CRISPR-dCas9-mediated knockdown of prtR, an essential gene in Pseudomonas aeruginosa

Pseudomonas aeruginosa is a widely distributed non-fermentative Gram-negative opportunistic pathogen that is often responsible for nosocomial infections. Gene interference is a potentially valuable tool for investigating essential genes in P. aeruginosa. To establish a gene interference platform in P. aeruginosa, CRISPR system was used with an inactive Cas9 protein. The CRISPR-dCas9 system was cloned into pHERD20T, a shuttle vector with arabinose inducible promoter, and was further modified to target a regulatory gene prtR that is essential for the viability of P. aeruginosa. Cells expressing the prtR-targeting CRISPR interference (CRISPRi) showed growth defect in an arabinose dose-dependent manner. A high-throughput RNA sequencing analysis of bacterial cells with or without the CRISPRi-mediated prtR inhibition indicated that prtRis a global regulator affecting multiple biological processes. In conclusion, the CRISPR-dCas9-based gene knockdown system has been successfully implemented in P. aeruginosa and demonstrated to be an effective tool in the investigation of essential or difficult-to-inactivate genes in this species.

0714 Effect of One-Week Velopharyngeal-Task Training on Genioglossus Corticomotor Excitability and Sleep Apnea Severity

Introduction

The effectiveness of the contraction of the UA dilator muscles plays a crucial role in the maintenance of UA patency. This study aimed to assess the effects of one-week velopharyngeal-task training (VTT) on sleep apnea severity and its genioglossus (GG) corticomotor excitability.

Methods

Ten patients with sleep apnea underwent 1 h VTT on seven consecutive days. During the VTT protocol, subjects were asked to develop repetitive intra-oral positive pressure using cheek-bulging maneuvers while wearing a mouth piece to keep the jaw opened and maintaining an exclusive nasal breathing. They were encouraged to generate approximately 4% of Max pressure by maintaining the pressure inside the corresponding pre-set pressure target window for 2 sec every 10 sec. PSG recording and GG transcranial magnetic stimulation (TMS) response was obtained before and after the one-week VTT.

Results

One-week VTT was associated with a global AHI decrease by 33.8% (pre-VTT: 34.5±31.9 n/h; post-VTT: 25.5±26.7 n/h; p< 0.05) and progressed from moderate/severe to mild/moderate in 40% of patients. Although the bulging pressure remained unchanged (pre-VTT: 17.1±5.6 kPa, post-VTT: 19.4±5.4 kPa, p> 0.05), the amplitude of GG motor evoked potential in response to TMS significantly increased after the one-week VTT (pre-VTT: 639.4±380.9mV; post-VTT: 1128.5±623.9mV; p< 0.05).

Conclusion

One-week VTT is sufficient to confer clinical benefits on patients with sleep apnea. VTT protocol is not oriented toward strength gain, but rather toward an enhancement in the upper airway muscle cortical excitability and improvement in the coordination of their contraction. The authors consider these results to be potentially clinically relevant and worthy of further investigation in a large randomized trial.

Support

National Natural Science Foundation of China, Grant/Award Number: 81670085.

MSTN Mutant Promotes Myogenic Differentiation by Increasing Demethylase TET1 Expression via the SMAD2/SMAD3 Pathway

Myostatin (MSTN) is mostly expressed in skeletal muscle and plays crucial roles in the negative regulation of muscle mass development. The methylation and demethylation of myogenesis-specific genes are major regulatory factors in muscle satellite cell differentiation. The present study was designed to investigate the mechanism of myogenic differentiation regulated by MSTN mutation (MT) and the methylation/demethylation state of downstream genes. The results showed that, in the MSTN^-/+ satellite cells, a higher myotube fusion index and a larger myotube length were observed compared to the wild type controls; the genes associated with myogenesis were all up-regulated compared to the WT controls. The methylation of the promoters and gene bodies of PAX3, PAX7, MyoD, and MyoG were all down-regulated, while the expression of the key demethylase TET1 was significantly promoted. ChIP-qPCR was used to demonstrate that the SMAD2/SMAD3 complex combined with the promoter of TET1 to inhibit the activity of TET1 promoter, indicating that MSTN may regulate TET1 via SMAD2/SMAD3. The overexpression of TET1 in wild type cells promoted myogenic differentiation, increased the myotube index, and reduced the methylation of the associated genes. On the contrary, the knockdown of TET1 in the MSTN mutant cells resulted in the opposite phenomena as in the overexpressed cells. In conclusion, the myostatin mutant showed an increased transcriptional activity of TET1, inducing higher levels of demethylation and improving the transcriptional activity levels of myogenic differentiation-associated genes. The binding of SMAD2/SMAD3 directly to the TET1 promoter region indicated that the MSTN mutant demethylated the myogenesis-specific genes by up-regulating TET1, which is directly controlled by SMAD2/SMAD3.

Transcriptome-wide analysis of the SCNT bovine abnormal placenta during mid- to late gestation

The dysfunction of placenta is common in somatic cell nuclear transfer (SCNT) cloned cattle and would cause aberrant fetal development and even abortion, which occurred with highest rate at the mid- to late gestation. However, the mechanism of abnormal placentas was unclear. To analyze the transcriptome-wide characteristics of abnormal placentas in SCNT cloned cattle, the mRNA, lncRNA and miRNA of placental cotyledon tissue at day 180 after gestation were sequenced. A total of 19,055 mRNAs, 30,141 lncRNAs and 684 miRNAs were identified. Compared with control group, 362 mRNAs, 1,272 lncRNAs and nine miRNAs (six known and three novel miRNAs) were differentially expressed (fold change ≥ 2 and P-value < 0.05). The differentially expressed genes were functionally enriched in urea and ions transmembrane transport, which indicated that the maternal-fetal interactions were disturbed in impaired placentas. Furthermore, the competing endogenous RNAs (ceRNAs) networks were identified to illustrate their roles in abnormal placental morphology. The present research would be helpful to discover the mechanism of late gestational abnormality of SCNT cattle by provides important genomic information and insights.

Inhibiting repressive epigenetic modification promotes telomere rejuvenation in somatic cell reprogramming

The efficiency of somatic cell nuclear transfer (SCNT) reprogramming is extremely low in terms of production of cloned animals. Here, we found that telomere rejuvenation is a critical event for SCNT reprogramming. Through small-molecule screening, we identified that melatonin significantly improved the in vitro and in vivo developmental competence of SCNT-derived embryos. Through use of embryonic biopsy, single-cell RNA sequencing, and quantitative FISH experiments, we revealed that melatonin not only attenuated the zygotic genome activation defect but also facilitated telomere elongation in the SCNT embryos. Further investigation indicated that melatonin inhibited heterochromatic epigenetic modification related to gene silencing including DNA methylation and histone H3 lysine 9 trimethylation. In addition, melatonin could increase the level of activation markers such as acetylated histone H3. This is the first study to characterize melatonin-treatment and telomere rejuvenation in SCNT-mediated reprogramming. Moreover, combinational use of melatonin-treated donor embryos and pseudopregnant recipients achieved synergistic enhancement of the production of cloned animals.-Yang, L., Liu, X., Song, L., Su, G., Di, A., Bai, C., Wei, Z., Li, G. Inhibiting repressive epigenetic modification promotes telomere rejuvenation in somatic cell reprogramming.

Microcatheter shaping using three-dimensional printed models for intracranial aneurysm coiling

Background and purpose

Microcatheterization is an important, but also difficult, technique used for the embolization of intracranial aneurysms. The purpose of this study was to investigate the application of three-dimensional (3D) printing technology in microcatheter shaping.

Methods

Nine cases of internal carotid artery posterior communicating artery aneurysm diagnosed by CT angiography were selected, and 3D printing technology was used to build a 3D model including the aneurysm and the parent artery. The hollow and translucent model had certain flexibility; it was immersed in water and the microcatheter was introduced into the water to the target position in the aneurysm, followed by heating the water temperature to 50°C. After soaking for 5 min, the microcatheter was taken out and the shaping was completed. After sterilization, the shaped microcatheter was used for arterial aneurysm embolization and evaluation was conducted.

Results

Nine cases of microcatheter shaping were satisfactory and shaping the needle was not necessary; no rebound was observed. The microcatheter was placed in an ideal position, and the stent-assisted method was used in three cases of wide-neck aneurysm. There were no complications related to surgery.

Conclusion

A new microcatheter shaping method using 3D printing technology makes intracranial artery aneurysm embolization more stable and efficient.

Histone Demethylase UTX is an Essential Factor for Zygotic Genome Activation and Regulates Zscan4 Expression in Mouse Embryos

Following fertilization, the zygotic genome is activated through a process termed zygotic genome activation (ZGA), which enables zygotic gene products to replace the maternal products and initiates early embryonic development. During the ZGA period, the embryonic epigenome experiences extensive recodifications. The H3K27me3 demethylase UTX is essential for post-implantation embryonic development. However, it remains unclear whether UTX participates in preimplantation development, especially during the ZGA process. In the present study, we showed that either knockdown or overexpression of UTX led to embryonic development retardation, whereas simultaneous depletion of UTX and overexpression of ZSCAN4D rescued the embryonic development, indicating that UTX positively regulated Zscan4d expression. Using a transgenic mice model, we also found that UTX was required for preimplantation embryonic development. In conclusion, these results indicate that UTX functions as a novel regulator and plays critical roles during ZGA in addition to early embryonic development.

Graphene oxide-film-coated splitting ratio-adjustable Mach-Zehnder interferometer for relative humidity sensing

In this paper, a splitting ratio-adjustable Mach-Zehnder interferometer (MZI) for the measurement of relative humidity (RH) is proposed and experimentally demonstrated. The sensing head contains three sections of single mode fiber (SMF) and two sections of multimode fiber (MMF), in which the two MMFs are spliced among the three SMFs. The MMFs are corroded with hydrofluoric acid and act as mode couplers to split and recombine light owing to the core diameter mismatch with the SMF. A layer of graphene oxide (GO) is coated on the MMFs by dip-coating and natural evaporation. The effective refractive index of the GO will vary when it absorbs the water molecules. As a result, the intensity of the transmission light in the core and cladding of the single mode fiber can be adjusted. Thus, the intensity of the resonant dip will vary when the relative humidity changes. The experimental results show that a humidity sensitivity of 0.263 dB/RH% with a linear correlation coefficient of 99% can be achieved in a relative humidity range of 35% to 85%.

DNA methylation subpatterns at distinct regulatory regions in human early embryos

DNA methylation has been investigated for many years, but recent technologies have allowed for single-cell- and single-base-resolution DNA methylation datasets and more accurate assessment of DNA methylation dynamics at the key genomic regions that regulate gene expression in human early embryonic development. In this study, the region from upstream 20 kb to downstream 20 kb of RefSeq gene was selected and divided into 12 distinct regions (up20, up10, up5, up2, 5'UTR, exon, intron, 3'UTR, down2, down5, down10 and down20). The candidate promoter region (TSS ± 2 kb) was further divided into 20 consecutive subregions, which were termed 'bins'. The DNA methylation dynamics of these regions were systematically analysed along with their effects on gene expression in human early embryos. The dynamic DNA methylation subpatterns at the distinct genomic regions with a focus on promoter regions were mapped. For the 12 distinct genomic regions, up2 and 5'UTR had the lowest DNA methylation levels, and their methylation dynamics were different with other regions. The region 3'UTR had the highest DNA methylation levels, and the correlation analysis with gene expression proved that it was a feature of transcribed genes. For the 20 bins in promoter region, the CpG densities showed a normal distribution pattern, and the trend of the methylated CpG counts was inverse with the DNA methylation levels, especially for the bin 1 (downstream 200 bp of the TSS). Through the correlation analysis between DNA methylation and gene expression, the current study finally revealed that the region bin -4 to 6 (800 bp upstream to 1200 bp downstream of the TSS) was the best candidate for the promoter region in human early embryos, and bin 1 was the putative key regulator of gene activity. This study provided a global and high-resolution view of DNA methylation subpatterns at the distinct genomic regions in human early embryos.

Comparative genomics and transcriptomics of Chrysolophus provide insights into the evolution of complex plumage coloration

Background

As one of the most recognizable characteristics in birds, plumage color has a high impact on understanding the evolution and mechanisms of coloration. Feather and skin are ideal tissues to explore the genomics and complexity of color patterns in vertebrates. Two species of the genus Chrysolophus, golden pheasant (Chrysolophus pictus) and Lady Amherst's pheasant (Chrysolophus amherstiae), exhibit brilliant colors in their plumage, but with extreme phenotypic differences, making these two species great models to investigate plumage coloration mechanisms in birds.

Results

We sequenced and assembled a genome of golden pheasant with high coverage and annotated 15,552 protein-coding genes. The genome of Lady Amherst's pheasant is sequenced with low coverage. Based on the feather pigment identification, a series of genomic and transcriptomic comparisons were conducted to investigate the complex features of plumage coloration. By identifying the lineage-specific sequence variations in Chrysolophus and golden pheasant against different backgrounds, we found that four melanogenesis biosynthesis genes and some lipid-related genes might be candidate genomic factors for the evolution of melanin and carotenoid pigmentation, respectively. In addition, a study among 47 birds showed some candidate genes related to carotenoid coloration in a broad range of birds. The transcriptome data further reveal important regulators of the two colorations, particularly one splicing transcript of the microphthalmia-associated transcription factor gene for pheomelanin synthesis.

Conclusions

Analysis of the golden pheasant and its sister pheasant genomes, as well as comparison with other avian genomes, are helpful to reveal the underlying regulation of their plumage coloration. The present study provides important genomic information and insights for further studies of avian plumage evolution and diversity.

[Epidemiologic survey on the prevalence and distribution of infants' common gastrointestinal symptoms in 7 cities in China: a population-based study]

Objective: Regurgitation, infantile colic, and functional constipation are common gastrointestinal symptoms in childhood, the aim of this study was to explore the prevalence and distribution of these symptoms in China. Methods: A screening program in infants aged 0 to 3 years selected through stratified cluster random sampling was carried out in 7 cities in China. Questionnaires were filled, and then diagnosis were made according to Rome Ⅳ criteria. Areas, (urban-rural), age and gender distribution of prevalence of childhood common gastrointestinal symptoms were analyzed. Results: Totally, 20 932 effective questionnaires were returned. The total number of infants aged 0 to 1 years was 10 193. Regurgitation was diagnosed in 1 960 infants, with the prevalence of 19.2%, among infants aged 0 to 3 months that had highest prevalence (29.8%). The prevalence decreased with age, and differences among different age groups showed significant. For infantile colic, 4 470 infants aged 0 to 5 months were analyzed and the prevalence of infantile colic was 7.3%. The prevalence of infantile colic was the highest in infants aged 1 to 2 months (10.0%). Age specific difference was significant. Of all the infants, functional constipation was diagnosed in 1 755 infants with the prevalence of 8.4%, and the lowest prevalence was found in infants aged 0 to 3 months (6.2%), and the highest prevalence was in infants aged 30 to 36 months (10.0%). The differences in different age group were significant. Conclusion: Symptoms of regurgitation, infantile colic, and functional constipation are common in infants in China, with age specific difference in prevalence of the symptoms.

Omega 3 polyunsaturated fatty acids inhibit cell proliferation by regulating cell cycle in fad3b transgenic mouse embryonic stem cells

Background

The consumption of omega 3 polyunsaturated fatty acids (PUFAs) is important for human health and is closely associated with cell proliferation and differentiation. This study aimed to investigate the influence of omega 3 PUFAs on embryonic stem cell (ESC) proliferation and explore potential mechanisms that mediate these effects.

Methods

In this study, we isolated ESCs from fad3b-expressing transgenic mice. We detected the fatty-acid composition of ESCs using gas chromatography-mass spectroscopy, analyzed cell-cycle phases using flow cytometry, and detected gene expression using real-time polymerase chain reaction (PCR) and western blots.

Results

The amount of omega 3 PUFAs significantly increased in fad3b versus control ESCs. However, the growth of fad3b ESCs was slower than that of control cells, and most fad3b ESCs were in a prolonged G0/G1 phase after being passaged for 18 h. Therefore, we hypothesized that fad3b expression inhibited the cell cycle in ESCs by increasing the expression of P21, which then decreased the expression of cyclin-dependent kinase 4 (Cdk4). We found that pretreatment of fad3b ESCs with PD0325901, a P21 inhibitor, clearly attenuated the inhibitory effects of P21 on Cdk4, and resumed the cell cycle.

Conclusions

Expression of the fad3b gene in ESCs increased the omega 3 PUFA content, which inhibited cell proliferation by prolonging the G1 phase but did not arrest the G0-to-G1 or G1-to-S transitions. The prolonged G1 phase in fad3b ESCs was probably induced by downregulation of Cdk4 expression via p21 upregulation. These results suggest that accumulation of omega 3 PUFAs in vivo may beneficially affect ESC differentiation and that fad3b ESCs may be a useful tool for investigating related mechanisms.

Electronic supplementary material

The online version of this article (10.1186/s12944-018-0862-x) contains supplementary material, which is available to authorized users.

Screening of exosomal miRNAs derived from subcutaneous and visceral adipose tissues: Determination of targets for the treatment of obesity and associated metabolic disorders

Exosomal micro (mi)RNAs have been suggested to have important roles in abdominal obesity, and to be associated with metabolic alterations via posttranscriptional regulation of target genes. However, exosomal miRNA profiles in subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT) have rarely been investigated. In the present study, microarray data were obtained from the Gene Expression Omnibus database with the following accession numbers: GSE68885 (exosomal miRNAs in SAT obtained from seven patients with obesity and five lean patients), GSE50574 (exosomal miRNAs in VAT obtained from seven patients with obesity and five lean patients) and GSE29718 [mRNAs in SAT (obtained from seven patients with obesity and eight lean patients) and VAT (obtained from three patients with obesity and two lean patients)]. Differentially expressed (DE)‑miRNAs and differentially expressed genes (DEGs) were identified using the Linear Models for Microarray Data method, and mRNA targets of DE‑miRNAs were predicted using the miRWalk2.0 database. Potential functions of DE‑miRNA target genes were determined using the Database for Annotation, Visualization and Integrated Discovery. As a result, 10 exosomal DE‑miRNAs were identified in SAT between patients with obesity and lean patients, while 58 DE‑miRNAs were identified in VAT between patients with obesity and lean patients. miRNA (miR)‑4517 was revealed to be a downregulated exosomal miRNA between SAT and VAT, while the other DE‑miRNAs were SAT‑(e.g. hsa‑miR‑3156‑5p and hsa‑miR‑4460) or VAT‑(e.g. hsa‑miR‑582‑5p, hsa‑miR‑566 and miR‑548) specific. Following overlapping with the target genes of DE‑miRNAs, only one DEG [cluster of differentiation 86 (CD86)] was identified in SAT samples, whereas 25 DEGs (e.g. fibroblast growth factor 2 (FGF2), FOS like 2, AP‑1 transcription factor subunit (FOSL2); and adenosine monophosphate deaminase 3 (AMPD3)] were identified in VAT samples. CD86 was revealed to be regulated by hsa‑miR‑3156‑5p; whereas FGF2, FOSL2 and AMPD3 were revealed to be regulated by hsa‑miR‑582‑5p, hsa‑miR‑566 and miR‑548, respectively. Functional enrichment analysis demonstrated that these target genes may be associated with inflammation. In conclusion, exosomal miRNAs may represent underlying therapeutic targets for the treatment of abdominal obesity and metabolic disorders via regulation of inflammatory genes.

Silver-modified octahedral anatase particles as plasmonic photocatalyst

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Octahedral anatase particles (OAPs) modified with silver NPs by photodeposition.

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Ag/OAPs with enhanced photocatalytic activity under both UV and vis irradiation.

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Electron traps as nucleation sites for silver NPs.

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Polydispersity of silver NPs results in broad LSPR and thus enhanced vis activity.

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TRMC data correlate with photocatalytic activity.

Octahedral anatase particles (OAPs) were modified with silver nanoparticles (NPs) by photodeposition method. The properties of OAPs influenced the properties of silver deposits, and thus the photocatalytic activity of the obtained silver-modified OAPs. Photocatalytic activities were tested under UV and vis irradiation for oxidative decomposition of acetic acid and oxidation of 2-propanol, respectively. The properties of silver-modified OAPs were investigated by XRD, STEM, DRS, XPS and time-resolved microwave conductivity (TRMC) method. It was found that electron traps (ETs) worked as nucleation sites for silver, resulting in formation of smaller silver NPs on smaller OAPs with larger content of ETs. The modification with silver resulted in enhanced photocatalytic activity under both UV and vis irradiation. It was found that larger crystallite size of silver NPs, and thus larger polydispersity of silver deposits resulted in broad and intense plasmon resonance peak causing enhanced visible activity. The correlation between photocatalytic activity and TRMC data, e.g., slower decay of TRMC signal for more active samples, allowed discussion on property-governed photocatalytic activities of silver-modified titania.

Characteristics and formation of typical winter haze in Handan, one of the most polluted cities in China

Handan, a city within the North China Plain (NCP) region, is a typical city influenced by regional particulate matter (PM) pollution. One-year hourly semi-continuous observation was carried out in 2015 in Handan with the aim of identifying the chemical composition and variations in PM_2.5. Moreover, the concentration of aerosol precursors, meteorological factors, and secondary transformations are considered. The results demonstrate that the annual average PM_2.5 concentration in Handan is 122.35μgm^-3, approximately 3.5 times higher than the Chinese National Ambient Air Quality Standard (NAAQS) (35μgm^-3), and only 12days were below the guideline. As expected, PM concentrations are highest in winter, especially in December. In addition, we measure the concentrations of five species commonly found in PM, nitrate, sulfate, ammonium, inorganic carbon, and organic carbon. Of these, nitrate and sulfate account for the largest proportion of PM_2.5; during periods when the PM_2.5 concentration was below 400μgm^-3, nitrate dominates, while above this concentration, sulfate dominate. This is likely related to the nitrogen and sulfur oxidation ratios, which are in turn, especially the sulfur oxidation ratio, driven by high relative humidity (>60%). In addition, haze events are driven by other meteorological conditions, wind speed and direction, where low wind speeds from the south and southwest enable pollutant accumulation, which are infrequently interspersed with brief periods with high wind speeds that promote pollutant dispersal. Even though Handan is among the ten most polluted cities in China with regard to air pollution, few studies beyond model simulations have analyzed air pollutant concentrations in this city. Therefore, this study makes a significant contribution to understanding air pollution in Handan, which can further be used to improve our understanding of regional pollution in the highly populated North China Plain. These results have implications for the creation of policies and legislation, as well as other pollution control measures.

Risk Factors Analysis and Death Prediction in Some Life-Threatening Ailments Using Chi-Square Case-Based Reasoning (χ2 CBR) Model

A wealth of data are available within the health care system, however, effective analysis tools for exploring the hidden patterns in these datasets are lacking. To alleviate this limitation, this paper proposes a simple but promising hybrid predictive model by suitably combining the Chi-square distance measurement with case-based reasoning technique. The study presents the realization of an automated risk calculator and death prediction in some life-threatening ailments using Chi-square case-based reasoning (χ² CBR) model. The proposed predictive engine is capable of reducing runtime and speeds up execution process through the use of critical χ² distribution value. This work also showcases the development of a novel feature selection method referred to as frequent item based rule (FIBR) method. This FIBR method is used for selecting the best feature for the proposed χ² CBR model at the preprocessing stage of the predictive procedures. The implementation of the proposed risk calculator is achieved through the use of an in-house developed PHP program experimented with XAMP/Apache HTTP server as hosting server. The process of data acquisition and case-based development is implemented using the MySQL application. Performance comparison between our system, the NBY, the ED-KNN, the ANN, the SVM, the Random Forest and the traditional CBR techniques shows that the quality of predictions produced by our system outperformed the baseline methods studied. The result of our experiment shows that the precision rate and predictive quality of our system in most cases are equal to or greater than 70%. Our result also shows that the proposed system executes faster than the baseline methods studied. Therefore, the proposed risk calculator is capable of providing useful, consistent, faster, accurate and efficient risk level prediction to both the patients and the physicians at any time, online and on a real-time basis.