Isolation, Identification, and Pathogenicity of a Goose Astrovirus Genotype 1 Strain in Goslings in China

Goose astrovirus genotype 1 (GAstV-1) has emerged in goose farms in some provinces of China in recent years and is considered to be one of the pathogens of gout in goslings in China. However, few studies have been conducted on the dynamic distribution, tissue tropism, and pathogenesis of GAstV-1 in goslings. In 2022, an epidemiological investigation of goose astrovirus (GAstV) in goslings was conducted in seven provinces of China. During the investigation, a GAstV-1 designated as GAstV-JSXZ was identified in the kidney of an 8-day-old gosling and was successfully isolated from a goose embryo. The full genome sequence of GAstV-JSXZ was determined using the next-generation sequencing technique. The complete genome of GAstV-JSXZ was 7299-nt-long. Interestingly, the phylogenetic analysis revealed that Chinese GAstV-1 has formed two distinct subgroups based on the ORF 2 genomes, designated GAstV-1 1a and GAstV-1 1b. The GAstV-JSXZ shared the highest identity with GAstV-1 1a strain FLX and TZ03 in nucleotides (ORF1a: 98.3-98.4%; ORF1b: 92.3-99.1%; ORF2: 95.8-98.8%) and amino acid sequences (ORF1a: 99.4-99.5%; ORF1b: 98.2-98.8%; ORF2: 97.0-99.4%). To evaluate the pathogenicity of GAstV-1, 1-day-old goslings were inoculated with the virus by oral and subcutaneous injection routes, respectively. The results revealed that the virus causes extensive pathological organ damage, especially in the kidney, liver, and thymus. Virus-specific genomic RNA could be detected in the cloacal swabs and tissues of infected goslings throughout the experiment. The viral copy numbers examined in the kidney and intestine were the highest, followed by the liver and spleen. These results are likely to provide a new understanding of the pathogenicity of GAstV-1 in geese.

Transcriptome-Based Identification of the Optimal Reference Genes for Quantitative Real-Time Polymerase Chain Reaction Analyses of Lingonberry Fruits throughout the Growth Cycle

(1) Background: Vaccinium vitis-idaea is a nutritionally and economically valuable natural wild plant species that produces berries useful for treating various diseases. There is growing interest in lingonberry, but there is limited information regarding lingonberry reference genes suitable for gene expression analyses of different tissues under various abiotic stress conditions. The objective of this study was to identify stable reference genes suitable for different lingonberry tissues in response to abiotic stress. (2) Methods: The delta Ct method and the GeNorm v3.5 and NormFinder v20 programs were used to comprehensively analyze gene expression stability. (3) Results: Actin Unigene23839 was the best reference gene for analyzing different cultivars, whereas Actin CL5740.Contig2 was the most suitable reference gene for analyzing different tissues and alkali stress. In contrast, 18S rRNA CL5051.Contig1 was the most stable reference gene under drought conditions. (4) Conclusions: These suitable reference genes may be used in future qRT-PCR analyses of different lingonberry tissues and the effects of abiotic stresses. Furthermore, the study data may be useful for functional genomics studies and the molecular breeding of lingonberry. In summary, internal reference genes or internal reference gene combinations should be carefully selected according to the experimental conditions to ensure that the generated gene expression data are accurate.

Selection and verification of reliable internal reference genes in stem development of herbaceous peony (Paeonia lactiflora Pall.)

Herbaceous peony (Paeonia lactiflora Pall.) has emerged in the cut flower market due to its beautiful appearance. The bending flower stems caused by a lack of mechanical strength is the main problem restricting the development of the cut P. lactiflora industry. So it is of great worth to reveal the basis of stem development changes in P. lactiflora to improve its cut flower quality. Quantitative research on gene expression characteristics can provide clues for understanding their biological functions, and the screening of relatively stable expression genes is a prerequisite for the quantitative study of gene expression characteristics. Thus, it is necessary to find appropriate genes during stem development so as to analyze the qRT‒PCR results. In this study, 10 genes were screened, and these genes expressed stably in stems of different stem strengths at three different developmental stages. Then, their expressions were evaluated by RefFinder, BestKeeper, NormFinder, and GeNorm programs. The results demonstrated that γ-tubulin (γ-TUB) was the most suitable gene, followed by α-tubulin (α-TUB) and β-D-glucosidase (β-GUS), whereas histone H3 (His) was the least suitable gene. Besides, the temporal and spatial expression characteristics of PlCOMT1, the key gene concerned with the synthesis of cell wall fillers in P. lactiflora, were also used to evaluate the suitability of genes. Consequently, γ-TUB and α-TUB are the two best combinations during stem development, and their combination can be used for the stem development of P. lactiflora. These findings will provide a reference for the selection of genes related to stem development and the study of molecular mechanisms related to stem development in P. lactiflora.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-023-01325-5.

Genome-Wide Identification of DUF668 Gene Family and Expression Analysis under Drought and Salt Stresses in Sweet Potato [Ipomoea batatas (L.) Lam]

The domain of unknown function 668 (DUF668) is a gene family that plays a vital role in responses to adversity coercion stresses in plant. However, the function of the DUF668 gene family is not fully understood in sweet potato. In this study, bioinformatics methods were used to analyze the number, physicochemical properties, evolution, structure, and promoter cis-acting elements of the IbDUF668 family genes, and RNA-seq and qRT-PCR were performed to detect gene expression and their regulation under hormonal and abiotic stress. A total of 14 IbDUF668 proteins were identified in sweet potato, distributed on nine chromosomes. By phylogenetic analysis, IbDUF668 proteins can be divided into two subfamilies. Transcriptome expression profiling revealed that many genes from DUF668 in sweet potato showed specificity and differential expression under cold, heat, drought, salt and hormones (ABA, GA3 and IAA). Four genes (IbDUF668-6, 7, 11 and 13) of sweet potato were significantly upregulated by qRT-PCR under ABA, drought and NaCl stress. Results suggest that the DUF668 gene family is involved in drought and salt tolerance in sweet potato, and it will further provide the basic information of DUF668 gene mechanisms in plants.

New Safety Aspects in Corneal Donation-Studies on SARS-CoV-2-Positive Corneal Donors

In the tissue donation field, to prevent pathogen transmission, all donors are screened by postmortem swabs for SARS-CoV-2 using qRT–PCR. Corneas from donors who tested positive for SARS-CoV-2 were subjected to further investigations. Corneal transplants and culture medium from positive donors were cultured under appropriate safety conditions for further analyses. Cornea tissue samples, including sclera/limbus/cornea, and culture media were taken at different time points for testing for SARS-CoV-2 using qRT–PCR, immunohistochemistry (IHC) and subgenomic RNA (sgRNA) analysis. Between January and May 2021, in four donors with initial negative premortem rapid tests, SARS-CoV-2 was detected post-mortem using qRT–PCR. In these cases, SARS-CoV-2 was observed at the beginning of cultivation in both tissue and culture medium using qRT–PCR and IHC. The virus was mainly localized in the limbus epithelial cells, with a stable detection level. Premortem rapid tests are potentially insufficient to exclude SARS-CoV-2 infection in corneal donors. While, for SARS-CoV-2, the risk of infection via transplants is considered low, a residual risk remains for presymptomatic new infections. However, our investigations provide the first indications that, with organ cultures, the risk of virus transmission is minimized due to the longer minimum culture period.

Genetic interference exerted by Salmonella-delivered CRISPR/Cas9 significantly reduces the pathological burden caused by Marek's disease virus in chickens

Efficient in vivo delivery of a CRISPR/Cas9 plasmid is of paramount importance for effective therapy. Here, we investigated the usability of Salmonella as a plasmid carrier for in vivo therapy against virus-induced cancer using Marek’s disease virus (MDV) as a model for study in chickens. A green fluorescent protein-expressing CRISPR/Cas9 plasmid encoding the virulence gene pp38 was constructed against Marek’s disease virus. Therapeutic plasmids were transformed into Salmonella carrying lon and sifA gene deletions. The animals in 5 groups were intraperitoneally inoculated with phosphate-buffered saline, vector control, or Salmonella before or after MDV infection, or left uninfected as a naïve control. Therapeutic effectiveness was evaluated by observing disease outcomes and the viral copy number in peripheral blood mononuclear cells. The efficacy of plasmid delivery by Salmonella was 13 ± 1.7% in the spleen and 8.0 ± 1.8% in the liver on the 6^th day post-infection. The Salmonella-treated groups showed significant resistance to MDV infection. The maximum effect was observed in the group treated with Salmonella before MDV infection. None of the chickens fully recovered; however, the results suggested that timely delivery of Salmonella could be effective for in vivo CRISPR/Cas9-mediated genetic interference against highly pathogenic MDV. The use of Salmonella in CRISPR systems provides a simpler and more efficient platform for in vivo therapy with CRISPR than the use of conventional in vivo gene delivery methods and warrants further development.

Identification of Differentially Expressed Plasma lncRNAs As Potential Biomarkers for Breast Cancer

BACKGROUND

Breast cancer is the most common malignant tumor in women and is not easy to diagnose. Increasing evidence has underscored that long non-coding RNAs (lncRNAs) play important regulatory roles in the occurrence and progression of many cancers, including breast cancer. We aimed to identify lncRNAs in plasma as potential biomarkers for breast cancer.

PATIENTS AND METHODS

We analyzed the Gene Expression Omnibus (GEO) datasets GSE22820, GSE42568, and GSE65194 to identify the common differential genes between cancer tissues and adjacent tissues. Then 14 lncRNAs were identified among the common differential genes and validated by using real-time quantitative polymerase chain reaction in 92 patients with breast cancer and 100 healthy controls. Receiver operating characteristic (ROC) curves were constructed to evaluate their diagnostic value for breast cancer.

RESULTS

Integrated analysis of the GEO datasets identified three significantly upregulated and 11 downregulated lncRNAs in breast cancer tissues. Compared with healthy controls, MIAT was significantly upregulated in breast cancer patient plasma, and LINC00968 and LINC01140 were significantly downregulated. ROC curve analysis suggested that these three lncRNAs can discriminate breast cancer from healthy individual with high specificity and sensitivity.

CONCLUSION

This research identified three differentially expressed lncRNAs in breast cancer patient plasma. Our data suggest that these three lncRNAs can be used as potential diagnostic biomarkers of breast cancer.

Evaluation of Appropriate Reference Genes For Investigating Gene Expression in Chlorops oryzae (Diptera: Chloropidae)

Reverse transcription quantitative polymerase chain reaction (PCR) has become an invaluable technique for analyzing gene expression in many insects. However, this approach requires the use of stable reference genes to normalize the data. Chlorops oryzae causes significant economic damage to rice crops throughout Asia. The lack of suitable reference genes has hindered research on the molecular mechanisms underlying many physiological processes of this species. In this study, we used quantitative real-time PCR to evaluate the expression of eight C. oryzae housekeeping genes glyceraldehyde-3-phosphate dehydrogenase (GAPDH), β-actin (βACT), beta-tubulin (βTUB), Delta Elongation factor-1 (EF1δ), ribosomal protein S11 (RPS11), RPS15, C-terminal-Binding Protein (CtBP), and ribosomal protein 49 (RP49) in different developmental stages and tissues in both larvae and adults. We analyzed the data with four different software packages: geNorm, NormFinder, BestKeeper, and RefFinder and compared the results obtained with each method. The results indicate that PRS15 and RP49 can be used as stable reference genes for quantifying gene expression in different developmental stages and larval tissues. GAPDH and βACT, which have been considered stable reference genes by previous studies, were the least stable of the candidate genes with respect to larval tissues. GAPDH was, however, the most stable reference gene for adult tissues. We verified the candidate reference genes identified and found that the expression levels of Cadherins (Cads) changed when different reference genes were used to normalize gene expression. This study provides a valuable foundation for future research on gene function, and investigating the molecular basis of physiological processes, in C. oryzae.

Circulating miRNAs as biomarkers for oral squamous cell carcinoma recurrence in operated patients

MicroRNAs (miRNAs) are small regulatory non-coding RNAs for which altered expression in cancers can serve as potential biomarkers for diseases. We here investigated whether circulating miRNAs can serve as biomarkers for predicting post-operational recurrence of oral squamous cell carcinoma (OSCC) in patients. Plasma samples from 8 Danish OSCC patients were collected before, and one year after surgical operation, as well as from 3 Danish healthy controls and subjected to miRNA profiling by next generation sequencing. Disease recurrence did not occur in the 8 patients when the post-operative plasma samples were collected. Based on the sequencing data, three up-regulated miRNAs (miR-148a-3p, miR-26a-5p and miR-21-5p) and three down-regulated miRNAs (miR-375, miR-92b-3p and miR-486-5p) in the OSCC samples compared to healthy controls were selected for qRT-PCR validation in a Chinese cohort of 20 plasma samples collected before, and 9-12 months after surgical operation, and 18 healthy controls. Disease recurrence had occurred in 8 out of the 20 Chinese patients at the time their post-operative plasma samples were collected. The results of qRT-PCR showed that down-regulation of miR-486-5p, miR-375 and miR-92b-3p were highly associated with OSCC recurrence. This study indicates that the plasma miRNA profile is altered in OSCC during its progression and can be used to monitor the likelihood of OSCC recurrence in patients after surgery.

Quantitative RT-PCR Platform to Measure Transcript Levels of C and N Metabolism-Related Genes in Durum Wheat: Transcript Profiles in Elevated [CO2] and High Temperature at Different Levels of N Supply

Only limited public transcriptomics resources are available for durum wheat and its responses to environmental changes. We developed a quantitative reverse transcription-PCR (qRT-PCR) platform for analysing the expression of primary C and N metabolism genes in durum wheat in leaves (125 genes) and roots (38 genes), based on available bread wheat genes and the identification of orthologs of known genes in other species. We also assessed the expression stability of seven reference genes for qRT-PCR under varying environments. We therefore present a functional qRT-PCR platform for gene expression analysis in durum wheat, and suggest using the ADP-ribosylation factor as a reference gene for qRT-PCR normalization. We investigated the effects of elevated [CO(2)] and temperature at two levels of N supply on C and N metabolism by combining gene expression analysis, using our qRT-PCR platform, with biochemical and physiological parameters in durum wheat grown in field chambers. Elevated CO(2) down-regulated the photosynthetic capacity and led to the loss of N compounds, including Rubisco; this effect was exacerbated at low N. Mechanistically, the reduction in photosynthesis and N levels could be associated with a decreased transcription of the genes involved in photosynthesis and N assimilation. High temperatures increased stomatal conductance, and thus did not inhibit photosynthesis, even though Rubisco protein and activity, soluble protein, leaf N, and gene expression for C fixation and N assimilation were down-regulated. Under a future scenario of climate change, the extent to which C fixation capacity and N assimilation are down-regulated will depend upon the N supply.

Disruption of murine Tcte3-3 induces tissue specific apoptosis via co-expression of Anxa5 and Pebp1

Programmed cell death or apoptosis plays a vital physiological role in the development and homeostasis. Any discrepancy in apoptosis may trigger testicular and neurodegenerative diseases, ischemic damage, autoimmune disorders and many types of cancer. Tcte3 (T-complex testis expressed 3) is an accessory component of axonemal and cytoplasmic dynein which expresses predominantly in meiotic and postmeiotic germ cells. It plays an essential role during spermatogenesis; however, to explore its diverse and complex functioning in male germ cell apoptosis, requires further prosecution. Here, 2D-gel electrophoresis, mass spectrometry and qRT-PCR analyses were performed to elucidate the differential expression of genes, in both wild-type and homozygous Tcte3-3 mice. We observed an increased expression of Tcte3 in homozygotes as compared to wild-type testes. Perpetually, an increased expression of Anxa5 and Pebp1, while a lower expression of Rsph1 was detected in Tcte3-3^-/- mice. We propose that over-expression of Pebp1 and Anxa5 in Tcte3-3^-/- testes might be due to increased apoptosis. To evaluate this possibility, testes specific microarray data set extracted from NCBI gene ontology omnibus (GEO) was used to cluster the possible co-expression partners of Tcte3. Further functional coherence of compiled candidate genes was monitored computationally by studying the common TFBS overlapped at the regulatory regions. Differential expression of Tcte3-3 and its involvement in apoptosis may provide a basis for the investigation of transcriptional specificities of other Tcte3 paralogs (Tcte3-1 and Tcte3-2). A complete understanding of controlling factors which have implications in regulating tissue-specific Tcte3 expression would provide additional insights into the gene control events. The collective knowledge may prove useful for the development of novel therapeutic regimen and would open new avenues in defining selective roles of Tcte3 in germ cell development.

Development of colistin resistance in pmrA-, phoP-, parR- and cprR-inactivated mutants of Pseudomonas aeruginosa

OBJECTIVES

Colistin susceptibility in Pseudomonas aeruginosa is associated with a lipopolysaccharide (LPS) structure that is controlled by the modulation of several two-component regulatory systems. In this study, we attempted to elucidate the role of these two-component systems in the development of colistin resistance in P. aeruginosa.

METHODS

pmrA-, phoP-, parR- or cprR-inactivated mutants were constructed from a colistin-susceptible P5 strain. Colistin-resistant mutants (P5R, P5ΔpmrA-R, P5ΔphoP-R, P5ΔparR-R and P5ΔcprR-R) were developed in vitro from a wild-type strain (P5) and pmrA-, phoP-, parR- or cprR-inactivated mutants by serial passage in colistin-containing media. Expression levels of the pmrA, phoP, parR, cprR and arnB genes were determined and amino acid alterations of two-component regulatory systems during development of colistin resistance were also investigated.

RESULTS

While P5ΔpmrA-R, P5ΔparR-R and P5ΔcprR-R showed elevated expression of the phoP gene, the expression levels of the pmrA, parR and cprR genes were not different between gene-inactivated mutants and the adapted colistin-resistant mutants. P5ΔphoP-R showed no significant elevation in expression of any of the pmrA, parR or cprR genes. The arnB gene was overexpressed in all in vitro-selected colistin-resistant mutants compared with colistin-susceptible wild-type and gene-inactivated mutants. Three amino acid alterations in PhoQ and three in ParS were identified in induced colistin-resistant mutants.

CONCLUSIONS

Our data suggest that individual two-component systems may not be essential for the acquisition of colistin resistance in P. aeruginosa. The PhoPQ two-component system may play a major role in the development of colistin resistance in our strains, but alternative or compensatory pathways may exist.

Validation of endogenous normalizing genes for expression analyses in adult human testis and germ cell neoplasms

The measurement of gene expression levels in cells and tissues typically depends on a suitable point of reference for inferring biological relevance. For quantitative (or real-time) RT-PCR assays, the method of choice is often to normalize gene expression data to an endogenous gene that is stably expressed across the samples analysed: a so-called normalizing or housekeeping gene. Although this is a valid strategy, the identification of stable normalizing genes has proved challenging and a gene showing stable expression across all cells or tissues is unlikely to exist. Therefore, it is necessary to define suitable normalizing genes for specific cells and tissues. Here, we report on the performance of a panel of nine commonly employed normalizing genes in adult human testis and testicular pathologies. Our analyses revealed significant variability in transcript abundance for commonly used normalizers, highlighting the importance of selecting appropriate normalizing genes as comparative measurements can yield variable results when different normalizing genes are employed. Based on our results, we recommend using RPS20, RPS29 or SRSF4 when analysing relative gene expression levels in human testis and associated testicular pathologies. OCT4 and SALL4 can be used with caution as second-tier normalizers when determining changes in gene expression in germ cells and germ cell tumour components, but the relative transcript abundance appears variable between different germ cell tumour types. We further recommend that such studies should be accompanied by additional assessment of histology and cellularity of each sample.

Astaxanthin and omega-3 fatty acids individually and in combination protect against oxidative stress via the Nrf2-ARE pathway

Oxidative stress is a major driver of many diseases, including cancer. The induction of Nrf2-ARE-mediated antioxidant enzymes provides a cellular defense against oxidative stress. Astaxanthin (AST), a red dietary carotenoid, possesses potent antioxidant activity, and inhibits oxidative damages. Polyunsaturated fatty acids (PUFAs), docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA), are important nutritional essentials and potent antioxidants found in fish oil. In the present study, we investigated whether AST in combination with low concentrations of DHA or EPA has a synergistic antioxidant effect in a HepG2-C8-ARE-luciferase cell line system. Using free radical scavenging DPPH assay, AST was more potent DPPH radical scavenger than DHA and EPA. MTS assay revealed that AST was non-toxic up to 100μM compared with more toxic DHA and EPA. The three compounds alone and in combination elevated cellular GSH levels, increased the total antioxidant activity, induced mRNA expression of Nrf2 and Nrf2 downstream target genes NQO1, HO-1, and GSTM2. Lower concentrations of AST show synergistic effects when combined with DHA or EPA. In summary, our study shows synergistic antioxidant effects of AST and PUFAs at low concentrations. The Nrf2/ARE pathway plays an important role in the antioxidative effects induced by AST, DHA, and EPA.