Terminal Poly Research Articles

Amphiphilic Polyurethane with Cluster-Induced Emission for Multichannel Bioimaging in Living Cell Systems.

The development of single-component materials with low cytotoxicity and multichannel fluorescence imaging capability is a research hotspot. In the present work, highly electron-deficient pyrazine monomers were covalently connected into a polyurethane backbone using addition polymerization with terminal poly(ethylene glycol) monomethyl ether units containing a high density of electron pairs. Thereby, an amphiphilic polyurethane-pyrazine (PUP) derivative has been synthesized. The polymer displays cluster-induced emission through compact inter- and/or intramolecular noncovalent interactions and extensive through-space electron coupling and delocalization. Molecular rigidity facilitates red-shifted emission. Based on hydrophilic/hydrophobic interactions and excitation dependence emission at low concentrations, PUP has been self-assembled into fluorescent nanoparticles (PUP NPs) without additional surfactant. PUP NPs have been used for cellular multicolor imaging to provide a variety of switchable colors on demand. This work provides a simple molecular design for environmentally sustainable, luminescent materials with excellent photophysical properties, biocompatibility, low cytotoxicity, and color modulation.

THE COMPLETE NUCLEOTIDE SEQUENCE OF THE GENOMIC RNA OF BEAN COMMON MOSAIC VIRUS STRAIN NL4

The complete nucleotide sequence of the genomic RNA of the NL4 strain of Bean common mosaic virus (BCMV-NL4) was determined. The viral genome is 10037 nucleotides in length, excluding the 3’ terminal poly (A) tail, and contains a single open reading frame (ORF) of 9666 nucleotides encoding a polyprotein of 3222 amino acids. The ORF is flanked by 5’ and 3’ untranslated regions (UTRs) of 133 and 235 nucleotides, respectively. Comparative analyses of the predicted BCMV-NL4 polyprotein with other species of the genus Potyvirus revealed nine cleavage sites resulting in ten functional proteins. Nucleotide and amino acid sequence identities indicated a close relationship between BCMV-NL4 and BCMV-NL1. Blast comparisons using coat protein (CP) and 3’UTR sequences showed 100% identity between BCMV-NL4 and the Mexican variant (US6) of this strain.

Complete genome sequence of Paris polyphylla chlorotic mottle virus infecting Paris polyphylla var. yunnanensis in southwest China.

A novel virus infecting a Paris polyphylla var. yunnanensis plant, tentatively named "Paris polyphylla chlorotic mottle virus" (PpCMV), was discovered in the city of Lijiang, Yunnan Province, China. Its genome consists of 6384 nucleotides (nt), excluding the 3'-terminal poly(A) tail, and contains two open reading frames: ORF1 and ORF2. ORF1 is 6150 nt in length, encoding a large 2050-aa polyprotein with at least two conserved regions encoding a replication-associated protein and a coat protein, the latter of which is located at the 3' end of ORF1. ORF2, consisting of 1185 nt, is located within ORF1 but has a different reading frame. It encodes a 394-aa-long putative movement protein. Phylogenetic analysis based on amino acid sequences revealed that the newly discovered virus exhibited the closest relationship to Hobart betaflexivirus 1 and rhodiola betaflexivirus 1, both of which belong to the genus Capillovirus, sharing 48.8% and 36.5% amino acid sequence identity, respectively, in the structural protein. This is the first report of the complete genome sequence of PpCMV in China.

Development of CO2-responsive supramolecular drug carrier system for potential application in anticancer treatment

A strategy to construct carbon dioxide (CO2)-responsive supramolecular drug delivery systems for effective cancer treatment was successfully confirmed using self-assembled supramolecular nanoparticles containing water-soluble terminal uracil-functionalized poly(ethylene glycol) (U-PEG) as a functional carrier and CO2-sensitive imidazole-functionalized rhodamine 6 G (I-R6G) as a potent anticancer agent. Owing to the high-affinity interactions between I-R6G and U-PEG, U-PEG can effectively encapsulate I-R6G and spontaneously co-assembles into spherical nanoparticles in water, which possess tunable drug loading contents and particle sizes, unique intense fluorescence features, and good structural stability and anti-hemolytic capacity in aqueous biological environments, as well as rapid, selective CO2-responsiveness and well-controlled CO2-responsive drug release. Cytotoxicity evaluations revealed I-R6G-loaded U-PEG nanoparticles exhibited highly selective cytotoxic activity towards cancer cells, without affecting normal cells. In addition, in CO2-rich media, I-R6G-loaded nanoparticles led to higher cytotoxicity at lower doses than I-R6G-loaded nanoparticles in pristine media or pristine I-R6G in CO2-rich media. Crucially, cellular assays confirmed the presence of CO2 in the culture media substantially increased selective cell internalization of the I-R6G-loaded nanoparticles by cancer cells, and subsequently promoted intracellular release of I-R6G from the disassembled nanoparticles and subsequent reaction of I-R6G with CO2, which ultimately resulted in more rapid induction of apoptotic cancer cell death than I-R6G-loaded nanoparticles in pristine media. Therefore, the introduction of the CO2-sensitive agent I-R6G within this self-assembled nanocarrier system is an essential factor that may provide a potential way to enhance efficacy and reduce the side effects of chemotherapy.

Complete nucleotide sequence of hackberry virus A, a tentative member of the genus Waikavirus

The complete genomic sequence of a waikavirus from Chinese hackberry in Zhejiang province, China, named "hackberry virus A" (HVA), was determined using high-throughput sequencing (HTS) combined with reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. The bicistronic genomic RNA of HVA was found to consist of 12,691 nucleotides (nt), excluding the 3'-terminal poly(A) tail, and to encode a large polyprotein of 3783 amino acids (aa) and an additional 10.3-kDa protein. The aa sequences of the Pro-Pol and the CP regions of this virus share 39.8-44.2% and 25.5-36.4% identity, respectively, with currently known waikaviruses. These values are significantly below the current species demarcation threshold (< 75% and < 80% aa identity for the CP and Pro-Pol region, respectively) for the family Secoviridae, indicating that HVA represents a new species in the genus Waikavirus. This is the first report of a virus infecting Chinese hackberry.

Genome sequence and characterization of a novel fabavirus infecting Cirsium setidens (gondre) in South Korea.

The complete nucleotide sequence of a novel gondre (Cirsium setidens)-infecting virus, provisionally named "cirsium virus A" (CiVA), was determined by high-throughput and Sanger sequencing, revealing a genome organization typical of fabaviruses. RNA1 and RNA2 are 5,828 and 3,478 nucleotides long, excluding the 3'-terminal poly(A) tails, each containing a single open reading frame. The highest sequence identity values for the CiVA coat protein and proteinase-polymerase, compared with known fabavirus sequences, were 59.09% and 69.68%, respectively, falling below the current thresholds for Fabavirus species demarcation. Our findings support classifying CiVA as a novel putative member of the genus Fabavirus, subfamily Comovirinae, family Secoviridae.

Complete genome sequence analysis of a new potyvirus isolated from Paris polyphylla var. yunnanensis

The complete genome sequence of a new potyvirus from Paris polyphylla var. yunnanensis was determined. Its genomic RNA consists of 9571 nucleotides (nt), excluding the 3'-terminal poly(A) tail, containing the typical open reading frame (ORF) of potyviruses and encoding a putative large polyprotein of 3061 amino acids. The virus shares 54.20%-59.60% nt sequence identity and 51.80%-57.90% amino acid sequence identity with other potyviruses. Proteolytic cleavage sites and conserved motifs of potyviruses were identified in the polyprotein and within individual proteins. Phylogenetic analysis indicated that the virus was most closely related to lily yellow mosaic virus. The results suggest that the virus should be classified as a member of a novel species within the genus Potyvirus, and we have tentatively named this virus "Paris yunnanensis mosaic chlorotic virus" (PyMCV).

Complete genome sequence and genome characterization of a novel potyvirus from Lamprocapnos spectabilis.

The genome of a new potyvirus from a Lamprocapnos spectabilis plant in South Korea was sequenced by high-throughput sequencing and confirmed by Sanger sequencing. The new potyvirus was tentatively named "lamprocapnos virus A" (LaVA); its complete genome contains 9,745 nucleotides, excluding the 3'-terminal poly(A) tail. The LaVA genome structure is similar to that of members of the genus Potyvirus and contains an open reading frame encoding a large putative polyprotein of 3,120 amino acids (aa) with conserved motifs. The complete genome shared 48%-56% nucleotide sequence identity and the polyprotein shared 41%-52% aa sequence identity with those of other potyviruses. These values are below the standard thresholds for potyvirus species demarcation. Phylogenetic analysis based on polyprotein sequences showed that LaVA belongs to the genus Potyvirus. To our knowledge, this is the first report of the complete genome sequence and genome characterization of a potyvirus infecting Lamprocapnos spectabilis.

A Supramolecular Hydrogel Enabled by the Synergy of Hydrophobic Interaction and Quadruple Hydrogen Bonding.

The increasing preference for minimally invasive surgery requires novel soft materials that are injectable, with rapid self-healing abilities, and biocompatible. Here, by utilizing the synergetic effect of hydrophobic interaction and quadruple hydrogen bonding, an injectable supramolecular hydrogel with excellent self-healing ability was synthesized. A unique ABA triblock copolymer was designed containing a central poly(ethylene oxide) block and terminal poly(methylmethacrylate) (PMMA) block, with ureido pyrimidinone (UPy) moieties randomly incorporated (termed MA-UPy-PEO-UPy-MA). The PMMA block could offer a hydrophobic microenvironment for UPy moieties in water and thus boost the corresponding quadruple hydrogen bonding interaction of Upy–Upy dimers. Owing to the synergetic effect of hydrophobicity and quadruple hydrogen bonding interaction, the obtained MA-UPy-PEO-UPy-MA hydrogel exhibited excellent self-healing properties, and injectable capability, as well as superior mechanical strength, and therefore, it holds great promise in tissue engineering applications, including in cell support and drug release.

Mussel-inspired polymeric coatings with the antifouling efficacy controlled by topologies.

Block copolymers with different topologies (linear, loop, 3-armed and 4-armed polymers) containing poly(N-vinylpyrrrolidone) (PVP) antifouling blocks and terminal poly(dopamine-acrylamide) (PDAA) anchoring blocks were synthesized. These polymers can form a robust antifouling nanolayer on various surfaces. The morphologies of the polymer-modified surfaces are strongly dependent on the topologies of the polymers: with the increase of arm numbers, the morphology evolves from the smooth surface to the nanoscale coarse surface. As a result, the hydrophilicity of the coatings increases with the increase of degree of nanoscale roughness, and the 4-armed block copolymer forms a superhydrophilic surface with a water contact angle (WCA) as low as 8.7°. Accordingly, the linear diblock copolymer exhibits the worst antifouling efficiency, while the 4-armed polymer exhibits the best antifouling efficiency. This is the first example systematically showing that the antifouling efficacy could be adjusted simply by the topology of the coatings. Cell viability studies revealed that all of the copolymers exhibit excellent cytocompatibility. These biocompatible polymers with narrowly distributed molecular weight might find niches for antifouling applications in various areas such as anti-protein absorption, anti-bacterial and anti-marine fouling.

Research Progress of circRNAs in Glioblastoma.

Circular RNAs (circRNAs) are a class of single-stranded covalently closed non-coding RNAs without a 5′ cap structure or 3′ terminal poly (A) tail, which are expressed in a variety of tissues and cells with conserved, stable and specific characteristics. Glioblastoma (GBM) is the most aggressive and lethal tumor in the central nervous system, characterized by high recurrence and mortality rates. The specific expression of circRNAs in GBM has demonstrated their potential to become new biomarkers for the development of GBM. The specific expression of circRNAs in GBM has shown their potential as new biomarkers for GBM cell proliferation, apoptosis, migration and invasion, which provides new ideas for GBM treatment. In this paper, we will review the biological properties and functions of circRNAs and their biological roles and clinical applications in GBM.

Complete genome sequence of a recombinant isolate of yambean mosaic virus from Canavalia ensiformis.

The complete genome sequence of a Brazilian isolate of yambean mosaic virus (YBMV) is presented. High-throughput sequencing (Illumina HiSeq) and Sanger sequencing revealed the complete genome sequence of the YBMV-BRA-6 isolate, found in Canavalia ensiformis. The de novo contigs were assembled into a 9612 nucleotides (nt) long scaffold, excluding the 3'-terminal poly(A) tail, covering the complete genome. The genomic RNA contains an open reading frame (ORF) typical of members of the genus Potyvirus, family Potyviridae, encoding a large putative polyprotein of 3078 amino acids (aa) and a small overlapping PIPO ORF. Pairwise comparisons showed that the YBMV-BRA-6 isolate sequence shares 88.1% nt identity for the complete genome and 90.6% aa identity for the polyprotein with the YBMV-SR isolate. Phylogenetic analysis grouped both isolates together and close to bean common mosaic virus (BCMV). The polyprotein cleavage sites were predicted and a recombination event is described.

Complete genome sequence and genome organization of scorzonera virus A (SCoVA), a novel member of the genus Potyvirus.

The complete genomic sequence of scorzonera virus A (SCoVA) from a Scorzonera austriaca Willd. plant in South Korea was determined by high-throughput sequencing and confirmed by Sanger sequencing. The SCoVA genome contains 9867 nucleotides, excluding the 3'-terminal poly(A) tail. The SCoVA genome structure is typical of potyviruses and contains a single open reading frame encoding a large putative polyprotein of 3168 amino acids. Pairwise comparison analysis of the complete genome and polyprotein sequences of SCoVA with those of other potyviruses showed that they shared the highest nucleotide and amino acid sequences identity (54.47% and 49.57%, respectively) with those of lettuce mosaic virus (GenBank accession number KJ161185). Phylogenetic analysis of the amino acid sequence of the polyprotein confirmed that SCoVA belongs to the genus Potyvirus. These findings suggest that SCoVA should be considered a novel member of the genus Potyvirus, family Potyviridae.

The unique genome organization of two novel fusariviruses hosted by the true morel mushroom Morchella esculenta

Two putative mycoviruses belonging to the proposed family “Fusariviridae” were identified in Morchella esculenta by sequencing of double-stranded RNAs extracted from the morel mushroom. These viruses were tentatively named “Morchella esculenta fusarivirus 1″ (MeFV1) and “Morchella esculenta fusarivirus 2″ (MeFV2). Including the poly(A) tail the complete genomes of MeFV1 and MeFV2 are composed of 9096 and 9011 nucleotides (nt) respectively. Both genomes contain four non-overlapping open reading frames (ORFs) in which the largest and the smallest ORFs are ORF2 and ORF3 for both genomes respectively. The ORF1 of MeFV1 and MeFV2 are preceded by the 5′ untranslated regions (UTRs) of 27 and 37 nt respectively and encode 341 and 339 aa long proteins that do not exhibit significant similarity to any of the protein sequences present in GenBank database. The 1502 and 1511 aa long proteins encoded by ORF2 of MeFV1 and MeFV2 share 84.42% sequence identity to each other and are 58.54% and 58.57% identical to the RNA-dependent RNA polymerase (RdRp) of Morchella importuna fusarivirus 1 (MiFV1) respectively. Interestingly, a Promethin/LDAF1 protein domain that is associated with the endoplasmic reticulum (ER) and lipid droplet (LD) membranes was identified at the N terminal regions of MeFV1 and MeFV2 RdRps, implying that the replication of these viruses is linked to the lipid membranes. The ORF3 and ORF4 of MeFV1 and MeFV2 encode proteins (268 and 333 aa long, and 645 and 647 aa long respectively) that only share significant sequence similarities with the proteins encoded by the ORF2 and ORF3 of MiFV1 respectively. The 3′ UTRs of MeFV1 and MeFV2 are 162 and 159 nt long respectively and both of them have 51 nt long terminal poly(A) traits. To our knowledge, MeFV1 and MeFV2 are the first fusariviruses identified in M. esculenta and this is the first study reporting on the presence of Promethin/LDAF1 domain in viral RdRps.

Complete genome sequence of viola mottle virus, revealing its synonymous relationship to tulip virus X.

Viola mottle virus (VMoV) was discovered in Viola odorata showing symptoms of reduced growth, leaf mottling, and whitish stripes on flowers in northern Italy in 1977. This virus has been provisionally classified as a member of the genus Potexvirus based on its morphological, serological, and biological characteristics. However, since genetic information of VMoV has never been reported, the taxonomic status of this virus is unclear. Here, we report the first complete genome sequence of VMoV to clarify its taxonomic position. Its genomic RNA is 6,052 nucleotides long, excluding the 3'-terminal poly(A) tail, and has five open reading frames (ORFs) typical of potexviruses. Among potexviruses, VMoV showed the most similarity to tulip virus X (TVX) with 81.1-81.2% nucleotide and 90.4-90.7% amino acid sequence identity in ORF1 and 82.9-83.5% nucleotide and 93.2-95.2% amino acid sequence identity in ORF5. These values are much higher than the species demarcation threshold for the genus. Phylogenetic analysis also indicated that VMoV is nested within the clade of TVX isolates. These data demonstrate that VMoV and TVX are members of the same species.

Molecular and biological characterization of Potato virus Y detected in zucchini in China.

The online version contains supplementary material available at 10.1007/s13337-020-00647-2.

Complete genome analysis of a divergent isolate of narcissus yellow stripe virus from China

The complete sequence of ZZ-2, a narcissus yellow stripe virus (NYSV) isolate identified from Chinese narcissus sample in China, was determined. Its entire RNA genomes comprised 9654 nucleotides (nt) in length, excluding the 3′-terminal poly(A) tail and encoded a polyprotein of 3105 amino acids (aa), flanked by 5′ and 3′ untranslated regions (UTR) of 130 and 206 nts, respectively. Sequence analyses indicated that ZZ-2 shared highest 94% nt and 97% aa sequence identities with NYSV NY-CB5 and NY-EH173 isolates at the polyprotein level, whereas only 75% nt and 79% aa identities respectively with the representative of NYSV isolate (NYSV-Zhangzhou), which are less than the threshold values of the proposed species demarcation for the genus Potyvirus. However, ZZ-2 shared more than 81%–97% nt and 83%–99% aa sequence identities with all NYSV isolates in the coat protein, respectively, but less than 80% aa sequences with NLSYV isolates. Phylogenetic analysis revealed that ZZ-2 clustered together with NY-CB5 and NY-EH173. This suggests that ZZ-2, NY-CB5 and NY-EH173 represent a divergent group of NYSV isolates but share specific motifs in the cleavage sites at the junction of P1/HC-Pro and P3/6K1, which are differed from those of NLSYV isolates.

Complete genome sequence of a novel foveavirus isolated from Allium sativum L. in China

The complete genome sequence of a novel foveavirus identified in garlic (Allium sativum L.) in China was determined using RNA-seq, reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. The entire genomic RNA (GenBank accession MT981417) is 8748 nucleotides long excluding the 3'-terminal poly(A) tail and contains five open reading frames (ORFs). These ORFs encode the viral replicase, a triple gene block, and a coat protein. The virus was tentatively named "garlic yellow stripe associated virus" (GarYSaV). Pairwise comparisons of protein sequences show that GarYSaV encodes proteins that share less than 47% identity with those of other foveaviruses, suggesting that it represents a new species in the genus. Phylogenetic analysis of amino acid sequences of the replicase and CP confirm that GarYSaV is a member of the genus Foveavirus. To our knowledge, this is the first report of a foveavirus in a monocot plant.

Complete genome sequence of pleioblastus mosaic virus, a distinct member of the genus Potyvirus.

Pleioblastus mosaic virus (PleMV) is a tentative member of the genus Potyvirus in the family Potyviridae and was discovered in bamboo with mosaic symptoms in Tokyo, Japan. Since no information on the genome sequence of PleMV has been reported, its taxonomic position has long been uncertain. Here, we report the first complete genome sequences of two distinct PleMV isolates. Excluding the 3'-terminal poly(A) tail, their genomic RNA sequences consist of 9,634 and 9,643 nucleotides (nt); both contain a large open reading frame (ORF) encoding a polyprotein and a small ORF termed PIPO. The large ORFs of the two isolates share 79.2% and 87.6% sequence identity at the nucleotide (nt) and amino acid (aa) level, respectively, and were found to have the highest nt and aa sequence identity (69.0% and 69.9%) to the potyvirus johnsongrass mosaic virus (JGMV). Phylogenetic analysis showed that PleMV is most closely related to JGMV but forms its own clade. These results suggest that PleMV is a distinct member of the genus Potyvirus.

Complete genome sequence of a new achyranthes virus A isolate from Achyranthes bidentata in China.

We have determined the complete genomic sequence of a potyvirus from Achyranthes bidentata in Zhejiang, China, using reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE) PCR. The genomic RNA is 9482 nucleotides (nt) long excluding the 3'-terminal poly(A) tail and encodes a putative large polyprotein with 3073 amino acids (aa). It has 75.4-53.5% nt sequence identity and 84.0-49.1% polyprotein sequence identity to other potyviruses and is probably a distantly related isolate of the same species as the recently reported achyranthes virus A isolate from South Korea (AcVA-SK). This is the first report of the occurrence of a potyvirus infecting A. bidentata in China.