Morphological Transitions of a Photoswitchable Aramid Amphiphile Nanostructure.

Self-assembly of small amphiphilic molecules in water can lead to nanostructures of varying geometries with pristine internal molecular organization. Here we introduce a photoswitchable aramid amphiphile (AA), designed to exhibit extensive hydrogen bonding and robust mechanical properties upon self-assembly, while containing a vinylnitrile group for photoinduced cis-trans isomerization. We demonstrate spontaneous self-assembly of the vinylnitrile-containing AA in water to form nanoribbons. Upon UV irradiation, trans-to-cis isomerizations occur concomitantly with a morphological transition from nanoribbons to nanotubes. The nanotube structure persists in water for over six months, stabilized by strong and collective intermolecular interactions. We demonstrate that the nanoribbon-to-nanotube transition is reversible upon heating and that switching between states can be achieved repeatedly. Finally, we use electron microscopy to capture the transition and propose mechanisms for nanoribbon-to-nanotube rearrangement and vice versa. The stability and switchability of photoresponsive AA nanostructures make them viable for a range of future applications.

Genetic differences between Korean and American isolates of Petunia vein clearing virus.

Petunia plants are used for urban landscaping in many parts of the world, including South Korea. In this study, we aimed to investigate the occurrence of petunia vein clearing virus (PVCV) infection in petunia plants in Seoul, South Korea. PVCV was detected from 23 of 79 petunia samples collected from Seoul. We obtained the complete genome sequences of the Korean isolates in this study (called PVCV-Kr, Kr2, and Kr3), which were compared with the genome sequence of the USA isolate of the virus (PVCV-USA). The genomic DNA of the three PVCV isolates was found to comprise 7210-7267 nucleotides (nts), which is 4-15 nts longer than the PVCV-USA genome. The genomes of the Kr and Kr2 isolates encode a large polyprotein of 252 kDa (2180 amino acids (aa)). The genome of the Kr3 isolate encodes a large polyprotein of 255 kDa (2203 aa). The polyprotein has six protein domains: a movement protein (MP; 72 aa), a coiled-coil domain (CC; 33 aa), an RNA-binding domain (RB; 18 aa), a protease (PR; 21 aa), a reverse transcriptase (RT; 196 aa), and an RNase H (RH; 121 aa). The large polyprotein and six domains of the three isolates showed 93.9-100.0% sequence homology with those of PVCV-USA. Furthermore, the polymerase polyprotein gene (PR, RT, and RH) of the four PVCV isolates containing the USA isolate grouped with those of Rice tungro bacilliform virus and Soybean chlorotic mottle virus, which belong to the same family (Caulimoviridae). Our findings suggested that the Korean isolates represent a new isolate of PVCV. To our knowledge, this is the first report of PVCV detection in South Korea.

ICTV Virus Taxonomy Profile: Virgaviridae.

The family Virgaviridae is a family of plant viruses with rod-shaped virions, a ssRNA genome with a 3'-terminal tRNA-like structure and a replication protein typical of alpha-like viruses. Differences in the number of genome components, genome organization and the mode of transmission provide the basis for genus demarcation. Tobacco mosaic virus (genus Tobamovirus) was the first virus to be discovered (in 1886); it is present in high concentrations in infected plants, is extremely stable and has been extensively studied. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the taxonomy of the Virgaviridae, which is available at www.ictv.global/report/virgaviridae.

Acetic acid chromoendoscopy for determining the extent of gastric intestinal metaplasia.

BACKGROUND AND AIMS: The diagnosis of gastric intestinal metaplasia (IM) is currently performed by histologic assessment of multiple endoscopic biopsies, methylene blue chromoendoscopy, or narrow-band imaging with magnification. However, practical and readily available methods are lacking. We assessed the diagnostic accuracy and reproducibility of acetic acid chromoendoscopy (AAC) for determining the extent of gastric IM. METHODS: One hundred twenty-six participants were enrolled. The participants underwent screening EGD with 1.5% acetic acid instillation for the detection of acetowhite reaction. Subsequently, targeted biopsies were performed at the 5 standard intra-gastric locations of the updated Sydney system. The accuracy of AAC was calculated using the histology results as a reference. Two endoscopists, each of whom was blinded to the other's result, determined the presence or absence of acetowhite reaction. RESULTS: The overall diagnostic accuracy of AAC was 89.0%, and the sensitivity and specificity were 77.6% and 94.4%, respectively. The specificity for the gastric body was >94%. The proportion of extensive IM, a strong risk factor for gastric cancer, increased from 0.9% to 18.1% when AAC was used instead of conventional EGD alone (P < .001). Endoscopically determined atrophy had a negative effect on the diagnosis of AAC (odds ratio, 3.012; 95% confidence interval, 1.625-5.583). There was substantial inter- and intra-observer agreement. CONCLUSIONS: AAC is a valid and reproducible tool for determining the extent of gastric IM and may serve as a practical method of identifying populations at high risk of gastric cancer. (Clinical trial registration number: NCT01499576.).

A pepper mottle virus-based vector enables systemic expression of endoglucanase D in non-transgenic plants.

Plant-virus-based expression vectors have been used as an alternative to the creation of transgenic plants. Using a virus-based vector, we investigated the feasibility of producing the endoglucanase D (EngD) from Clostridium cellulovorans in Nicotiana benthamiana. This protein has endoglucanase, xylanase, and exoglucanase activities and may be of value for cellulose digestion in the generation of biofuels from plant biomass. The EngD gene was cloned between the nuclear inclusion b (NIb)- and coat protein (CP)-encoding sequences of pSP6PepMoV-Vb1. In vitro transcripts derived from the clone (pSP6PepMoV-Vb1/EngD) were infectious in N. benthamiana but caused milder symptoms than wild-type PepMoV-Vb1. RT-PCR amplification of total RNA from non-inoculated upper leaves infected with PepMoV-Vb1/EngD produced the target band for the CP, partial NIb and EngD-CP regions of PepMoV-V1/EngD, in addition to nonspecific bands. Western blot analysis showed the CP target bands of PepMoV-Vb1/EngD as well as non-target bands. EngD enzymatic activity in infected plants was detected using a glucose assay. The plant leaves showed increased senescence compared with healthy and PepMoV-Vb1-infected plants. Our study suggests the feasibility of using a viral vector for systemic infection of plants for expression of heterologous engD for the purpose of digesting a cellulose substrate in plant cells for biomass production.

The complete genome sequence of a member of a new species of tobamovirus (rattail cactus necrosis-associated virus) isolated from Aporcactus flagelliformis.

In this study, we identified a new tobamovirus from diseased Aporcactus flagelliformis cactus plants, named it rattail cactus necrosis-associated virus (RCNaV), and determined its complete genome sequence. The full RCNaV genome consisted of 6,506 nucleotides and contained four open reading frames coding for proteins of M(r) 128 kDa (3,441 nt), 185 kDa (4,929 nt), 55 kDa (1452 nt), 36 kDa (1,005 nt) and 19 kDa (513 nt) from the 5' to 3' end, respectively. The overall similarities for the four ORFs of RCNaV were from 32.5% to 64.1% and from 17.0% to 67.3% to those of the other tobamoviruses, at the nucleotide and amino acid level, respectively. Comparison of the coding and non-coding regions of the virus with those of other tobamoviruses showed that RCNaV is the most closely related to cactus mild mottle virus.

An effective instillation method for water-assisted colonoscopy as performed by in-training endoscopists in terms of volume and temperature.

BACKGROUND AND STUDY AIMS: There is general consensus that water instillation helps insert a colonoscope. However, the most effective method for water instillation has not yet been established, especially for endoscopists-in-training. The aim of this study was to determine volume and temperature for effective water instillation colonoscopy. PATIENTS AND METHODS: This is a prospective, randomized, controlled trial that was carried out at a single center, and a total of 207 consecutive subjects who underwent colonoscopic examination for health checkup were included in the study. Water instillation of supplied water was conducted under four different conditions: 100 and 300 ml at room temperature, 300 ml at 30 °C and no use of water instillation. The following parameters were recorded and analyzed: intubation success rate, independent predictors of successful intubation and intubation time to reach the cecum. RESULTS: The intubation success rate was not significantly different between individual groups. Independent predictors of successful intubation were younger age (P = 0.004) and later examined subjects (P = 0.016). The 300-ml warm water instillation during colonoscopy significantly reduced intubation time over the conventional method without water instillation (P = 0.034). CONCLUSIONS: Instillation of 300-ml warm (30 °C) water during colonoscopy can reduce cecal intubation time for in-training endoscopists without improving the intubation success rate.

Comparison of one-stage laparoscopic common bile duct exploration plus cholecystectomy and two-stage endoscopic sphincterotomy plus laparoscopic cholecystectomy for concomitant gallbladder and common bile duct stones in patients over 80 years old.

Purpose: This study was performed to compare the safety and efficacy of one-stage laparoscopic common bile duct exploration (LCBDE) plus laparoscopic cholecystectomy (LC) with those of endoscopic sphincterotomy (EST) plus LC for concomitant gallbladder (GB) and common bile duct (CBD) stones in elderly patients. Methods: This single-center retrospective study reviewed the medical records of patients aged >80 years who were diagnosed with concomitant GB and CBD stones between January 2010 and December 2020. Results: Of the 137 patients included in this study, 46 underwent one-stage LCBDE + LC and 91 underwent two-stage EST + LC. The frequency of previous gastrectomy (23.9% vs. 5.5%, p = 0.002) and multiple stones (76.1% vs. 49.5%, p = 0.003) was higher in the LCBDE + LC group than in the EST + LC group. Further, patients in LCBDE + LC group had larger CBD stones (11.9 mm vs. 6.0 mm, p < 0.001). There were no significant differences in the clearance (91.3% vs. 95.6%, p = 0.311) and recurrence (4.3% vs. 8.8%, p = 0.345) rates between the groups. The incidence of posttreatment overall complications (17.4% vs. 22.0%, p = 0.530) and total hospital stay (12.7 days vs. 11.7 days, p = 0.339) were similar in the two groups. Conclusion: One-stage LCBDE + LC is a safe and effective treatment for concomitant GB and CBD stones, even in elderly patients, and may be considered as the first treatment option in elderly patients with previous gastrectomy, multiple large (≥ 15 mm) CBD stones, or inability to cooperate with endoscopic procedures.

The complete genome sequence and genome structure of passion fruit mosaic virus.

In this study, we determined the complete sequence of the genomic RNA of a Florida isolate of maracuja mosaic virus (MarMV-FL) and compared it to that of a Peru isolate of the virus (MarMV-P) and those of other known tobamoviruses. Complete sequence analysis revealed that the isolate should be considered a member of a new species and named passion fruit mosaic virus (PafMV). The genomic RNA of PafMV consists of 6,791 nucleotides and encodes four open reading frames (ORFs) coding for proteins of 125 kDa (1,101 aa), 184 kDa (1,612 aa), 34 kDa (311 aa) and 18 kDa (164 aa) in consecutive order from the 5' to the 3' end. The sequence homologies of the four ORFs of PafMV were from 78.8% to 81.6% to those of MarMV-P at the amino acid level. The sequence homologies of the four ORFs of PafMV ranged from 36.0% to 77.9% and from 21.7% to 81.6% to those of other tobamoviruses, at the nucleotide and amino acid level, respectively. Phylogenetic analysis revealed that these PafMV-encoded proteins are closely related to those of MarMV-P. In conclusion, the results indicate that PafMV and MarMV-P belong to different species within the genus Tobamovirus.

A multiplex PCR assay for the simultaneous detection of five potexviruses infecting cactus plants using dual-priming oligonucleotides (DPOs) primers.

Five potexviruses, namely, cactus virus X (CVX), opuntia virus X, pitaya virus X (PiVX), schlumbergera virus X (SchVX) and zygocactus virus X (ZyVX), have been reported in cactus plants. In this report, a multiplex RT-PCR assay, based on specific dual-priming oligonucleotide (DPO) primers, was developed to detect these five viruses simultaneously in field samples. Using 18 field plants comprising 16 cactus species, these viruses were detected among nine of the 18 plants, including the simultaneous detection of CVX, PiVX, SchVX and ZyVX co-infecting an Aporocactus flagelliformis and a Notocactus leninghausii f. cristatus plant. The multiplex PCR assay was thus applied successfully in the field plants and it would be useful in the diagnosis of viral infections in cactus plants.

The Prognostic Impact of HER2 Genetic and Protein Expression in Pancreatic Carcinoma-HER2 Protein and Gene in Pancreatic Cancer.

Pancreatic ductal adenocarcinoma (PDAC) is a lethal and clinically heterogeneous disease with a limited benefit from human epidermal growth factor receptor 2 (HER2)-targeted therapy. Recently, some studies have addressed the antitumoral effect of novel anti-HER2 drugs in HER2 low-expressing tumors. However, there have been few studies on the significance of low HER2 expression and genetic heterogeneity in PDAC. Using immunohistochemistry and dual-color silver-enhanced in situ hybridization based on the Trastuzumab for a gastric cancer scoring scheme, we evaluated HER2 protein expression, gene amplification, and genetic heterogeneity in three groups (HER2-neg, HER2-low, HER2-pos) of 55 patients. Among the 55 cases, 41.8% (23/55) showed HER2 expression of any intensity. HER2 amplification independent of HER2 expression was 25.5% (14/55). Patients in both these groups had a shorter overall survival than did patients in the HER2-neg group. HER2 genetic heterogeneity was identified in 37 (70.9%) of the 55 cases, mainly in HER2-neg and HER2-low groups. HER2 genetic heterogeneity significantly correlated with worse survival in the HER2-low and HER2-neg groups of PDAC. These findings support the hypothesis that low-level HER2 expression and heterogeneity have significant clinical implications in PDAC. HER2 heterogeneity might indicate the best strategies of combination therapies to prevent the development of subdominant clones with resistance potential.

Subcellular localization of the barley stripe mosaic virus triple gene block proteins.

Barley stripe mosaic virus (BSMV) spreads from cell to cell through the coordinated actions of three triple gene block (TGB) proteins (TGB1, TGB2, and TGB3) arranged in overlapping open reading frames (ORFs). Our previous studies (D. M. Lawrence and A. O. Jackson, J. Virol. 75:8712-8723, 2001; D. M. Lawrence and A. O. Jackson, Mol. Plant Pathol. 2:65-75, 2001) have shown that each of these proteins is required for cell-to-cell movement in monocot and dicot hosts. We recently found (H.-S. Lim, J. N. Bragg, U. Ganesan, D. M. Lawrence, J. Yu, M. Isogai, J. Hammond, and A. O. Jackson, J. Virol. 82:4991-5006, 2008) that TGB1 engages in homologous interactions leading to the formation of a ribonucleoprotein complex containing viral genomic and messenger RNAs, and we have also demonstrated that TGB3 functions in heterologous interactions with TGB1 and TGB2. We have now used Agrobacterium tumefaciens-mediated protein expression in Nicotiana benthamiana leaf cells and site-specific mutagenesis to determine how TGB protein interactions influence their subcellular localization and virus spread. Confocal microscopy revealed that the TGB3 protein localizes at the cell wall (CW) in close association with plasmodesmata and that the deletion or mutagenesis of a single amino acid at the immediate C terminus can affect CW targeting. TGB3 also directed the localization of TGB2 from the endoplasmic reticulum to the CW, and this targeting was shown to be dependent on interactions between the TGB2 and TGB3 proteins. The optimal localization of the TGB1 protein at the CW also required TGB2 and TGB3 interactions, but in this context, site-specific TGB1 helicase motif mutants varied in their localization patterns. The results suggest that the ability of TGB1 to engage in homologous binding interactions is not essential for targeting to the CW. However, the relative expression levels of TGB2 and TGB3 influenced the cytosolic and CW distributions of TGB1 and TGB2. Moreover, in both cases, localization at the CW was optimal at the 10:1 TGB2-to-TGB3 ratios occurring in virus infections, and mutations reducing CW localization had corresponding effects on BSMV movement phenotypes. These data support a model whereby TGB protein interactions function in the subcellular targeting of movement protein complexes and the ability of BSMV to move from cell to cell.

[Gut Microbiota and Pancreatobiliary System].

The gut microbiota is part of the human body that is involved in body metabolism and the occurrence of various diseases. Detecting and analyzing their genetic information (microbiome) is as important as analyzing human genes. The core microbiome, the key functional genes shared by all humans, helps better understand the physiology of the human body. Information on the gut microbiome of a diseased person can help diagnose and treat disease. The pancreatobiliary system releases functional antimicrobial substances, such as bile acids and antimicrobial peptides, which affect the gut microbiota directly. In response, the gut microbiota influences pancreatobiliary secretion by controlling the generation and emission of substances through indirect signaling. This crosstalk maintains homeostasis of the pancreatobiliary system secretion and microbiota. Dysbiosis and disease can occur if this fails to work properly. Bile acid therapy has been used widely and may affect the microbial environment in the intestine. An association of the gut microbiota has been reported in many cases of pancreatobiliary diseases, including malignant tumors. Traditionally, most pancreatobiliary diseases are accompanied by infections from the gut microbiota, which is an important target for treatment. The pancreatobiliary system can control its function through physical and drug therapy. This may be a new pioneering field in the study or treatment of the gut microbiota.

The role of the Cucumber mosaic virus 2b protein in viral movement and symptom induction.

The Cucumber mosaic virus (CMV) 2b protein is a counter-defense factor and symptom determinant. Conserved domains in the 2b protein sequence were mutated in the 2b gene of strain Fny-CMV. The effects of these mutations were assessed by infection of Nicotiana tabacum, N. benthamiana, and Arabidopsis thaliana (ecotype Col-0) with mutant viruses and by expression of mutant 2b transgenes in A. thaliana. We confirmed that two nuclear localization signals were required for symptom induction and found that the N-terminal domain was essential for symptom induction. The C-terminal domain and two serine residues within a putative phosphorylation domain modulated symptom severity. Further infection studies were conducted using Fny-CMVdelta2b, a mutant that cannot express the 2b protein and that induces no symptoms in N. tabacum, N. benthamiana, or A. thaliana ecotype Col-0. Surprisingly, in plants of A. thaliana ecotype C24, Fny-CMVdelta2b induced severe symptoms similar to those induced by the wild-type virus. However, C24 plants infected with the mutant virus recovered from disease while those infected with the wild-type virus did not. Expression of 2b transgenes from either Fny-CMV or from LS-CMV (a mild strain) in Col-0 plants enhanced systemic movement of Fny-CMVdelta2b and permitted symptom induction by Fny-CMVdelta2b. Taken together, the results indicate that the 2b protein itself is an important symptom determinant in certain hosts. However, they also suggest that the protein may somehow synergize symptom induction by other CMV-encoded factors.

Generation of infectious transcripts from Korean strain and mild mottle strain of potato virus X.

Full-length cDNAs of two different strains of Potato virus X (PVX-Kr and PVX-Mo) have been directly amplified by long template reverse transcription polymerase chain reaction (RT-PCR) using the 5'-end primer containing a SP6 or T7 RNA promoter sequence and the virus-specific 3'-end primer, and then constructed in plasmid vectors. Capped in vitro transcripts from cloned full-length cDNAs as well as those RT-PCR amplicons proved to be infectious systemically on tobacco plants. Symptom expression on tobacco plants from PVX-Mo transcripts was faster and severer than that from PVX-Kr. In replication stability test of transcripts derived from PVX clones, progeny viruses showed stable replication according to sequencing through passages. This highly infectious transcript system from the full-length cDNA clones for PVX can be useful for recombinant molecules for functional analysis of viral proteins in plant-virus interaction study as well as for expression of foreign protein in planta.

Abnormal cell division caused by inclusion bodies in E. coli; increased resistance against external stress.

Inclusion body formation occurs naturally in prokaryotic cells, but is particularly common when heterologous foreign proteins are overexpressed in bacterial systems. The plant disease virus protein CMV 3a (cucumber mosaic virus movement protein) and the 56 kDa Orientia tsutsugamushi (OT56) protein (an outer membrane protein), which causes tsutsugamushi disease, were expressed in Escherichia coli, and found to form inclusion bodies. Confocal laser scanning microscopy revealed that these inclusion bodies are localized at the cellular poles within E. coli. Cells expressing inclusion bodies appeared to be interconnected, and divided abnormally. The clustered cells exhibited biofilm-like characteristics in that the interior cells of the community were protected by the antibiotic resistance of the outer cells. We compared the number of colony-forming units in inclusion body-forming versus non-forming E. coli to demonstrate the effects of lysozyme, sonication or antibiotic treatment. E. coli clustering provided significantly improved protection against cell disruption/lysis by physical and biochemical stress. This is the first report that shows that abnormal cell division caused by inclusion body formation can cause cellular clustering, resulting in improved resistance to stress in vitro.

Detection of Co-Infection of Notocactus leninghausii f. cristatus with Six Virus Species in South Korea.

Co-infection with two virus species was previously reported in some cactus plants. Here, we showed that Notocactus leninghausii f. cristatus can be co-infected with six different viruses: cactus mild mottle virus (CMMoV)-Nl, cactus virus X (CVX)-Nl, pitaya virus X (PiVX)-Nl, rattail cactus necrosis-associated virus (RCNaV)-Nl, schlumbergera virus X (SchVX)-Nl, and zygocactus virus X (ZyVX)-Nl. The coat protein sequences of these viruses were compared with those of previously reported viruses. CMMoV-Nl, CVX-Nl, PiVX-Nl, RCNaV-Nl, SchVX-Nl, and ZyVX-Nl showed the greatest nucleotide sequence homology to CMMoV-Kr (99.8% identity, GenBank accession NC_011803), CVX-Jeju (77.5% identity, GenBank accession LC12841), PiVX-P37 (98.4% identity, GenBank accession NC_024458), RCNaV (99.4% identity, GenBank accession NC_016442), SchVX-K11 (95.7% identity, GenBank accession NC_011659), and ZyVX-B1 (97.9% identity, GenBank accession NC_006059), respectively. This study is the first report of co-infection with six virus species in N. leninghausii f. cristatus in South Korea.

Quassinoids isolated from Brucea javanica inhibit pepper mottle virus in pepper.

A green fluorescent protein (GFP)-tagged pepper mottle virus (PepMoV) based leaf-disc method and systemic host method were developed to identify antiviral agents. Preliminary experiments using a PepMoV-GFP based leaf-disc method led to the isolation of five quassinoids, including brusatol (1), bruceantin (2), brucein A (3), bruceantinol (4), and brucein B (5), from the CH3OH extract of Brucea javanica. All isolated compounds exhibited inactivation effects in systemic host plants, and compounds 3 and 4 were potent, with a minimum inhibitory concentration of 10µM. Furthermore, compound 3 was found to have a protective effect at the tested concentration of 40µM.

Antiviral Activities of Trichothecenes Isolated from Trichoderma albolutescens against Pepper Mottle Virus.

A bioassay-guided isolation using a green fluorescence protein (GFP)-tagged pepper mottle virus (PepMoV-GFP) based leaf-disk method to obtain new antiviral agents led to the isolation of trichodermin, 1, and a new compound trichoderminol, 2, from EtOAc extract of Trichoderma albolutescens culture medium. The structures of compounds 1 and 2 were determined by MS and NMR experiments, and the absolute configurations of the compounds were established by experimental and calculated vibrational circular dichroism spectra. Compounds 1 and 2 were evaluated for their anti-PepMoV potential in systemic host plants, such as tobacco and pepper, by PepMoV-GFP based systemic host method. All compounds exhibited inactivation effects against PepMoV. Furthermore, compound 1 showed protective effects against PepMoV.