CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

Abstract Background The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. Results We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR) are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. Conclusions CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas

The phytochemicals and health benefits of Cyclocarya paliurus (Batalin) Iljinskaja

Cyclocarya paliurus (C. paliurus), a nutritional and nutraceutical resource for human and animal diets, has been constantly explored. The available biological components of C. paliurus were triterpenoids, polysaccharides, and flavonoids. Recent studies in phytochemical-phytochemistry; pharmacological-pharmacology has shown that C. paliurus performed medicinal value, such as antihypertensive, antioxidant, anticancer, antimicrobial, anti-inflammatory and immunological activities. Furthermore, C. paliurus and its extracts added to drinks would help to prevent and mitigate chronic diseases. This review provides an overview of the nutritional composition and functional applications of C. paliurus, summarizing the research progress on the extraction methods, structural characteristics, and biological activities. Therefore, it may be a promising candidate for developing functional ingredients in traditional Chinese medicine. However, a more profound understanding of its active compounds and active mechanisms through which they perform biological activities is required. As a result, the plant needs further investigation in vitro and in vivo

The impact of road environments on rural periodic market travel satisfaction: a heterogeneity analysis of travel modes

IntroductionTravel satisfaction as experienced by rural residents is closely related to personal physical and mental health, as well as rural economic conditions. An improved rural road environment can be expected to enhance villagers’ satisfaction with regards to visits to markets, but to date this has not been established empirically.MethodsIn this study, a questionnaire was designed to obtain local residents’ evaluations of road environment characteristics for periodic market travel. And we use an Oprobit regression model and Importance-Performance Map Analysis (IPMA) to explore the heterogeneity of the 14 key elements of the “home-to-market” road environment impact on villagers’ satisfaction under different modes of travel.ResultsThe results of the study reveal that villagers expressed dissatisfaction with the current lack of sidewalks and non-motorized paths, and except for road traffic disturbances and road deterioration, which did not significantly affect mode of travel, other factors proved significant. Significantly, bus services are associated with a significant positive effect on walking, non-motorized and bus travel satisfaction, while distance travel also affects walking, non-motorized and motorized travel satisfaction. It is worth noting that greening and service facilities negatively affect motorized travel satisfaction. In summary, road width, sidewalks, bus service, and road deterioration, are among the elements most in need of urgent improvement for all modes of travel.DiscussionThe characteristics of the road environment that influence satisfaction with travel to the periodic market vary by travel mode, and this study is hoped to provide data support and optimization recommendations for the improvement of the rural road environment in China and other countries

Unlocking the mystery of the hard-to-sequence phage genome: PaP1 methylome and bacterial immunity

BACKGROUND: Whole-genome sequencing is an important method to understand the genetic information, gene function, biological characteristics and survival mechanisms of organisms. Sequencing large genomes is very simple at present. However, we encountered a hard-to-sequence genome of Pseudomonas aeruginosa phage PaP1. Shotgun sequencing method failed to complete the sequence of this genome. RESULTS: After persevering for 10 years and going over three generations of sequencing techniques, we successfully completed the sequence of the PaP1 genome with a length of 91,715 bp. Single-molecule real-time sequencing results revealed that this genome contains 51 N-6-methyladenines and 152 N-4-methylcytosines. Three significant modified sequence motifs were predicted, but not all of the sites found in the genome were methylated in these motifs. Further investigations revealed a novel immune mechanism of bacteria, in which host bacteria can recognise and repel modified bases containing inserts in a large scale. This mechanism could be accounted for the failure of the shotgun method in PaP1 genome sequencing. This problem was resolved using the nfi(-) mutant of Escherichia coli DH5α as a host bacterium to construct a shotgun library. CONCLUSIONS: This work provided insights into the hard-to-sequence phage PaP1 genome and discovered a new mechanism of bacterial immunity. The methylome of phage PaP1 is responsible for the failure of shotgun sequencing and for bacterial immunity mediated by enzyme Endo V activity; this methylome also provides a valuable resource for future studies on PaP1 genome replication and modification, as well as on gene regulation and host interaction. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/1471-2164-15-803) contains supplementary material, which is available to authorized users

Protocol for bacterial typing using Fourier transform infrared spectroscopy

[EN]The Fourier transform infrared (FT-IR) signals obtained from bacterial samples are specific and reproducible, making FT-IR an efficient tool for bacterial typing at a subspecies level. However, the typing accuracy could be affected by many factors, including sample preparation and spectral acquisition. Here, we present a unified protocol for bacterial typing based on FT-IR spectroscopy. We describe sample preparation from bacterial culture and FT-IR spectrum collection. We then detail FT-IR spectrum preprocessing and multivariate analysis of spectral data for bacterial typing.SIThis work was supported by Moutai Group Research and Development Project (no. 2018023) and the National Natural Science Foundation of China (nos. 31470786, U1904196, 82073699, and 21275032)

Altered Brain Fraction Amplitude of Low Frequency Fluctuation at Resting State in Patients With Early Left and Right Bell’s Palsy: Do They Have Differences?

Purpose: Bell’s palsy refers to acute idiopathic unilateral facial nerve palsy. It is a common disorder of the main motor pathway to the facial muscles. This study aimed to investigate the abnormal fraction amplitude of low frequency fluctuation (fALFF) of the brain in patients with early left and right Bell’s palsy.Materials and Methods: Sixty-seven patients (left 33, right 34) and 37 age- and sex-matched healthy controls underwent resting-state functional magnetic resonance imaging (R-fMRI) examination. The fALFF values were measured from all subjects and were compared among the left palsy, right palsy, and control groups. Then, correlations between the Toronto Facial Grading System (TFGS) scores of the patients and the fALFF values of abnormal brain regions were analyzed.Results: Significant group differences in fALFF values among the three groups were observed mainly in the cerebral cortical, subcortical, and deep gray matter regions. Compared with the right Bell’s palsy group, the left Bell’s palsy group showed significantly decreased fALFF values in the left temporal pole of the superior temporal gyrus (TPOsup), right supramarginal, left and right middle cingulate cortex (MCC), left superior frontal gyrus (SFG), and left precentral gyrus (PreCG), and increased fALFF values were observed in the right SFG and PreCG. Furthermore, altered fALFF values correlated positively with the TFGS scores in the left superior TPO, bilateral MCC, and right PreCG, and correlated negatively with the TFGS scores in the right SFG of the left Bell’s palsy group. Altered fALFF values correlated positively with the TFGS scores in the bilateral MCC and right PreCG and correlated negatively with the TFGS scores in the left superior TPO and SFG of the right Bell’s palsy group.Conclusion: Regulatory mechanisms seem to differ between patients with left and right early Bell’s palsy. The severity of the disease is associated with these functional alterations

Small interfering RNA targeting mcl-1 enhances proteasome inhibitor-induced apoptosis in various solid malignant tumors

<p>Abstract</p> <p>Background</p> <p>Targeting the ubiquitin-proteasome pathway is a promising approach for anticancer strategies. Recently, we found Bik accumulation in cancer cell lines after they were treated with bortezomib. However, recent evidence indicates that proteasome inhibitors may also induce the accumulation of anti-apoptotic Bcl-2 family members. The current study was designed to analyze the levels of several anti-apoptotic members of Bcl-2 family in different human cancer cell lines after they were treated with proteasome inhibitors.</p> <p>Methods</p> <p>Different human cancer cell lines were treated with proteasome inhibitors. Western blot were used to investigate the expression of Mcl-1 and activation of mitochondrial apoptotic signaling. Cell viability was investigated using SRB assay, and induction of apoptosis was measured using flow cytometry.</p> <p>Results</p> <p>We found elevated Mcl-1 level in human colon cancer cell lines DLD1, LOVO, SW620, and HCT116; human ovarian cancer cell line SKOV3; and human lung cancer cell line H1299, but not in human breast cancer cell line MCF7 after they were treated with bortezomib. This dramatic Mcl-1 accumulation was also observed when cells were treated with other two proteasome inhibitors, MG132 and calpain inhibitor I (ALLN). Moreover, our results showed Mcl-1 accumulation was caused by stabilization of the protein against degradation. Reducing Mcl-1 accumulation by Mcl-1 siRNA reduced Mcl-1 accumulation and enhanced proteasome inhibitor-induced cell death and apoptosis, as evidenced by the increased cleavage of caspase-9, caspase-3, and poly (ADP-ribose) polymerase.</p> <p>Conclusions</p> <p>Our results showed that it was not only Bik but also Mcl-1 accumulation during the treatment of proteasome inhibitors, and combining proteasome inhibitors with Mcl-1 siRNA would enhance the ultimate anticancer effect suggesting this combination might be a more effective strategy for cancer therapy.</p

PIEZO1 acts as a cancer suppressor by regulating the ROS/Wnt/β‐catenin axis

Abstract Background PIEZO1 works differently in different cancers and at different stages of development. The objective of the current study was to explore the function and underlying mechanism of PIEZO1 in lung adenocarcinoma (LUAD) cells. Methods Different LUAD cell lines were treated with PIEZO1 inhibitor (GsMTx4) and agonist (Yoda1), and the expression of PIEZO1 in LUAD cells was detected using real‐time quantitative PCR (RT‐qPCR) and western blotting. The effects of PIEZO1 on invasion, migration and epithelial‐mesenchymal transition (EMT) markers protein expression of LUAD cells were detected using the MTT assay, flow cytometry, transwell assay, wound‐healing assay, and western blotting. Reactive oxygen species (ROS) agonists (BAY 87–2243) and inhibitors (NAC) and Wnt/β‐catenin pathway inhibitors (iCRT3) were selected to treat A549 cells to investigate the mechanism of PIEZO1 on ROS production and Wnt/β‐catenin expression in A549 cells. Results In A549, NCI‐H1395, and NCI‐H1975 cells, GsMTx4 promoted cell proliferation, invasion, migration, upregulated EMT‐related marker protein expression, and inhibited cell apoptosis, while Yoda1 exerted effects opposite to those of GsMTx4. In A549 cells, GsMTx4 can reduce ROS production, it also inhibited ROS production, apoptosis, and downregulated proapoptotic markers induced by BAY 87–2243. Importantly, BAY 87–2243 blocked the effect of GSMTX4‐induced Wnt/β‐catenin overexpression. Similarly, Yoda1 can reduce the effect of NAC. In addition, iCRT3 can block the upregulation of EMT‐related marker proteins by GsMTx4, and increase apoptosis and decrease cell invasion and migration. Conclusion In summary, PIEZO1 acts as a cancer suppressor by regulating the ROS/Wnt/β‐catenin axis, providing a new perspective on the role of mechanosensitive channel proteins in cancer

Glucose conversion to 5-hydroxymethylfurfural on zirconia : tuning surface sites by calcination temperatures

The influence of calcination temperature on ZrO2 and its catalytic activity in glucose conversion was studied in this research. It shows that different structure of ZrO2 can be obtained by tuning calcination temperature, which results in the various surface catalytic properties. Quantitative evaluation of acidity by NH3-TPD and solid-state NMR spectroscopy shows that ZrO2 calcined at 300 °C, which is in amorphous state and has a higher BET surface area, possesses more Brønsted and Lewis acid sites than ZrO2 samples calcined at other temperatures. Amorphous ZrO2 shows a better catalytic performance in glucose conversion, nearly 100% glucose conversion with an HMF selectivity of about 40%. Increasing calcination temperature leads to a result of sintering, crystallizing, and pore collapsing of ZrO2. There is a distinct decrease in Brønsted acid sites, along with a decrease of the total number of acid sites in ZrO2 as calcination temperature increases. At the same time, a new type of Lewis acid appears at a downfield shift, resulting in different reaction rates