signals of population differentiation at the locus of hypoxia-related genes including endothelial Per-Arnt-Sim (PAS) domain protein 1 (EPAS1) and beta hemoglobin cluster. Notably, four novel nonsynonymous mutations specific to high-altitude dogs are identified at EPAS1, one of which occurred at a quite conserved site in the PAS domain. The association testing between EPAS1 genotypes and blood-related phenotypes on additional high-altitude dogs reveals that the homozygous mutation is associated with decreased blood flow resistance, which may help to improve hemorheologic fitness. Interestingly, EPAS1 was also identified as a selective target in Tibetan highlanders, though no amino acid changes were found. Thus, our results not only indicate parallel evolution of humans and dogs in adaptation to high-altitude hypoxia, but also provide a new opportunity to study the role of EPAS1 in the adaptive processes.

Genetic characterization of MHC class II DQB exon 2 variants in gayal (Bos frontalis).

In the present study, exon 2 of major histocompatibility complex (MHC) class II DQB gene from 39 gayals (Bos frontalis) was isolated, characterized and compared with previously reported patterns for other bovidae. It was revealed by sequence analyses that there are 36 DQB exon 2 variants among 39 gayals. These variants exhibited a high degree of nucleotide and amino acid substitutions with most amino acid variations occurring at positions forming the peptide-binding sites (PBS). The DQB loci were analysed for patterns of synonymous (dS) and non-synonymous (dN) substitution. The gayals were observed to be under strong balancing selection in the DQB exon 2 PBS (dN = 0.094, P = 0.001). It appears that this variability among gayals could confer the ability to mount immune responses to a wide variety of peptides or pathogens.

Concise synthesis of the oxapentacyclic core of cortistatin A.

A concise synthetic approach for constructing the oxapentacyclic framework of cortistatin A is described. The synthesis features a furan-oxyallyl [4 + 3] cycloaddition and double-intramolecular aldol reactions. In addition, an interesting core structure was obtained in 11 steps from furan by using our method.

Total synthesis of (-)-5,6-dihydrocineromycin B.

An asymmetric total synthesis of (-)-5,6-dihydrocineromycin B has been accomplished in 13 steps from (-)-linalool O-triethylsilyl ether or 12 steps from geraniol. The present synthesis features (i) an intermolecular Wittig reaction involving an aldehyde possessing a ketophosphonate functionality and (ii) an intramolecular Horner-Wadsworth-Emmons olefination.