The Challenges of Long-Term Transcriptional Gene Silencing by RNA Viruses.

Since the past few decades, the small RNA (sRNA) technologies including small interfering RNA and miRNA have been widely explored for therapeutic development. Classically, these sRNAs target the coding regions of mRNA to exert temporal gene silencing in a post-transcriptional manner. Interestingly, sRNAs targeting gene promoters have been recently described to mediate long-term transcriptional gene silencing (TGS) by epigenetic modifications. This has further harnessed the potential applications in gene therapy. However, efficient delivery is a common hurdle for almost any types of gene therapy approaches. In a recent issue of Trends in Biochemical Sciences, Baltusnikas et al. have proposed to use RNA viruses to deliver sRNA for long-term TGS, suggesting long-term therapy by a single administration approach for various diseases, including chronic, incurable, and fatal illnesses. Being a novel and ambitious gene therapy strategy, we hereby would like to emphasize three major challenges and propose potential solutions.

(±)-Involucrasins A and B, two pairs of flavanone enantiomers from Shuteria involucrata and their inhibitory effects on the proliferation of various cancer cell lines.

(±)-Involucrasins A (1) and B (2), two pairs of flavanone enantiomers were isolated from Shuteria involucrata. Structurally, both 1 and 2 are rare representatives of 5-dehydroxy/5-demethoxy 2',3',4'-trisubstituted flavanones. Their structures were elucidated on the basis of comprehensive spectroscopic data analysis and comparison with the literature data. Involucrasin B (2) exhibited moderate anti-proliferative activity against Caco-2, MCF-7, MDA-MB-468, and HCT116 cell lines with IC50 values ranging from 7.9-22.7 µM. Involucrasin A (1) exhibited weak inhibitory activity against Caco-2 and MCF-7 cell lines with IC50 values of 25.8 and 26.5 µM, respectively.

Effect of mangrove restoration on sediment properties and bacterial community.

Mangrove reconstruction is an efficient approach for mangrove conservation and restoration. The present study aimed to explore the effects of mangrove reconstruction on sediment properties and bacterial community. The results showed that mangrove restoration greatly promoted sediment fertility, whereas the improvements were more obvious induced by Kandelia obovata when compared to Avicennia marina. In all the samples, the dominant top5 bacterial group were Proteobacteria (48.31-54.52%), Planctomycetes (5.98-8.48%), Bacteroidetes (4.49-11.14%) and Acidobacteria (5.69-8.16%). As for the differences among the groups, the relative abundance of Chloroflexi was higher in the sediments of K. obovata, while Bacteroidetes was more abundant in A. marina group. Furthermore, the two bacterial genera (Rhodoplanes and Novosphingobium) were more dominant in the sediments of K. obovata, while the sediments of A. marina contained higher abundance of Vibrio and Marinobacterium. Besides, bacterial community was highly correlated with mangrove species and sediment property and nutrient status. The results of this study would provide a better understanding of the ecological benefits of mangroves and highlighted the information on biogeochemical processes driven by mangrove restoration and microorganisms.

The nucleotide usages significantly impact synonymous codon usage in Mycoplasma hyorhinis.

Five annotated genomes of Mycoplasma hyorhinis were analyzed for clarifying evolutionary dynamics driving the overall codon usage pattern. Information entropy used for estimating nucleotide usage pattern at the gene level indicates that multiple evolutionary dynamics participate in forcing nucleotide usage bias at every codon position. Moreover, nucleotide usage bias directly contributes to synonymous codon usage biases with two different extremes. The overrepresented codons tended to have A/T in the third codon position, and the underrepresented codons strongly used G/C in the third position. Furthermore, correspondence analysis and neutrality plot reflect an obvious interplay between mutation pressure and natural selection mediating codon usage in M. hyorhinis genome. Due to significant bias in usages between A/T and G/C at the gene level, different selective forces have been proposed to contribute to codon usage preference in M. hyorhinis genome, including nucleotide composition constraint derived from mutation pressure, translational selection involved in natural selection, and strand-specific mutational bias represented by different nucleotide skew index. The systemic analyses of codon usage for M. hyorhinis can enable us to better understand the mechanisms of evolution in this species.

Nitrogen dynamics in the mangrove sediments affected by crabs in the intertidal regions.

Crab is an important benthonic animal in mangrove ecosystem, however, the potential function of crabs on nitrogen (N) transformation in mangrove ecosystems is still poorly understood. The present study aimed to explore the potential effect of crab burrows on nitrification/denitrification within the sediments. The results showed that the presence of crab burrows could directly promote soil nitrification, the regions within more crab burrows appeared to possess higher nitrification. Higher AOA and AOB gene copies were also observed in the sediments surrounding crab burrows than those in the sediments without crab burrow. On the contrary, lower nirS copies, a denitrification related gene, were detected in the sediments surrounding crab burrows. In summary, the present study proposed new evidences of nitrification enhancement deriving by crabs, the presence of crabs might be significant in alleviating nitrification inhibition and benefits the growth of mangroves under tidal flooding.

Significance and roles of synonymous codon usage in the evolutionary process of Proteus.

Proteus spp. bacteria frequently serve as opportunistic pathogens that can infect many animals and show positive survival and existence in various natural environments. The evolutionary pattern of Proteus spp. is an unknown topic, which benefits understanding the different evolutionary dynamics for excellent bacterial adaptation to various environments. Here, the eight whole genomes of different Proteus species were analyzed for the interplay between nucleotide usage and synonymous codon usage. Although the orthologous average nucleotide identity and average nucleotide identity display the genetic diversity of these Proteus species at the genome level, the principal component analysis further shows that these species sustain the specific genetic niche at the aspect of synonymous codon usage patterns. Interestingly, although these Proteus species have A/T rich genes with underrepresented G (guanine) or C (cytosine) at the third codon positions and overrepresented A or T at these positions, some synonymous codons with A or T end are obviously suppressed in usage. The overall codon usage pattern reflected by the effective number of codons (ENC) has a significantly positive correlation with GC3 content (GC content at the third codon position), and ENC has a significantly negative correlation with the adaptation index for these species. These results suggest that the mutation pressure caused by nucleotide composition constraint serves as a dominant evolutionary dynamic driving evolutionary trend of Proteus spp., along with other selections related to natural selection, replication and fine-tune translation, and so on. Taken together, the analyses help to understand the evolutionary interplay between nucleotide and codon usage at the gene level of Proteus.

The Burden of Human Papillomavirus and Chlamydia trachomatis Coinfection in Women: A Large Cohort Study in Inner Mongolia, China.

Background: Chlamydia trachomatis may coinfect with human papillomavirus (HPV) and complicate the cervical pathogenesis. This study aimed to evaluate the prevalence, risk factors, and clinical outcomes of HPV/C. trachomatis coinfection in women from Inner Mongolia, China. Methods: We performed a polymerase chain reaction (PCR)-based HPV/C. trachomatis screening and cervical samples were analyzed by thinprep cytologic test. Statistical analysis was used to assess the association between demographic factors and coinfection. Results: Among the 2345 women recruited, the prevalences of HPV, C. trachomatis, and HPV/C. trachomatis coinfection were 36.0%, 14.3%, and 4.8%, respectively. The rate of multiple HPV genotypes was higher in coinfected women. HPV66 was the most frequently identified genotype in coinfected participants. The HPV DNA load was significantly higher in HPV monoinfected cases. In contrast, the DNA load of C. trachomatis was significantly higher in the coinfection group. Risk factors, including single women (odds ratio [OR] = 6.0, 95% confidence interval [CI], 4.044-8.782) and women with multiple sex partners (OR = 1.9, 95% CI, 1.324-2.824), were associated with coinfection. Importantly, coinfection was associated with increased risk for high-grade squamous intraepithelial lesions. Conclusions: HPV and C. trachomatis coinfection is an important risk factor for the progression of cervical lesions.

Comparative genomic analysis for nucleotide, codon, and amino acid usage patterns of mycoplasmas.

The evolutionary factors in influencing the genetic characteristics of nucleotide, synonymous codon, and amino acid usage of 18 mycoplasma species were analyzed. The nucleotide usage at the 1st and 2nd codon position which determines amino acid composition of proteins has a significant correlation with the total nucleotide composition of gene population of these mycoplasma species, however, the nucleotide usage at the 3rd codon position which affects synonymous codon usage patterns has a slight correlation with either the total nucleotide composition or the nucleotide usage at the 1st and 2nd codon position. Other evolutionary factors join in the evolutionary process of mycoplasma apart from mutation pressure caused by nucleotide usage constraint based on the relationships between effective number of codons/codon adaptation index and nucleotide usage at the 3rd codon position. Although nucleotide usage of gene population in mycoplasma dominates in forming the overall codon usage trends, the relative abundance of codon with nucleotide context and amino acid usage pattern show that translation selection involved in translation accuracy and efficiency play an important role in synonymous codon usage patterns. In addition, synonymous codon usage patterns of gene population have a bigger power to represent genetic diversity among different species than amino acid usage. These results suggest that although the mycoplasmas reduce its genome size during the evolutionary process and shape the form, which is opposite to their hosts, of AT usages at high levels, this kind organism still depends on nucleotide usage at the 1st and 2nd codon positions to control syntheses of the requested proteins for surviving in their hosts and nucleotide usage at the 3rd codon position to develop genetic diversity of different mycoplasma species. This systemic analysis with 18 mycoplasma species may provide useful clues for further in vivo genetic studies on the related species.

Adaptation of Borrelia burgdorferi to its natural hosts by synonymous codon and amino acid usage.

Lyme disease, caused by Borrelia burgdorferi, is a focally endemic tick-transmitted zoonotic infection. In this study, the major factors underlying synonymous codon-related amino acid usage in the B. burgdorferi genome and bias in synonymous codon usage of the translation initiation region of coding sequences were analyzed. Additionally, adaptation of B. burgdorferi to several of its hosts was analyzed in the context of synonymous codon usage. Principal component analysis (PCA) revealed that nucleotide content at the third synonymous position of a codon influenced the synonymous codon usage pattern, but the strand-specific factor did not influence the synonymous codon usage pattern of B. burgdorferi. In terms of the low GC content of B. burgdorferi coding sequences, the effective number of codons (ENC) showed a significant correlation with GC3 content (at the synonymous position). For the amino acid usage pattern for B. burgdorferi, PCA showed that the strand-specific factor did not contribute to this pattern, while the properties (aromaticity and hydrophobicity) of the amino acids themselves showed strong correlations with this pattern. Under-represented codons, which were frequently selected in the translation initiation region, possibly play roles in regulating gene expression in B. burgdorferi. In terms of co-evolution and synonymous codon usage patterns, adaptation of B. burgdorferi to different intermediate hosts was apparent to different degrees, and the degree of adaptation of this spirochete to wild animals was stronger than that of humans or mice.

Sweritranslactones A-C: Unusual Skeleton Secoiridoid Dimers via [4 + 2] Cycloaddition from Swertiamarin.

Skeleton-diversity-oriented chemical conversion from pure natural products is a valuable method to obtain natural product-like compounds, especially those with novel architecture. The application of phytochemical methods to iridoids yielded three novel secoiridoid dimers: sweritranslactones A-C (1-3). These molecules possess a 6/6/6/6/6/6-fused hexacyclic skeleton and were obtained from swertiamarin, one of the major constituents of the genus Swertia, via a [4 + 2] cycloaddition and intramolecular nucleophilic addition under aqueous conditions. The structures were established based on extensive spectroscopic characterization and X-ray crystallographic diffraction analysis.

[Chemical Constituents from Processed Products of Aconitum Vilmoriniani Radix].

OBJECTIVE: To investigate the chemical constituents of the processed products of Aconitum Vilmorinian Radix. METHODS: The constituents were isolated by repeated column chromatography over silica gel, alumina and RP-C18 as well as recrystallization. The structures were elucidated on the basis of spectral analysis and physicochemical properties. RESULTS: Ten compounds were obtained from the methanol extract, and they were identified as yunaconitine (1), 8-deacetyl-yunaconitine (2), geniculatine C (3), vilmorrianine B (4), vilmorrianine C(5), vilmorrianine D (6), talatisamine (7), ß-sitosterol (8), ß-daucosterol (9) and ß-sitosterol acetate (10). CONCLUSION: All compounds are obtained from the processed products of Aconitum Vilmoriniani Radix for the first time.

Immunosuppressants exert antiviral effects against influenza A(H1N1)pdm09 virus via inhibition of nucleic acid synthesis, mRNA splicing, and protein stability.

Influenza A virus (IAV) poses a threat to patients receiving immunosuppressive medications since they are more susceptible to infection with severe symptoms, and even death. Understanding the direct effects of immunosuppressants on IAV infection is critical for optimizing immunosuppression in these patients who are infected or at risk of influenza virus infection. We profiled the effects of 10 immunosuppressants, explored the antiviral mechanisms of immunosuppressants, and demonstrated the combined effects of immunosuppressants with the antiviral drug oseltamivir in IAV-infected cell models. We found that mycophenolic acid (MPA) strongly inhibits viral RNA replication via depleting cellular guanosine pool. Treatment with 6-Thioguanine (6-TG) promoted viral protein degradation through a proteasomal pathway. Filgotinib blocked mRNA splicing of matrix protein 2, resulting in decreased viral particle assembly. Furthermore, combined treatment with immunosuppressants and oseltamivir inhibits IAV viral particle production in an additive or synergic manner. Our results suggest that MPA, 6-TG, and filgotinib could be the preferential choices for patients who must take immunosuppressants but are at risk of influenza virus infection.

[Chemical constituents of Aconitum bulleyanum].

OBJECTIVE: To study the chemical constituents of chloroform fraction from Aconitum bulleyanum. METHODS: The compounds were isolated by various chromatographic techniques and identified by spectroscopic methods. RESULTS: 7 compounds were obtained and identified as yunaconitine (1), crassicaudine (2), foresaconitine (3), chasmaconitine (4), bulleyaconitine A (5), franchetine (6), and beta-sitosterol (7), CONCLUSION: Compounds 2-7 are isolated from this plant for the first time.

An Innovative model of magnetically intercalated expanded graphite for calculating radar attenuation performance at 2-18 GHz.

With the emergence of various filtering technologies, the radar jamming efficiency of the technology based on radar cross section is ever lower, therefore cannot meet military requirements. In this context, the jamming technology based on attenuation mechanism has been developed and plays an increasingly important role in disturbing radar detecting. Magnetically expanded graphite (MEG) has excellent attenuation efficiency because it can cause dielectric loss as well as magnetic loss. Moreover, MEG features good impedance matching, which makes more incidence of electromagnetic waves into the material; and its multi-layer structure is conducive for electromagnetic wave reflection and absorption. In this work, the structure model of MEG was established by analyzing the layered structure of expanded graphite (EG) and the dispersion of intercalated magnetic particles. The electromagnetic parameters of thus-modeled MEG were calculated based on the equivalent medium theory; and effects of EG size, magnetic particle type and volume fraction on the attenuation performance were studied by the variational method. It is indicated that MEG with 500-µm diameter has the best attenuation effect and the highest increment of absorption cross section appears at 50% volume fraction of the magnetic particles at 2 GHz. The imaginary part of complex permeability of the magnetic material has the most significant influence on the attenuation effect of MEG. This study provides guidance for the design and application of MEG materials in disturbing radar detecting field.

Antiviral triterpenoid saponins from the roots of Ilex asprella.

Two new sulfur-containing triterpenoid saponins, asprellanosides A (1) and B (2), were isolated from the roots of Ilex asprella, together with 10 known compounds (3-12). An in vitro anti-HSV-1 activity test of the isolates (1-4, 6-7, and 9-12) showed that only asprellanoside A (1) and oblonganoside H (6) exhibited anti-HSV-1 activity with TIC values of 0.14 and 0.18 mM, respectively.

Mapping codon usage of the translation initiation region in porcine reproductive and respiratory syndrome virus genome.

BACKGROUND: Porcine reproductive and respitatory syndrome virus (PRRSV) is a recently emerged pathogen and severely affects swine populations worldwide. The replication of PRRSV is tightly controlled by viral gene expression and the codon usage of translation initiation region within each gene could potentially regulate the translation rate. Therefore, a better understanding of the codon usage pattern of the initiation translation region would shed light on the regulation of PRRSV gene expression. RESULTS: In this study, the codon usage in the translation initiation region and in the whole coding sequence was compared in PRRSV ORF1a and ORFs2-7. To investigate the potential role of codon usage in affecting the translation initiation rate, we established a codon usage model for PRRSV translation initiation region. We observed that some non-preferential codons are preferentially used in the translation initiation region in particular ORFs. Although some positions vary with codons, they intend to use codons with negative CUB. Furthermore, our model of codon usage showed that the conserved pattern of CUB is not directly consensus with the conserved sequence, but shaped under the translation selection. CONCLUSIONS: The non-variation pattern with negative CUB in the PRRSV translation initiation region scanned by ribosomes is considered the rate-limiting step in the translation process.

Inhibiting pyrimidine biosynthesis impairs Peste des Petits Ruminants Virus replication through depletion of nucleoside pools and activation of cellular immunity.

Replication of peste des petits ruminants virus (PPRV) strongly depends on the cellular environment and resources of host cells including nucleoside pool. Thus, enzymes involved in nucleoside biosynthesis (such as pyrimidine biosynthesis pathway) are regarded as attractive targets for antiviral drug development. Here, we demonstrate that brequinar (BQR) and leflunomide (LFM) which are two specific inhibitors of DHODH enzyme and 6-azauracil (6-AU) which is an ODase enzyme inhibitor robustly inhibit PPRV replication in HEK293T cell line as well as in peripheral blood mononuclear cells isolated from goat. We further demonstrate that these agents exert anti-PPRV activity via the depletion of purimidine nucleotide. Interestingly, these inhibitors can trigger the transcription of antiviral interferon-stimulated genes (ISGs). However, the induction of ISGs is largely independent of the classical JAK-STAT pathway. Combination of BQR with interferons (IFNs) exerts enhanced ISG induction and anti-PPRV activity. Taken together, this study reveals an unconventional novel mechanism of crosstalk between nucleotide biosynthesis pathways and cellular antiviral immunity in inhibiting PPRV replication. In conclusion, targeting pyrimidine biosynthesis represents a potential strategy for developing antiviral strategies against PPRV.

Codon Usage Bias in Autophagy-Related Gene 13 in Eukaryotes: Uncovering the Genetic Divergence by the Interplay Between Nucleotides and Codon Usages.

Synonymous codon usage bias is a universal characteristic of genomes across various organisms. Autophagy-related gene 13 (atg13) is one essential gene for autophagy initiation, yet the evolutionary trends of the atg13 gene at the usages of nucleotide and synonymous codon remains unexplored. According to phylogenetic analyses for the atg13 gene of 226 eukaryotic organisms at the nucleotide and amino acid levels, it is clear that their nucleotide usages exhibit more genetic information than their amino acid usages. Specifically, the overall nucleotide usage bias quantified by information entropy reflected that the usage biases at the first and second codon positions were stronger than those at the third position of the atg13 genes. Furthermore, the bias level of nucleotide 'G' usage is highest, while that of nucleotide 'C' usage is lowest in the atg13 genes. On top of that, genetic features represented by synonymous codon usage exhibits a species-specific pattern on the evolution of the atg13 genes to some extent. Interestingly, the codon usages of atg13 genes in the ancestor animals (Latimeria chalumnae, Petromyzon marinus, and Rhinatrema bivittatum) are strongly influenced by mutation pressure from nucleotide composition constraint. However, the distributions of nucleotide composition at different codon positions in the atg13 gene display that natural selection still dominates atg13 codon usages during organisms' evolution.

Prevalence and clinical features of hepatitis E virus infection in pregnant women: A large cohort study in Inner Mongolia, China.

BACKGROUND AND AIM: Hepatitis E virus (HEV) infection causes severe maternal and fetal outcomes in pregnant women. These patients are exclusively from resource-limited regions with genotype 1 HEV infection, but not from western countries with genotype 3 prevalence. Since the circulating strains in China have evolved from the waterborne genotype 1 to the zoonotic genotype 4 HEV in the past decades, this study aims to evaluate the prevalence and clinical features of HEV infection in a large cohort of pregnant women in Inner Mongolia, China. METHODS: A total of 3278 pregnant women who visited the Inner Mongolia Maternal and Child Care hospital during 2018 were enrolled. Serum samples were examined for anti-HEV IgG and anti-HEV IgM antibodies using ELISA. Demographic information, results of clinical biochemical tests, maternal and neonatal outcomes were collected. RESULTS: Among the recruited 3278 pregnant women, 6.0% were anti-HEV IgG antibody positive, 0.3% were anti-HEV IgM antibody positive and 0.3% were positive for both anti-HEV IgG and anti-HEV IgM antibodies. HEV viral RNA was not detected. Pregnant women with recent/ongoing HEV infection indicated by anti-HEV IgM positivity have slightly higher ALT level, and potential risk of developing hyperlipidemia, preterm delivery and neonatal jaundice. CONCLUSIONS: These findings indicated that HEV infection is associated with a possible increase in adverse maternal, fetal and neonatal outcomes in our cohort. Thus, the burden of HEV infection in pregnant women in China appears distinct from resource-limited regions and western countries. Nevertheless, future studies are required to confirm and extend our findings.