Direct sequencing and analysis of the genomes of newly emerging GII.17 norovirus strains in South China

AIMS

This study aims to develop a quick and sensitive method for obtaining GII.17 norovirus genome sequences based on a novel amplification strategy.

METHODS AND RESULTS

Based on multiple alignments of GII.17 norovirus genome sequences available in GenBank, a set of primer pairs were first rationally designed, which could amplify six overlapping fragments encompassing the whole genome. Two sequencing primers II.17-Seq1R and II.17-Seq6F were also designed to complement sequences at both ends. The sensitivity of new primers was then evaluated by end-point dilution RT-PCR that was comparable to detection primers G2SKF/G2SKR. In practice, genome sequences of nine Guangzhou GII.17 strains were successfully obtained by the new method in one working day. All genomes comprised 7495 nucleotides with three complete ORFs, and their phylogenetic relationships were verified with other GII norovirus reference strains.

CONCLUSIONS

Based on the new amplification strategy, a quick and sensitive method for direct sequencing of GII.17 norovirus genomes was successfully established.

SIGNIFICANCE AND IMPACT OF THE STUDY

The newly developed method can be used as an important tool to collect genetic information of GII.17 noroviruses, and new obtained viral genomes in Guangzhou also provide reference data for norovirus research in future.

Emittance and lifetime measurement with damping wigglers

National Synchrotron Light Source II (NSLS-II) is a new third-generation storage ring light source at Brookhaven National Laboratory. The storage ring design calls for small horizontal emittance (<1 nm-rad) and diffraction-limited vertical emittance at 12 keV (8 pm-rad). Achieving low value of the beam size will enable novel user experiments with nm-range spatial and meV-energy resolution. The high-brightness NSLS-II lattice has been realized by implementing 30-cell double bend achromatic cells producing the horizontal emittance of 2 nm rad and then halving it further by using several Damping Wigglers (DWs). This paper is focused on characterization of the DW effects in the storage ring performance, namely, on reduction of the beam emittance, and corresponding changes in the energy spread and beam lifetime. The relevant beam parameters have been measured by the X-ray pinhole camera, beam position monitors, beam filling pattern monitor, and current transformers. In this paper, we compare the measured results of the beam performance with analytic estimates for the complement of the 3 DWs installed at the NSLS-II.

Functional traits contributed to the superior performance of the exotic species Robinia pseudoacacia: a comparison with the native tree Sophora japonica

Functional traits determine the ecological strategies of plants and therefore are widely considered to feature in the success of invasive species. By comparing a widespread exotic invasive species Robinia pseudoacacia L. with a related native one Sophora japonica L., this research aimed to study strategies of R. pseudoacacia for superior performance from the perspective of functional traits. We conducted a greenhouse experiment in which seedlings of R. pseudoacacia and S. japonica were grown separately under a factorial combination of two light regimes and three levels of nitrogen (N) fertilization, including a control and two levels intended to represent ambient and future levels of N deposition in Chinese forests. After 90 days of treatment, performance and functional traits were determined for the two species, the former referred to as the total biomass (TB) that directly affected fitness. Trait plasticity and integration (the pattern and extent of functional covariance among different plant traits) were analyzed and compared. We found that the two species showed significantly different plastic responses to light increase: in the low-light regime, they were similar in performance and functional traits, while in the high-light regime, R. pseudoacacia achieved a significantly higher TB and a suite of divergent but advantageous functional traits versus S. japonica, such as significantly greater photosynthetic capacity and leaf N concentration, and lower carbon-to-N ratio and root-to-shoot ratio, which conferred it the greater performance. Moreover, across the light gradient, R. pseudoacacia showed higher correlations between photosynthetic capacity and other functional traits than S. japonica. In contrast, N deposition showed little impact on our experiment. Our results suggested that across light regimes, three aspects of functional traits contributed to the superior performance of R. pseudoacacia: functional trait divergence, significantly different plasticity of these traits, as well as greater overall trait coordination.

Comparison of human dental follicle cells and human periodontal ligament cells for dentin tissue regeneration

AIM

To compare the odontogenic potential of human dental follicle cells (DFCs) and periodontal ligament cells (PDLCs).

MATERIALS & METHODS

In vitro and in vivo characterization studies of DFCs and PDLCs were performed comparatively. DFCs and PDLCs were subcutaneously implanted into the dorsum of mice for 8 weeks after combined with treated dentin matrix scaffolds respectively.

RESULTS

Proteomic analysis identified 32 differentially expressed proteins in DFCs and PDLCs. Examination of the harvested grafts showed PDLCs could form the dentin-like tissues as DFCs did. However, the structure of dentin tissues generated by DFCs was more complete.

CONCLUSION

PDLCs could contribute to regenerate dentin-like tissues in the inductive microenvironment of treated dentin matrix. DFCs presented more remarkable dentinogenic capability than PDLCs did.

¹³C Pathway Analysis for the Role of Formate in Electricity Generation by Shewanella Oneidensis MR-1 Using Lactate in Microbial Fuel Cells

Microbial fuel cell (MFC) is a promising technology for direct electricity generation from organics by microorganisms. The type of electron donors fed into MFCs affects the electrical performance, and mechanistic understanding of such effects is important to optimize the MFC performance. In this study, we used a model organism in MFCs, Shewanella oneidensis MR-1, and (13)C pathway analysis to investigate the role of formate in electricity generation and the related microbial metabolism. Our results indicated a synergistic effect of formate and lactate on electricity generation, and extra formate addition on the original lactate resulted in more electrical output than using formate or lactate as a sole electron donor. Based on the (13)C tracer analysis, we discovered decoupled cell growth and electricity generation in S. oneidensis MR-1 during co-utilization of lactate and formate (i.e., while the lactate was mainly metabolized to support the cell growth, the formate was oxidized to release electrons for higher electricity generation). To our best knowledge, this is the first time that (13)C tracer analysis was applied to study microbial metabolism in MFCs and it was demonstrated to be a valuable tool to understand the metabolic pathways affected by electron donors in the selected electrochemically-active microorganisms.

Metabolic engineering of Saccharomyces cerevisiae to produce 1-hexadecanol from xylose

Background

An advantageous but challenging approach to overcome the limited supply of petroleum and relieve the greenhouse effect is to produce bulk chemicals from renewable materials. Fatty alcohols, with a billion-dollar global market, are important raw chemicals for detergents, emulsifiers, lubricants, and cosmetics production. Microbial production of fatty alcohols has been successfully achieved in several industrial microorganisms. However, most of the achievements were using glucose, an edible sugar, as the carbon source. To produce fatty alcohols in a renewable manner, non-edible sugars such as xylose will be a more appropriate feedstock.

Results

In this study, we aim to engineer a Saccharomyces cerevisiae strain that can efficiently convert xylose to fatty alcohols. To this end, we first introduced the fungal xylose utilization pathway consisting of xylose reductase (XR), xylitol dehydrogenase (XDH), and xylulose kinase (XKS) into a fatty alcohol-producing S. cerevisiae strain (XF3) that was developed in our previous studies to achieve 1-hexadecanol production from xylose at 0.4 g/L. We next applied promoter engineering on the xylose utilization pathway to optimize the expression levels of XR, XDH, and XKS, and increased the 1-hexadecanol titer by 171 %. To further improve the xylose-based fatty alcohol production, two optimized S. cerevisiae strains from promoter engineering were evolved with the xylose as the sole carbon source. We found that the cell growth rate was improved at the expense of decreased fatty alcohol production, which indicated 1-hexadecanol was mainly produced as a non-growth associated product. Finally, through fed-batch fermentation, we successfully achieved 1-hexadecanol production at over 1.2 g/L using xylose as the sole carbon source, which represents the highest titer of xylose-based 1-hexadecanol reported in microbes to date.

Conclusions

A fatty alcohol-producing S. cerevisiae strain was engineered in this study to produce 1-hexadecanol from xylose. Although the xylose pathway we developed in this study could be further improved, this proof-of-concept study, for the first time to our best knowledge, demonstrated that the xylose-based fatty alcohol could be produced in S. cerevisiae with potential applications in developing consolidated bioprocessing for producing other fatty acid-derived chemicals.

Electronic supplementary material

The online version of this article (doi:10.1186/s12934-016-0423-9) contains supplementary material, which is available to authorized users.

Utilization of native oxygen in Eu(RE)-doped GaN for enabling device compatibility in optoelectronic applications

The detrimental influence of oxygen on the performance and reliability of V/III nitride based devices is well known. However, the influence of oxygen on the nature of the incorporation of other co-dopants, such as rare earth ions, has been largely overlooked in GaN. Here, we report the first comprehensive study of the critical role that oxygen has on Eu in GaN, as well as atomic scale observation of diffusion and local concentration of both atoms in the crystal lattice. We find that oxygen plays an integral role in the location, stability, and local defect structure around the Eu ions that were doped into the GaN host. Although the availability of oxygen is essential for these properties, it renders the material incompatible with GaN-based devices. However, the utilization of the normally occurring oxygen in GaN is promoted through structural manipulation, reducing its concentration by 2 orders of magnitude, while maintaining both the material quality and the favorable optical properties of the Eu ions. These findings open the way for full integration of RE dopants for optoelectronic functionalities in the existing GaN platform.

Amidoxime-functionalized hydrothermal carbon materials for uranium removal from aqueous solution

Amidoxime-functionalized hydrothermal carbon (AO-HTC) has been synthesized and applied to adsorb U(vi) from aqueous solutions, exhibiting a high selectivity above 60% for a wide pH range from 1.0 to 5.0.

An outbreak of Candida parapsilosis fungemia among preterm infants

In this article, we describe the first outbreak of Candida parapsilosis fungemia in our hospital. We examined a cluster of four nosocomial cases of C. parapsilosis fungemia that occurred in the neonatal intensive care unit (NICU) of the Affiliated Xingtai People's Hospital of Hebei Medical University over a two-week period. We ascertained patient parameters including clinical characteristics, blood and sputum cultures, and drug sensitivity test results. Cultures from eight blood samples obtained from the four infected preterm infants showed identical characteristics and were identified as C. parapsilosis. In order to determine the infection-related factors and to control the spread of the infection among the population, we immediately initiated the emergency plan. All four of the preterm infants recovered from the infection; there were no deaths. Outbreaks of C. parapsilosis, mostly involving preterm infants of very low birth weight or extremely low birth weight, can and do occur in NICUs. Cultures prepared using multiple samples taken from different patients contribute to a more definitive diagnosis. Established measures that control and prevent the infection, as well as effective and comprehensive treatments, can lead to a favorable outcome. That is to say, improving both disinfection and isolation, as well as interrupting the pathway of transmission, is the key to controlling the spread of infection.

Cytoskeletal binding proteins distinguish cultured dental follicle cells and periodontal ligament cells

Human dental follicle cells (DFCs) and periodontal ligament cells (PDLCs) derived from the ectomesenchymal tissue, have been shown to exhibit stem/progenitor cell properties and the ability to induce tissue regeneration. Stem cells in dental follicle differentiate into cementoblasts, periodontal ligament fibroblasts and osteoblasts, these cells form cementum, periodontal ligament and alveolar bone, respectively. While stem cells in dental follicle are a precursor to periodontal ligament fibroblasts, the molecular changes that distinguish cultured DFCs from PDLCs are still unknown. In this study, we have compared the immunophenotypic features and cell cycle status of the two cell lines. The results suggest that DFCs and PDLCs displayed similar features related to immunophenotype and cell cycle. Then we employed an isobaric tag for relative and absolute quantitation (iTRAQ) proteomics strategy to reveal the molecular differences between the two cell types. A total of 2138 proteins were identified and 39 of these proteins were consistently differentially expressed between DFCs and PDLCs. Gene ontology analyses revealed that the protein subsets expressed higher in PDLCs were related to actin binding, cytoskeletal protein binding, and structural constituent of muscle. Upon validation by real-time PCR, western blotting, and immunofluorescence staining. Tropomyosin 1 (TPM1) and caldesmon 1 (CALD1) were expressed higher in PDLCs than in DFCs. Our results suggested that PDLCs display enhanced actin cytoskeletal dynamics relative to DFCs while DFCs may exhibit a more robust antioxidant defense ability relative to PDLCs. This study expands our knowledge of the cultured DFCs and PDLCs proteome and provides new insights into possible mechanisms responsible for the different biological features observed in each cell type.

iTAP: integrated transcriptomics and phenotype database for stress response of Escherichia coli and Saccharomyces cerevisiae

BACKGROUND

Organisms are subject to various stress conditions, which affect both the organism's gene expression and phenotype. It is critical to understand microbial responses to stress conditions and uncover the underlying molecular mechanisms. To this end, it is necessary to build a database that collects transcriptomics and phenotypic data of microbes growing under various stress factors for in-depth systems biology analysis. Despite of numerous databases that collect gene expression profiles, to our best knowledge, there are few, if any, databases that collect both transcriptomics and phenotype data simultaneously. In light of this, we have developed an open source, web-based database, namely integrated transcriptomics and phenotype (iTAP) database, that records and links the transcriptomics and phenotype data for two model microorganisms, Escherichia coli and Saccharomyces cerevisiae in response to exposure of various stress conditions.

RESULTS

To collect the data, we chose relevant research papers from the PubMed database containing all the necessary information for data curation including experimental conditions, transcriptomics data, and phenotype data. The transcriptomics data, including the p value and fold change, were obtained through the comparison of test strains against control strains using Gene Expression Omnibus's GEO2R analyzer. The phenotype data, including the cell growth rate and the productivity, volumetric rate, and mass-based yield of byproducts, were calculated independently from charts or graphs within the reference papers. Since the phenotype data was never reported in a standardized format, the curation of correlated transcriptomics-phenotype datasets became extremely tedious and time-consuming. Despite the challenges, till now, we successfully correlated 57 and 143 datasets of transcriptomics and phenotype for E. coli and S. cerevisiae, respectively, and applied a regression model within the iTAP database to accurately predict over 93 and 73 % of the growth rates of E. coli and S. cerevisiae, respectively, directly from the transcriptomics data.

CONCLUSION

This is the first time that transcriptomics and phenotype data are categorized and correlated in an open-source database. This allows biologists to access the database and utilize it to predict the phenotype of microorganisms from their transcriptomics data. The iTAP database is freely available at https://sites.google.com/a/vt.edu/biomolecular-engineering-lab/software .

Prediabetes Enhances Periodontal Inflammation Consistent With Activation of Toll-Like Receptor-Mediated Nuclear Factor-κB Pathway in Rats

BACKGROUND

Clinical studies have showed that prediabetes (preDM) is a predisposing factor for periodontitis. However, the pathogenic mechanism involved is unclear. Because it is known that the activation of Toll-like receptor (TLR)-mediated nuclear factor-kappa B (NF-κB) signaling pathway plays a crucial role in periodontitis, it is hypothesized that preDM enhances periodontal inflammation by activation of the TLR-mediated NF-κB pathway.

METHODS

In this study, a preDM rat model is established by feeding a high-fat diet (HFD). HFD-induced rats with preDM (n = 7) and normal chow-fed rats (n = 7) were studied. The animal model was characterized in terms of body weight and the glycemic and insulinemic profiles. The following parameters were assessed to evaluate possible early periodontal alterations and underlying mechanisms: 1) histology analysis of periodontal tissue; and 2) serum and mRNA levels and/or the tissue protein expression of TLRs, myeloid differentiation factor 88 (MyD88), tumor necrosis factor (TNF) receptor-associated factor 6 (TRAF6), NF-κB, cytokines, advanced glucose ends (AGEs), and free fatty acids (FFAs).

RESULTS

Rats with preDM presented higher expression of TLR2 and TLR4 in periodontal tissue in the HFD group compared with the control group. The TLR2 and TLR4 was mostly expressed in gingiva, and TLR4 was expressed in periodontal ligament in rats. Furthermore, the MyD88 and TRAF6 protein levels were significantly increased in gingiva in rats with preDM compared with normal rats. The activity of NF-κB signals was higher in rats with preDM than in normal rats. Regarding cytokines expression, the TNF-α protein levels and interleukin-1β mRNA levels were significantly increased in the HFD group compared with the control group. In the serum, AGEs levels were significantly increased in the rats with preDM. Mean FFAs concentrations were increased in rats with preDM compared with normal rats, but it did not reach statistical significance.

CONCLUSION

In rats with preDM, TLR2 and TLR4 gene and protein levels were higher in periodontal tissue, and the activation of NF-κB may, through TLRs/MyD88, cause more cytokine secretion, which is associated with the onset or development of periodontal disease.

Periodontal Ligament and Alveolar Bone in Health and Adaptation: Tooth Movement

The periodontal ligament (PDL) and alveolar bone are two critical tissues for understanding orthodontic tooth movement. The current literature is replete with descriptive studies of multiple cell types and their matrices in the PDL and alveolar bone, but is deficient with how stem/progenitor cells differentiate into PDL and alveolar bone cells. Can one type of orthodontic force with a specific magnitude and frequency activate osteoblasts, whereas another force type activates osteoclasts? This chapter will discuss the biology of not only mature cells and their matrices in the periodontal ligament and alveolar bone, but also stem/progenitor cells that differentiate into fibroblasts, osteoblasts and osteoclasts. Key advances in tooth movement rely on further understanding of osteoblast and fibroblast differentiation from mesenchymal stem/progenitor cells, and osteoclastogenesis from the hematopoietic/monocyte lineage.

Association of Resting Heart Rate with Infrarenal Aortic Diameter: A Cross Sectional Study in Chinese Hypertensive Adults

OBJECTIVE

Elevated resting heart rate (RHR) has been shown to be a risk marker for cardiovascular disease. Results from studies on the effects of RHR in large arteries are limited to the functional changes of those arteries, while the association between RHR and aortic diameter remains largely understudied.

METHODS

This was a cross sectional study of hypertensive Chinese adults from rural areas. The maximum infrarenal aortic diameter (maxIAD) from renal arteries to the iliac bifurcation was obtained by ultrasound. MaxIADs in different RHR groups were compared in males and females separately because of the significant differences between sexes. Multiple regression analysis was used to determinate the correlation between RHR and maxIAD. Further interactions between three factors (BMI, smoking, and anti-hypertensive regimens) and RHR for maxIAD were examined using subgroup analysis.

RESULTS

19,200 subjects were enrolled in the study, with an average age of 64.8±7.4 years and 61.6% females. Only 22 cases (0.11%) were detected with AAA, with males (n = 17) presenting a higher AAA incidence than females (n = 5). In subjects ≥65 years, there were 18 (0.19%) AAA, and 15 (83.3%) had a history of smoking. In the total subjects, the mean maxIAD ranged from 15.7±2.1 mm to 15.2±2.2 mm as RHR changed from the lowest quartile to the highest (≥84 bpm) in males, with a similar tendency observed in females. The correlation coefficient of RHR on maxIAD was -0.17 in males and -0.12 in females. Further subgroup analysis revealed that smoking exaggerated the correlation between RHR and maxIAD, but only in females.

CONCLUSIONS

A low AAA incidence was observed in this hypertensive Chinese population. There was a negative association between RHR and maxIAD, potentially exaggerated by smoking, especially in females.

Caspase-3 feedback loop enhances Bid-induced AIF/endoG and Bak activation in Bax and p53-independent manner

Chemoresistance in cancer has previously been attributed to gene mutations or deficiencies. Bax or p53 deficiency can lead to resistance to cancer drugs. We aimed to find an agent to overcome chemoresistance induced by Bax or p53 deficiency. Here, we used immunoblot, flow-cytometry analysis, gene interference, etc. to show that genistein, a major component of isoflavone that is known to have anti-tumor activities in a variety of models, induces Bax/p53-independent cell death in HCT116 Bax knockout (KO), HCT116 p53 KO, DU145 Bax KO, or DU145 p53 KO cells that express wild-type (WT) Bak. Bak knockdown (KD) only partially attenuated genistein-induced apoptosis. Further results indicated that the release of AIF and endoG also contributes to genistein-induced cell death, which is independent of Bak activation. Conversely, AIF and endoG knockdown had little effect on Bak activation. Knockdown of either AIF or endoG alone could not efficiently inhibit apoptosis in cells treated with genistein, whereas an AIF, endoG, and Bak triple knockdown almost completely attenuated apoptosis. Next, we found that the Akt-Bid pathway mediates Bak-induced caspase-dependent and AIF- and endoG-induced caspase-independent cell death. Moreover, downstream caspase-3 could enhance the release of AIF and endoG as well as Bak activation via a positive feedback loop. Taken together, our data elaborate the detailed mechanisms of genistein in Bax/p53-independent apoptosis and indicate that caspase-3-enhanced Bid activation initiates the cell death pathway. Our results also suggest that genistein may be an effective agent for overcoming chemoresistance in cancers with dysfunctional Bax and p53.

Interferon-α-2b as an adjuvant therapy prolongs survival of patients with previously resected oral muscosal melanoma

Two major subtypes of melanoma include cutaneous melanoma and mucosal melanoma. The latter type is rare and usually occurs in the head and neck region. High-dose interferon-α-2b (IFN-α-2b) has proven effective in the treatment of cutaneous melanoma. Recently, a regimen of temozolomide plus cisplatin was reported more likely to improve relapse-free survival and overall survival than high-dose IFN-α-2b for mucosal melanoma. We conducted this study to analyze the therapeutic effect of high-dose IFN-α-2b for patients with oral mucosal melanoma who had received prior chemotherapy. One hundred and seventeen patients with stage III-IVa oral mucosal melanoma who had received chemotherapy were analyzed. The overall survival and relapse-free survival were compared between the patients with/without high-dose IFN-α-2b. The results indicate that the IFN-α-2b treatment group had a longer relapse-free survival rate (P = 0.0169) as compared to the control group. However, the overall survival was not significant between the two groups (P = 0.096), except in patients in stage IVa, whose overall survival increased by 20 months (P = 0.0146). The adverse reactions included a drug-induced influenza-like syndrome, gastrointestinal responses, myelosuppression, and hepatoxicity, which were predominantly of grade 1-2 and reversible. Thus, patients with resected oral mucosal melanoma, even those who have received chemotherapy, could benefit from the treatment of high-dose IFN-α-2b.

Learning curve and outcome of laparoscopic transcystic common bile duct exploration for choledocholithiasis

BACKGROUND

The best approach for cholecystocholedocholithiasis remains a matter of debate. The aim of this study was to evaluate the technical aspects, learning curve and outcome of laparoscopic transcystic common bile duct exploration (LTCBDE).

METHODS

Patients who underwent laparoscopic cholecystectomy with LTCBDE between January 2007 and December 2012 were identified from an institutional database. Data on preoperative investigations, intraoperative and postoperative findings were retrieved retrospectively from the patients' hospital notes.

RESULTS

There were 399 women (56·4 per cent) and 309 men (43·6 per cent), with a median age of 58 (range 18-87) years. Microincision (incision of the cystic duct at the confluence with the common bile duct (CBD) with extension of only 3-5 mm at the lateral margin of the CBD) and lithotripsy were used in the transcystic exploration in 119 patients, and increased the success rate of LTCBDE from 74·2 to 91·0 per cent. The median duration of operation was 85 (i.q.r. 65-120) min and the median postoperative hospital stay was 2 (1-3) days. Retained common bile duct stones were observed in 13 patients, and postoperative complications developed in 27 patients. The cumulative sum duration of operation learning curve comprised two phases; phase 1 included the first 250 patients and phase 2 the remaining 458 patients. Duration of operation and postoperative hospital stay decreased with increasing volume per surgeon. Recurrence of common bile duct stones was diagnosed in 26 patients during a median follow-up of 4 years.

CONCLUSION

LTCBDE with or without microincision and/or lithotripsy is a safe and effective approach.

Gene mutations in gastric cancer: a review of recent next-generation sequencing studies

Gastric cancer (GC) is one of the most common malignancies worldwide. Although some driver genes have been identified in GC, the molecular compositions of GC have not been fully understood. The development of next-generation sequencing (NGS) provides a high-throughput and systematic method to identify all genetic alterations in the cancer genome, especially in the field of mutation detection. NGS studies in GC have discovered some novel driver mutations. In this review, we focused on novel gene mutations discovered by NGS studies, along with some well-known driver genes in GC. We organized mutated genes from the perspective of related biological pathways. Mutations in genes relating to genome integrity (TP53, BRCA2), chromatin remodeling (ARID1A), cell adhesion (CDH1, FAT4, CTNNA1), cytoskeleton and cell motility (RHOA), Wnt pathway (CTNNB1, APC, RNF43), and RTK pathway (RTKs, RAS family, MAPK pathway, PIK pathway) are discussed. Efforts to establish a molecular classification based on NGS data which is valuable for future targeted therapy for GC are introduced. Comprehensive dissection of the molecular profile of GC cannot only unveil the molecular basis for GC but also identify genes of clinical utility, especially potential and specific therapeutic targets for GC.