Recent development of oral vaccines (Review).

Oral immunization can elicit an effective immune response and immune tolerance to specific antigens. When compared with the traditional injection route, delivering antigens via the gastrointestinal mucosa offers superior immune effects and compliance, as well as simplicity and convenience, making it a more optimal route for immunization. At present, various oral vaccine delivery systems exist. Certain modified bacteria, such as Salmonella, Escherichia coli and particularly Lactobacillus, are considered promising carriers for oral vaccines. These carriers can significantly enhance immunization efficiency by actively replicating in the intestinal tract following oral administration. The present review provided a discussion of the main mechanisms of oral immunity and the research progress made in the field of oral vaccines. Additionally, it introduced the advantages and disadvantages of the currently more commonly administered injectable COVID-19 vaccines, alongside the latest advancements in this area. Furthermore, recent developments in oral vaccines are summarized, and their potential benefits and side effects are discussed.

Single-cell transcriptomics reveals peripheral immune responses in non-segmental vitiligo.

Background: Vitiligo is a common autoimmune depigmented dermatology due to destruction of melanocytes. Much evidence suggests that vitiligo is associated with systemic immune activation. Previous studies have focused on immune cell infiltration in and around lesion areas, but few studies have investigated the cell types and function of circulating immune cells in peripheral blood. Here, single cell RNA-sequencing (scRNA-seq) was used to investigate the mechanisms of peripheral immune responses in vitiligo patients. Methods: Peripheral blood was collected from five patients with progressive non-segmental vitiligo and three healthy controls. Peripheral blood mononuclear cells (PBMCs) were obtained by Ficoll-Paque density gradient centrifugation, and scRNA-seq was performed on isolated cell populations to obtain single cell transcriptomes and characterize important genes and intracellular signaling pathways. The key findings were validated with qPCR and flow cytometry assays. Results: We identified 10 major cell types by scRNA-seq. Among these cell types, neutrophils were specifically observed in our scRNA-seq data from PBMCs. Peripheral blood effector CD8+ T cells from vitiligo patients did not show significant differences at the transcriptome level compared with healthy controls, whereas regulatory T cells showed pro-inflammatory TH1-like properties. Innate immune cells, including natural killer cells and dendritic cells, showed increased antigen processing and presentation as well as upregulated interferon responses. B cells, monocytes, and neutrophils all showed activation. B cells, especially memory B cells, had upregulated expression of genes related to humoral immunity. Monocytes showed production of proinflammatory cytokines and chemokines. Neutrophils showed strong chemokine ligand-receptor (L-R) pair (CXCR8-CXCR2) autocrine signaling pathway. Conclusion: This study revealed the genetic profile and signaling pathway characteristics of peripheral blood immune cells in vitiligo patients, providing new insights into its pathogenesis, which may facilitate identification of potential therapeutic targets.

Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo.

BACKGROUND: Vitiligo has been correlated with an abnormal gut microbiota. We aimed to systematically identify characteristics of the gut microbial compositions, genetic functions, and potential metabolic features in patients with non-segmental vitiligo. METHODS: Twenty-five patients with non-segmental vitiligo and 25 matched healthy controls (HCs) were enrolled. Metagenomic sequencing and bioinformatic analysis were performed to determine the gut microbiota profiles. Differences in gut microbiota diversity and composition between patients with vitiligo and HCs were analyzed. Gene functions and gut metabolic modules were predicted with the Kyoto Encyclopedia of Gene and Genomes (KEGG) and MetaCyc databases. RESULTS: Compared with HCs, alpha diversity of intestinal microbiome in vitiligo patients was significantly reduced. At the species level, the relative abundance of Staphylococcus thermophiles was decreased, and that of Bacteroides fragilis was increased in patients with vitiligo compared with those of the HCs. Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed representative microbial markers of Lachnospiraceae_bacterium_BX3, Massilioclostridium_coli, TM7_phylum_sp_oral_taxon_348 and Bacteroides_fragilis for patients with vitiligo. KEGG gene function analysis showed that the NOD-like receptor signaling pathway was significantly enriched in patients with vitiligo. Gut metabolic modules (GMMs) analysis showed that cysteine degradation was significantly down-regulated, and galactose degradation was up-regulated in patients with vitiligo. A panel of 28 microbial features was constructed to distinguish patients with vitiligo from HCs. CONCLUSIONS: The gut microbial profiles and genetic functions of patients with vitiligo were distinct from those of the HCs. The identified gut microbial markers may potentially be used for earlier diagnosis and treatment targets.

Laser-Induced Cavitation-Assisted True 3D Nano-Sculpturing of Hard Materials.

Femtosecond lasers enable flexible and thermal-damage-free ablation of solid materials and are expected to play a critical role in high-precision cutting, drilling, and shaping of electronic chips, display panels, and industrial parts. Although the potential applications are theoretically predicted, true 3D nano-sculpturing of solids such as glasses and crystals, has not yet been demonstrated, owing to the technical challenge of negative cumulative effects of surface changes and debris accumulation on the delivery of laser pulses and subsequent material removal during direct-write ablation. Here, a femtosecond laser-induced cavitation-assisted true 3D nano-sculpturing technique based on the ingenious combination of cavitation dynamics and backside ablation is proposed to achieve stable clear-field point-by-point material removal in real time for precise 3D subtractive fabrication on various difficult-to-process materials. As a result, 3D devices including free-form silica lenses, micro-statue with vivid facial features, and rotatable sapphire micro-mechanical turbine, all with surface roughness less than 10 nm are readily produced. The true 3D processing capability can immediately enable novel structural and functional micro-nano optics and non-silicon micro-electro-mechanical systems based on various hard solids.

SCSit: A high-efficiency preprocessing tool for single-cell sequencing data from SPLiT-seq.

SPLiT-seq provides a low-cost platform to generate single-cell data by labeling the cellular origin of RNA through four rounds of combinatorial barcoding. However, an automatic and rapid method for preprocessing and classifying single-cell sequencing (SCS) data from SPLiT-seq, which directly identified and labeled combinatorial barcoding reads and distinguished special cell sequencing data, is currently lacking. Here, we develop a high-efficiency preprocessing tool for single-cell sequencing data from SPLiT-seq (SCSit), which can directly identify combinatorial barcodes and UMI of cell types and obtain more labeled reads, and remarkably enhance the retained data from SCS due to the exact alignment of insertion and deletion. Compared with the original method used in SPLiT-seq, the consistency of identified reads from SCSit increases to 97%, and mapped reads are twice than the original. Furthermore, the runtime of SCSit is less than 10% of the original. It can accurately and rapidly analyze SPLiT-seq raw data and obtain labeled reads, as well as effectively improve the single-cell data from SPLiT-seq platform. The data and source of SCSit are available on the GitHub website https://github.com/shang-qian/SCSit.

Prevalence of Chlamydia in Pigs in China from 1985 to 2020: A Systematic Review and Meta-Analysis.

Chlamydia is a small gram-negative (G-) microorganism that can be dangerous to human and animals. In this study, we conducted a systematic review and meta-analysis of Chlamydia infection in swine in China. From PubMed, ScienceDirect, Chinese Web of knowledge (CNKI), VIP Chinese journal database, and Wanfang database, we collected a total of 72 publications reported in 1985-2020. The prevalence of Chlamydia was 22.48% in China. In the sampling year subgroup, the prevalence after 2011 was the highest (26.14%). In southern China, the prevalence was 30.97%. By contrast, the prevalence in northern China was only 10.79%. Also the difference was significant (p < 0.05). In the provincial level, Hubei had the highest rate of 36.23%. Boars had a higher prevalence (29.47%). The prevalence of Chlamydia detection in pigs with reproductive disorders (21.86%) was higher than that without reproductive disorders. Among the three age groups, finishing pigs (21.43%) had the highest prevalence. The prevalence in large-scale farmed pigs (28.58%) was the highest in the subgroup of feeding methods. The prevalence in farms was 24.29%, which was the highest in the survey areas. The prevalence in spring was the highest with 40.51%. Other methods had the highest prevalence (39.61%) than enzyme-linked immunosorbent assay (ELISA) and indirect hemagglutination assay. The prevalence of Chlamydia psittaci 18.41% was lower than the prevalence of Chlamydia abortus (41.35%). We also analyzed the impact of different climate factor subgroups (rainfall, temperature, and humidity) on the probability of pigs suffering from the disease. The results showed that Chlamydia was widespread in pigs in China. We suggest that we should strengthen the detection of Chlamydia in the semen of breeding pigs and pigs with reproductive disorders, and reasonably control the environment of large-scale pig farms, so as to reduce further infection of Chlamydia in pigs.

Characterization of Hibiscus Latent Fort Pierce Virus-Derived siRNAs in Infected Hibiscus rosa-sinensis in China.

Although limited progress have been made about pathogen system of Hibiscus rosa-sinensis and Hibiscus latent Fort Pierce virus (HLFPV), interaction between plant host and pathogen remain largely unknown, which led to deficiency of effective measures to control disease of hibiscus plants caused by HLFPV. In this study, infection of HLFPV in Hibiscus rosa-sinensis was firstly confirmed for the first time by traditional electron microscopy, modern reverse transcription polymerase chain reaction and RNA-seq methods in China (HLFPV-Ch). Sequence properties analyzing suggested that the full-length sequences (6,465 nt) of HLFPV-Ch had a high sequence identity and a similar genomic structure with other tobamoviruses. It includes a 5'-terminal untranslated region (UTR), followed by four open reading frames encoding for a 128.5-kDa replicase, a 186.5-kDa polymerase, a 31-kDa movement protein, 17.6-kDa coat protein, and the last a 3'-terminal UTR. Furthermore, HLFPV-Ch-derived virus-derived siRNAs (vsiRNAs) ant its putative target genes, reported also for the first time, were identified and characterized from disease Hibiscus rosa-sinensis through sRNA-seq and Patmatch server to investigate the interaction in this pathogen systems. HLFPV-Ch-derived vsiRNAs demonstrated several general and specific characteristics. Gene Ontology classification revealed predicted target genes by vsiRNAs are involved in abroad range of cellular component, molecular function and biological processes. Taken together, for first time, our results certified the HLFPV infection in China and provide an insight into interaction between HLFPV and Hibiscus rosa-sinensis.

Corrigendum: Distribution Patterns of DNA N6-Methyladenosine Modification in Non-coding RNA Genes.

[This corrects the article DOI: 10.3389/fgene.2020.00268.].

DNA N6-Methyladenine Modification in Wild and Cultivated Soybeans Reveals Different Patterns in Nucleus and Cytoplasm.

DNA 6mA modification, an important newly discovered epigenetic mark, plays a crucial role in organisms and has been attracting more and more attention in recent years. The soybean is economically the most important bean in the world, providing vegetable protein for millions of people. However, the distribution pattern and function of 6mA in soybean are still unknown. In this study, we decoded 6mA modification to single-nucleotide resolution in wild and cultivated soybeans, and compared the 6mA differences between cytoplasmic and nuclear genomes and between wild and cultivated soybeans. The motif of 6mA in the nuclear genome was conserved across the two kinds of soybeans, and ANHGA was the most dominant motif in wild and cultivated soybeans. Genes with 6mA modification in the nucleus had higher expression than those without modification. Interestingly, 6mA distribution patterns in cytoplasm for each soybean were significantly different from those in nucleus, which was reported for the first time in soybean. Our research provides a new insight in the deep analysis of cytoplasmic genomic DNA modification in plants.

Distribution Patterns of DNA N6-Methyladenosine Modification in Non-coding RNA Genes.

N6-methyladenosine (6mA) DNA modification played an important role in epigenetic regulation of gene expression. And the aberrational expression of non-coding genes, as important regular elements of gene expression, was related to many diseases. However, the distribution and potential functions of 6mA modification in non-coding RNA (ncRNA) genes are still unknown. In this study, we analyzed the 6mA distribution of ncRNA genes and compared them with protein-coding genes in four species (Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, and Homo sapiens) using single-molecule real-time (SMRT) sequencing data. The results indicated that the consensus motifs of short nucleotides at 6mA location were highly conserved in four species, and the non-coding gene was less likely to be methylated compared with protein-coding gene. Especially, the 6mA-methylated lncRNA genes were expressed significant lower than genes without methylation in A. thaliana (p = 3.295e-4), D. melanogaster (p = 3.439e-11), and H. sapiens (p = 9.087e-3).. The detection and distribution profiling of 6mA modification in ncRNA regions from four species reveal that 6mA modifications may have effects on their expression level.

Evaluating Structural Variation Detection Tools for Long-Read Sequencing Datasets in Saccharomyces cerevisiae.

Structural variation (SV) represents a major form of genetic variations that contribute to polymorphic variations, human diseases, and phenotypes in many organisms. Long-read sequencing has been successfully used to identify novel and complex SVs. However, comparison of SV detection tools for long-read sequencing datasets has not been reported. Therefore, we developed an analysis workflow that combined two alignment tools (NGMLR and minimap2) and five callers (Sniffles, Picky, smartie-sv, PBHoney, and NanoSV) to evaluate the SV detection in six datasets of Saccharomyces cerevisiae. The accuracy of SV regions was validated by re-aligning raw reads in diverse alignment tools, SV callers, experimental conditions, and sequencing platforms. The results showed that SV detection between NGMLR and minimap2 was not significant when using the same caller. The PBHoney was with the highest average accuracy (89.04%) and Picky has the lowest average accuracy (35.85%). The accuracy of NanoSV, Sniffles, and smartie-sv was 68.67%, 60.47%, and 57.67%, respectively. In addition, smartie-sv and NanoSV detected the most and least number of SVs, and SV detection from the PacBio sequencing platform was significantly more than that from ONT (p = 0.000173).

Haplotype diversity and phylogenetic characteristics for Guanzhong Han population from Northwest China via 38 Y-STRs using Yfiler™ Platinum Amplification System.

BACKGROUND: For better application in human forensic cases and population genetics research, it is imperative to investigate the genetic characteristics of Guanzhong Han population using enhanced Y-chromosomal short tandem repeats (Y-STR) detecting system with higher discriminating power than previous ones. METHODS: In this study, 38 Y-STRs were profiled in 430 unrelated Chinese Han male individuals from Guanzhong region of Shaanxi Province, Northwest China, using the Yfiler™ Platinum PCR Amplification Kit. Haplotype frequencies and forensic parameters were calculated. Comprehensive population comparisons with geographically/ethnically different populations in China and other worldwide countries were performed. RESULTS: A total of 422 different haplotypes were observed with the overall haplotype diversity (HD), discriminatory power (DC) and haplotype match probability (HMP) were 0.9999, 0.9814, and 0.0024, respectively. Guanzhong Han showed genetically affinity with Han ethnicity from Shanxi and Henan provinces, while far distant from Tibetan populations. CONCLUSION: This study offered a unique insight into Guanzhong Han population, the 38 Y-STRs included in the the Yfiler™ Platinum system are highly polymorphic and informative and can be used for forensic practice and human genetic research.

MDR: an integrative DNA N6-methyladenine and N4-methylcytosine modification database for Rosaceae.

Eukaryotic DNA methylation has been receiving increasing attention for its crucial epigenetic regulatory function. The recently developed single-molecule real-time (SMRT) sequencing technology provides an efficient way to detect DNA N6-methyladenine (6mA) and N4-methylcytosine (4mC) modifications at a single-nucleotide resolution. The family Rosaceae contains horticultural plants with a wide range of economic importance. However, little is currently known regarding the genome-wide distribution patterns and functions of 6mA and 4mC modifications in the Rosaceae. In this study, we present an integrated DNA 6mA and 4mC modification database for the Rosaceae (MDR, http://mdr.xieslab.org). MDR, the first repository for displaying and storing DNA 6mA and 4mC methylomes from SMRT sequencing data sets for Rosaceae, includes meta and statistical information, methylation densities, Gene Ontology enrichment analyses, and genome search and browse for methylated sites in NCBI. MDR provides important information regarding DNA 6mA and 4mC methylation and may help users better understand epigenetic modifications in the family Rosaceae.

DNA N6-Methyladenosine modification role in transmitted variations from genomic DNA to RNA in Herrania umbratica.

BACKGROUND: DNA methylation is an important epigenetic modification. Recently the developed single-molecule real-time (SMRT) sequencing technology provided an efficient way to detect DNA N6-methyladenine (6mA) modification that played an important role in epigenetic and positively regulated gene expression. In addition, the gene expression was also regulated by genetic variation. However, the relationship between DNA 6mA modification and variation is still unknown. RESULTS: We collected the SMRT long-reads DNA, Illumina short reads DNA and RNA datasets from the young leaves of Herrania umbratica, and used them to detect 35,654 6mA modification sites, 829,894 DNA variations and 60,672 RNA variations respectively, among which, there are 303 DNA variations and 19 RNA variations with 6mA modification, and 57,468 transmitted genetic variations from DNA to RNA. The results illustrated that the genes with 6mA modification were significant disadvantage to mutate than those genes without modification (p-value< 4.9e-08). And result from the linear regression model showed the 6mA densities of genes were associated with the transmitted variations type 0/1 to 1/1 (p-value < 0.001). CONCLUSIONS: The variations of DNA and RNA in genes with 6mA modification were significant less than those in unmodified genes. Furthermore, the variations in 6mA modified genes were easily transmitted from DNA to RNA, especially the transmitted variation from DNA heterozygote to RNA homozygote.

N 6-Methyladenine DNA Modification in the Woodland Strawberry (Fragaria vesca) Genome Reveals a Positive Relationship With Gene Transcription.

N 6-methyladenine (6mA) DNA modification has been detected in several eukaryotic organisms, where it plays important roles in gene regulation and epigenetic memory maintenance. However, the genome-wide distribution patterns and potential functions of 6mA DNA modification in woodland strawberry (Fragaria vesca) remain largely unknown. Here, we examined the 6mA landscape in the F. vesca genome by adopting single-molecule real-time sequencing technology and found that 6mA modification sites were broadly distributed across the woodland strawberry genome. The pattern of 6mA distribution in the long non-coding RNA was significantly different from that in protein-coding genes. The 6mA modification influenced the gene transcription and was positively associated with gene expression, which was validated by computational and experimental analyses. Our study provides new insights into the DNA methylation in F. vesca.

[Multispectral Radiation Algorithm Based on Emissivity Model Constraints for True Temperature Measurement].

Temperature measurement is one of the important factors for ensuring product quality, reducing production cost and ensuring experiment safety in industrial manufacture and scientific experiment. Radiation thermometry is the main method for non-contact temperature measurement. The second measurement (SM) method is one of the common methods in the multispectral radiation thermometry. However, the SM method cannot be applied to on-line data processing. To solve the problems, a rapid inversion method for multispectral radiation true temperature measurement is proposed and constraint conditions of emissivity model are introduced based on the multispectral brightness temperature model. For non-blackbody, it can be drawn that emissivity is an increasing function in the interval if the brightness temperature is an increasing function or a constant function in a range and emissivity satisfies an inequality of emissivity and wavelength in that interval if the brightness temperature is a decreasing function in a range, according to the relationship of brightness temperatures at different wavelengths. The construction of emissivity assumption values is reduced from multiclass to one class and avoiding the unnecessary emissivity construction with emissivity model constraint conditions on the basis of brightness temperature information. Simulation experiments and comparisons for two different temperature points are carried out based on five measured targets with five representative variation trends of real emissivity. decreasing monotonically, increasing monotonically, first decreasing with wavelength and then increasing, first increasing and then decreasing and fluctuating with wavelength randomly. The simulation results show that compared with the SM method, for the same target under the same initial temperature and emissivity search range, the processing speed of the proposed algorithm is increased by 19.16%-43.45% with the same precision and the same calculation results.

[Compensation method of broadband illuminant fluctuation based on spectrum linear fitting].

The intensity of broadband illuminant fluctuates when its' power supply output power changes. Spectral intensities at each wavelength within the band of broadband illuminant fluctuate at different levels. A method based on spectrum linear fitting is proposed to compensate the illuminant spectral intensity in its band when its intensity fluctuates. The spectral intensity fluctuation at each wavelength could be compensated simply by measuring the band intensity with this method. The linear relationship between spectral radiant exitance and whole radiant exitance of ideal blackbody was analysed by researching the radiant exitance at different temperatures. The linear model of broadband illuminant band intensity and spectral intensity was built. Experimental system is composed of a halogen light, a power supply, an aperture, a spectrometer, and a computer mainly. By adjusting the power output of the power supply, we obtained a set of halogen light relative spectral intensities at different power inputs. The spectral intensity of halogen light at different input powers was measured to test the compensation effect of this method. The relationship between spectral intensity and band intensity of halogen light was fitted with linear relation and the fitting errors were analysed. The experimental result shows a linear relationship between spectral intensity and band intensity of halogen light, so the spectral intensity fluctuation can be compensated using the band intensity according to their linear relation. The relative error absolute value of compensated spectral intensity decreases as the halogen light input power increases. Within the range of halogen light input power, the relative error absolute values of spectral intensity compensated with this method are within 5% at vast majority (92%) of the wavelengths.

Splenogonadal fusion: Report of four cases and review of the literature.

Splenogonadal fusion (SGF) is a rare congenital abnormality that affects children of both genders. Very few cases of SGF have been diagnosed preoperatively. In this study, the surgical findings and laparoscopic treatment of four children with SGF associated with intra-abdominal cryptorchidism are described. Laparoscopy was demonstrated to be the only accurate exploratory procedure for the diagnosis and surgical treatment of SGF with non-palpable testis.

[Synergistic effects of low temperature in winter and ebb tide at night on Sonneratia apetala seedlings growth and key eco-physiological traits].

By setting up a set of simulated tidal systems with different air- and water temperature and tidal flood conditions, this paper studied the synergistic effects of low temperature in winter and ebb tide at night on the growth and key eco-physiological traits of Sonneratia apetala seedlings. Low air temperature depressed the seedlings growth, but the reduction in the seedling height and basal stem diameter was compensated 41.2% and 44.6%, respectively by a 5 degrees C increase of water temperature. Low air temperature (15 degrees C) reduced the leaf Fv/Fm significantly, indicating a dramatic reduction in the leaf photosynthetic capacity, whereas the flooded tide with higher water temperature could not compensate this damage. The flooded tide with high air temperature increased the proline and soluble sugar contents in mature leaves, which could protect the mature leaves from cold damage. When extreme cold events occurred, the flooded tide at night worked as a heat storage medium, which alleviated the cold damage on the seedlings growth and leaf physiological traits, and promoted the survival rate of S. apetala seedlings.

Sublethal levels of cadmium down-regulate the gene expression of DNA mismatch recognition protein MutS homolog 6 (MSH6) in zebrafish (Danio rerio) embryos.

MutS homolog 6 (MSH6) is the major mismatch contacting component of the MSH2-MSH6 heterodimeric complex (MutSα) that mediates DNA mismatch repair (MMR) of simple mispairs and small insertion-deletion loops in eukaryotes. This study examined the potential of cadmium (Cd) to disturb the gene expression of MSH6 in vertebrates using zebrafish (Danio rerio) embryo as a model organism. Semiquantitative RT-PCR indicated that msh2 and msh6 expressions were suppressed in embryos at 1h post fertilization (hpf), then drastically up-regulated in 2 hpf embryos and actively expressed in 3-25 hpf embryos. In the presence of a constitutive ß-actin expression, exposure of 1 hpf embryos to sublethal concentrations of CdCl(2) at 0.5-3 µM for 4 or 9h caused a time and concentration-dependent down-regulation of msh6 transcription. Cd failed to inhibit msh2 transcription except at 3 µM, reflecting the higher sensitivity of msh6 than msh2 transcription to Cd. Whole mount in situ hybridization showed a wide distribution of msh6 transcripts in the front body portions of 10 hpf embryos and Cd-induced a general suppression of msh6 expression in zebrafish tissues. Cd-induced down-regulation of msh6 transcription paralleled with reduced levels of MSH6 protein synthesis and MSH6-mediated G-T mismatch binding activities identified by band shift assay using recombinant zebrafish MSH6 and an anti-human MSH6 antibody. Our results revealed the inhibition of Cd on MSH6 expression at both mRNA and protein levels and this mechanism may play a role in Cd genotoxicity.