Benzo[a]pyrene and a high-fat diet induce aortic injury and promote low-density lipoprotein accumulation in the endothelium.

Benzo[a]pyrene (BaP) is a ubiquitous environmental pollutant which mainly exposed though diet. High-fat diet (HFD) can induce atherosclerosis, as can BaP. Unhealthy dietary habits lead to high intake of both BaP and lipids. However, the combined effect of BaP and HFD on atherosclerosis and lipid accumulation in the arterial wall, the initial stage of atherosclerosis, is unclear. In this study, C57BL/6 J mice were subchronically exposed to BaP and a HFD, and the mechanism of lipid accumulation was investigated in EA.hy926 and HEK293 cells. Results showed that BaP and HFD increased blood lipids and damaged aortic wall synergistically. Meanwhile, LDL enhanced the toxicity of BaP, and BaP promoted the production of reactive oxygen species and malonaldehyde in EA.hy926 cells, which aggravated LDL-induced cell injury. Moreover, BaP and HFD/LDL induced LDL accumulation in the aortic wall of C57BL/6 J mice/EA.hy926, and the mechanism was by activating AHR/ARNT heterodimer to combine with the scavenger receptor BⅠ (SR-BⅠ) and activin receptor-like kinase 1 (ALK1) promoter regions to transcriptional upregulate its expression, which enhanced the uptake of LDL, and promoting the production of AGEs to inhibit reverse cholesterol transport by SR-BI. BaP and lipid synergistically promoted aortic and endothelial damage, and the health risk of their combined intake should be paid attention to.

Rapid identification of ultrathin amorphous damage on monocrystalline silicon surface.

Amorphous silicon (a-Si) is a type of common surface damages during the ultra-precision machining of monocrystalline Si. However, it is difficult to identify the amorphous damage of several nanometers by traditional detection methods, which severely hinders the performance improvement of Si-based products. In this study, ultrathin a-Si was found to act as a mask against etching in HF/HNO3 mixtures, resulting in the formation of protrusive hillocks. Reciprocating sliding on an atomic force microscope (AFM) was employed to simulate a material removal event in surface manufacturing. The effects of normal load, etching time and etchant concentration on selective etching were investigated to optimize the parameters for amorphous damage detection. The mechanisms for selective etching were further addressed based on high-resolution transmission electron microscopy (HRTEM) detection and comparative etching of different surface structures. Further analysis demonstrated that a lower dangling bond density of a-Si could result in the reduction of the dissolution rate, while deformed Si lattices, including stacking faults, dislocations and microcracks, could facilitate rapid selective etching. By the proposed selective etching, ultrathin amorphous damage and its spatial distributions can be rapidly identified with high resolution and low destruction. This study sheds new light on achieving a high-quality Si surface in ultra-precision machining.

Transcriptome analysis of Paecilomyces hepiali at different growth stages and culture additives to reveal putative genes in cordycepin biosynthesis.

Paecilomyces hepialid (PH) is an endoparasitic fungus of Cordyceps sinensis (CS) and has become a substitute for CS due to their similar pharmacological activities. Because the market demand for CS is difficult to satisfy, and cordycepin, the effective compound of CS, is difficult to industrially produce, we produced 5 samples of PH by culturing for different durations and adding different additives to the culture broth, and detected their cordycepin content with UPLC ESI MS/MS. Then we grouped these cultures into five transcriptome comparisons containing 3 time variable groups and 2 additive variable groups. We used next-generation (NG) sequencing methods to acquire transcriptomic information and investigated the response of gene expression to the additives and the influence of different growth stages. This work will contribute to a better understanding of purine metabolism in PH, and possibly in other Cordyceps species. It will provide a useful resource to further advance transcriptomics studies in Cordyceps species.

Genome-wide analysis of DNA methylation profiles in a senescence-accelerated mouse prone 8 brain using whole-genome bisulfite sequencing.

MOTIVATION: The pathogenesis of AD is complex and contributed by both genetic and environmental factors. Recent work revealed a potential link between DNA methylation and AD. However, a genome-wide study to identify potential DNA methylation sites involved in AD is still at an early stage. WGBS, an up-to-date technology, was used in this study. We investigated mouse brain genome-wide DNA methylation profiles between seven-month-old SAMP8 and SAMR1 models through deep WGBS. RESULTS: According to the results, the global ML slightly decreased in the SAMP8 mice than in the SAMR1 mice (4.12% versus 4.19%). A total of 1 307 172 280 clean reads were obtained. Subsequently, we identified 63 DMRs from all cases in SAMP8 mice relative to SAMR1 mice. In addition, 26 DMR-related genes were detected. GO analyses revealed that these DMR-related genes were involved in regulating the development of AD from different aspects. Finally, three differentially expressed DMR-related genes ( Dlgap1 , TMEM51 and Eif2ak2 ) that were most likely involved in AD were summarized and listed in detail. Our study provided a systematic exploration of DNA methylation profiles in SAMP8 mouse brain for the first time. These novel methylation sites may be considered strong future candidates to combat this life-threatening disease. AVAILABILITY AND IMPLEMENTATION: The WGBS sequencing clean data and RNA-seq clean data have been deposited in the NCBI Sequence Read Archive (SRA).The accession number of WGBS is SRP097054. The accession number of RNA-seq is SRP096779. CONTACT: zws@bnu.edu.cn. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Characterization of circRNA-Associated-ceRNA Networks in a Senescence-Accelerated Mouse Prone 8 Brain.

Alzheimer's disease (AD) is one of the most common neurodegenerative diseases. Although many researchers have attempted to explain the origins of AD, developing an effective strategy in AD clinical therapy is difficult. Recent studies have revealed a potential link between AD and circRNA-associated-ceRNA networks. However, few genome-wide studies have identified the potential circRNA-associated-ceRNA pairs involved in AD. In this study, we systematically explored the circRNA-associated-ceRNA mechanism in a 7-month-old senescence-accelerated mouse prone 8 (SAMP8) model brain through deep RNA sequencing. We obtained 235 significantly dysregulated circRNA transcripts, 30 significantly dysregulated miRNAs, and 1,202 significantly dysregulated mRNAs. We then constructed the most comprehensive circRNA-associated-ceRNA networks in SAMP8 brain. GO analysis revealed that these networks were involved in regulating the development of AD from various angles, for instance, axon terminus (GO: 0043679) and synapse (GO: 0045202). Following rigorous selection, we discovered that the circRNA-associated-ceRNA networks in this AD mouse model were mainly involved in the regulation of Aß clearance (Hmgb2) and myelin function (Dio2). This research is the first to provide a systematic dissection of circRNA-associated-ceRNA profiling in SAMP8 mouse brain. The selected circRNA-associated-ceRNA networks can profoundly affect the diagnosis and therapy of AD in the future.

Controlling amorphous silicon in scratching for fabricating high-performance micromixers.

As core parts of microfluidic chip analysis systems, micromixers show robust applications in wide fields. However, restricted by the fabrication technology, it remains challenging to achieve high-quality micromixers with both delicately designed structure and efficient mixing. In this study, based on the theory of chaotic mixing, sinusoidal structures with variable phases were designed and then fabricated through scanning probe lithography (SPL) and post-selective etching. It was found that scratches with phase differences can lead to the periodic formation of amorphous silicon (a-Si), which can resist etching. Consequentially, misaligned sine channels with thick-thin alternating 3D shapes can be generated in situ from the scratched traces after the etching. Further analysis showed that a thicker a-Si layer can be obtained by reducing the line spacing in the scratching, confirmed by Raman detections and simulations. With the proposed method, the misaligned sine micromixer was achieved with higher mixing efficiency than ever. The duplicating process was also investigated for high-precision production of micromixers. The study provided strategies for the miniaturization of high-performance microfluidic chips.

[Status of wild resource of medicine plant Lamiophlomis rotata and its problems in sustainable use].

OBJECTIVE: Lamiophlomis rotata is a common wild herb in Tibetan traditional medicine with important medicinal and economic value. The paper examines the wild distributions, exploitation regime, and situations. METHOD: A variety of research methods, such as literature survey, specimens inspection, market information collection in major Chinese herbal markets, questionnaire of herbalists and employers of local governments and institutions, and field quadrat survey and AcrGIS as well, have been used for this work. RESULT: Total stock of wild resources of L. rotata is ranging from 3 713.49 tons to 6 896.56 tons (2 519-3 314 t in Qinghai, 490-1 414 t in Gansu, 641-1 167 t in Sichuan, and 422-999 t in Tibet, respectively), acceptable harvest quantity of the herb is ranging from 908-1 675 t per year, and actual harvest quantity is 2 520 t annually far beyond the acceptable harvest quantity. CONCLUSION: Harvesting quantity of L. rotata is far more than that of acceptable, suggesting that utilization pattern of this wild resource plant is unsustainable. L. rotata seems to act as an indicating plant of degraded ecosystem of high-altitude grassland, shrub grassland, and wetland, and distributes in those degraded and degrading plateau ecosystems, and the plant is facing with pressure of ecological protection and wild resource population degradation. Wild population monitoring and standard cultivation are of importance for although they are far from implementation due to shortage of related basic studies.

[Differences of saikosaponin contents in Bupleurum chinense from habitats in Dongling Mountain & Wuling Mountain of Beijing].

The different growing habitats of Bupleurum chinense were investigated in Donglin mountain & Wuling mountain areas, the saikosaponin a and d in samples of B. chinense collected from different habitats were determined by HPLC. Results showed that B. chinense distributed in various habitats, such as meadow, understory and brushy. Significant differences of saikosaponin contents were observed. The higher saikosaponins contents were showed in samples from meadow habitats, while the lower saikosaponins contents in samples from understory and brushy habitats. The ventilation situation and light condition showed positive correlation with the saikosaponins accumulation in B. chinense. It could be concluded that growing habitats play an important role in accumulation of saikosaponins in B. chinense.

Royal jelly peptides: potential inhibitors of ß-secretase in N2a/APP695swe cells.

Royal jelly (RJ) is a type of natural health product with a long history of use. Royal jelly peptides (RJPs) obtained from RJ have numerous bioactivities. To study the neuroprotective effect of RJPs, major royal jelly proteins were digested into crude RJPs and subsequently purified by RP-HPLC. Purified RJP fractions were evaluated in N2a/APP695swe cells. Our results indicated that purified royal jelly peptides (RJPs) (1-9 µg/mL) could inhibit external beta-amyloid 40 (Aß1-40) and beta-amyloid 42 (Aß1-42) production through the down-regulation of ß-secretase (BACE1) in N2a/APP695 cells. The modulation of BACE1 may be related to histone acetylation modification. Our results demonstrated a neuroprotective function of RJPs, which indicates that RJPs may serve as potential ß-secretase inhibitors in ameliorating Aß-related pathology in Alzheimer's Disease.

Identification of functional tRNA-derived fragments in senescence-accelerated mouse prone 8 brain.

Transfer RNA-derived fragments (tRFs) are known to contribute to multiple illnesses, including cancers, viral infections, and age-related neurodegeneration. In this study, we used senescence-accelerated mouse prone 8 (SAMP8) as a model of neurodegenerative disorders such as Alzheimer's disease and Parkinson's disease, and a control, the senescence-accelerated mouse resistant 1 (SAMR1) model, to comprehensively explore differences in tRF expression between them. We discovered 570 tRF transcripts among which eight were differentially expressed. We then obtained 110 potential target genes in a miRNA-like pattern. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation suggest that these target genes participate in a variety of brain functions; e.g., synapse formation (GO: 0045202) and the synaptic vesicle cycle pathway. We further assessed in detail those tRFs whose miRNA-like pattern was most likely to promote the progression of either Alzheimer's or Parkinson's disease, such as AS-tDR-011775 acting on Mobp and Park2. Our findings suggest the eight dysregulated tRFs we uncovered here may be beneficially exploited as potential diagnostic biomarkers and/or therapeutic targets to treat age-related brain diseases.

Analyses of mRNA Profiling through RNA Sequencing on a SAMP8 Mouse Model in Response to Ginsenoside Rg1 and Rb1 Treatment.

Ginsenoside Rg1 and Rb1 are the major ingredients in two medicines called QiShengLi (Z20027165) and QiShengJing (Z20027164) approved by China. These ingredients are believed to mitigate forgetfulness. Numerous studies have confirmed that GRg1 and GRb1 offer protection against Alzheimer's disease (AD), and our morris water maze (MWM) experiment also indicated that GRg1 and GRb1 may attenuate memory deficits in the 7-month-old SAMP8 mice; however, comprehensive understanding of their roles in AD remains limited. This study systematically explored the mechanism at the genome level of the anti-AD effects of GRg1 and GRb1 in a senescence-accelerated mouse prone 8 (SAMP8) model through deep RNA sequencing. A total of 74,885 mRNA transcripts were obtained. Expression analysis showed that 1,780 mRNA transcripts were differentially expressed in SAMP8 mice compared with the SAMP8+GRg1 mice. Moreover, 1,066 significantly dysregulated mRNA transcripts were identified between SAMP8 and SAMP8+GRb1 mice. Analyses according to gene ontology and the Kyoto Encyclopedia of Genes and Genomes revealed that oral administration of GRg1 and GRb1 improved the learning performance of the SAMP8 mouse model from various aspects, such as nervous system development and mitogen-activated protein kinase signaling pathway. The most probable AD-related transcriptional responses after medication were predicted and discussed in detail. This study is the first to provide a systematic dissection of mRNA profiling in SAMP8 mouse brain in response to GRg1 and GRb1 treatment. We explained their efficacy thoroughly from the source (gene-level explanation). The findings serve as a theoretical basis for the exploration of GRg1 and GRb1 as functional drugs with anti-AD activity.

[High specific PCR identification of Bungarus multicinctus and its adulterants].

OBJECTIVE: To develop a convenient and effective method for the identification of Bungarus multicinctus. METHOD: Based on the sequence of Cyt b gene fragment of B. multicinctus and its adulterants, a pair of highly specific primer (HJL- and HJH-) were designed for distinguishing B. ulticinctus from other species of snake. To establish specific PCR reaction condition, the primers were employed to amplify the DNA templates extracted from B. multicinctus and 6 other species of snake, under different annealing temperature. Using this method, B. multicinctus was identified from 18 samples bought from many drugstores. RESULT: A 230 bp DNA fragment was amplified from B. multicinctus in PCR with annealed temperature at 67 degrees C, whereas no DNA fragment was amplified from other snake samples under the same reaction condition, B. multicinctus could be clearly distinguished from others by PCR reaction with the highly specific primers. In the present study, 18 sample, bought from different drugstores, were also identified by the highly specific PCR with the primers. The results indicated that 14 samples were B. multicinctus and the other 4 were adulterant, which was consistent with the conclusion of authentication based on morphological. CONCLUSION: The primers designed in the present study were highly specific for B. multicinctus.

Systematic Analysis of Long Noncoding RNAs in the Senescence-accelerated Mouse Prone 8 Brain Using RNA Sequencing.

Long noncoding RNAs (lncRNAs) may play an important role in Alzheimer's disease (AD) pathogenesis. However, despite considerable research in this area, the comprehensive and systematic understanding of lncRNAs in AD is still limited. The emergence of RNA sequencing provides a predictor and has incomparable advantage compared with other methods, including microarray. In this study, we identified lncRNAs in a 7-month-old mouse brain through deep RNA sequencing using the senescence-accelerated mouse prone 8 (SAMP8) and senescence-accelerated mouse resistant 1 (SAMR1) models. A total of 599,985,802 clean reads and 23,334 lncRNA transcripts were obtained. Then, we identified 97 significantly upregulated and 114 significantly downregulated lncRNA transcripts from all cases in SAMP8 mice relative to SAMR1 mice. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes analyses revealed that these significantly dysregulated lncRNAs were involved in regulating the development of AD from various angles, such as nerve growth factor term (GO: 1990089), mitogen-activated protein kinase signaling pathway, and AD pathway. Furthermore, the most probable AD-associated lncRNAs were predicted and listed in detail. Our study provided the systematic dissection of lncRNA profiling in SAMP8 mouse brain and accelerated the development of lncRNA biomarkers in AD. These attracting biomarkers could provide significant insights into AD therapy in the future.

The complete mitochondrial genome of Paecilomyces hepiali (Ascomycota, Eurotiomycetes).

Paecilomyces hepiali, belonging to the Eurotiales order Ascomycota, is an endoparasitic fungus that commonly exists in the natural Cordyceps sinensis anamorph stage. Here, we report the complete mitochondrial DNA sequences of P. hepiali for the first time. The genome is 24,245 bp in length, encoding 15 protein-coding genes (PCGs), 2 rRNA genes, 25 tRNA genes and 3 homing endonucleases. The overall AT composition is 73.37% and the average AT content of PCG, rRNA, tRNA and non-coding region are 74.21%, 66.07%, 62.83% and 75.96%, respectively. Phylogenetic analysis with eight Ascomycota species and thirteen Basidiomycota species revealed that P. hepiali is was more closely related to Cordyceps bassiana, Cordycep smilitaris and Cordyceps brongniartii. It is confirmed that P. hepiali is a derivative of Cordyceps sinensis. This study provided valuable information on the gene contents of the mitochondrial genome and would facilitate the study of function and evolution of P. hepiali.

Draft Genome Sequence of Paecilomyces hepiali, Isolated from Cordyceps sinensis.

Paecilomyces hepiali is an endoparasitic fungus that commonly exists in the natural Cordyceps sinensis Here, we report the draft genome sequence of P. hepiali, which will facilitate the exploitation of medicinal compounds produced by the fungus.