Objective To investigate the effects of Qingguang'anⅡFormula(QGAⅡ)on the gut micro-biota of mice with chronic high intraocular pressure(IOP)model,and explore its key micro-biota for protecting the optic nerve.Me...Objective To investigate the effects of Qingguang'anⅡFormula(QGAⅡ)on the gut micro-biota of mice with chronic high intraocular pressure(IOP)model,and explore its key micro-biota for protecting the optic nerve.Methods A total of 10 specific pathogen free(SPF)grade female DBA/2J mice were random-ly divided into model group and QGAⅡgroup(n=5 for each group),while additional 5 SPF-grade female C57BL/6J mice were assigned to control group.Mice presented spontaneous high IOP and showed elevated approximately at the age of seven months.The high IOP was maintained until week 38,when gavage was initiated.Mice in control group underwent the same intragastric treatment,while those in QGAⅡgroup were gavaged with QGAⅡ(9.67 g/kg),once a day for four weeks.Retinal morphology was examined using hematoxylin and eosin(HE)staining,with the number of retinal ganglion cells(RGCs)counted.The expression level of Brn3a protein,a specific marker for RGCs,was detected by immunofluorescence,with the mean optical density(OD)measured for quantitative analysis.In addition,16S rDNA se-quencing was leveraged to analyze changes in the diversity of gut microbiota,including theirα-diversity(Chao1,Shannon,Pielou’s evenness,and observed species index)andβ-diversity.Venn diagrams and linear discriminant analysis effect size(LEfSe)analysis was employed to investigate the number of amplicon sequence variants(ASVs),the abundance of differential gut microbiota species,and the classification of species at both the phylum and genus levels within the three groups of mice.Results HE staining revealed that compared with control group,model group showed signif-icant reduction in the number of RGCs(P<0.01),with intracellular vacuolar degeneration and nuclear pyknosis.After QGAⅡtreatment,the number of RGCs was significantly in-creased compared with model group(P<0.01),with notable improvements in intracellular vacuolar degeneration.Immunofluorescence analysis showed that the mean OD of Brn3a protein was significantly decreased in model group compared with control group(P<0.01),while QGAⅡtreatment significantly elevated its expression level(P<0.01).Analysis ofα-diversity showed that after QGAⅡintervention,the Chao1,Shannon,and Pielou’s evenness indices were significantly increased(P<0.01),and the observed species index was elevated(P<0.05).β-Diversity analysis demonstrated distinct clustering among the three groups,indicating relatively low similarity in bacterial community structures.ASV clustering identi-fied a total of 14061 ASVs across all groups,with 9514 ASVs shared between model and QGAⅡgroups.At the phylum level,the abundance of Bacteroidetes was significantly decreased in model group compared with control group(P<0.01),while Firmicutes and the Firmicutes/Bacteroidetes(F/B)ratio were significantly increased(P<0.01).QGAⅡtreatment significantly reduced both Firmicutes abundance and the F/B ratio(P<0.01).At the genus level,Lactobacillus was dominant across all groups,with its abundance significantly in-creased in model group(P<0.01)and subsequently decreased following QGAⅡintervention(P<0.05).Conclusion QGAⅡrestructured the gut microbiota of DBA/2J mice with chronic high IOP,bringing changes in their diversity and abundance of components.Firmicutes,Bacteroidetes,Lactobacillus,along with their associated microorganisms,are likely critical components of the gut microbiota that contribute to the optic neuroprotective effects of QGAⅡon chronic high IOP mice.展开更多
To fulfill the demands of applications under severe operational conditions,alloys should possess outstanding wear resistance at elevated temperatures.A Ti-Hf-Nb-V based refractory high entropy alloy(RHEA)was successfu...To fulfill the demands of applications under severe operational conditions,alloys should possess outstanding wear resistance at elevated temperatures.A Ti-Hf-Nb-V based refractory high entropy alloy(RHEA)was successfully produced using the directed energy deposition(DED)technique,which avoided the formation of fatal defects and showcased well-performed mechanical properties across a broad temperature spectrum.Strategic design of the oxidation sequence enabled the early formation of oxide nanolayers,which can form a polycrystalline oxide nanocoating under a complex stress condition to drastically reduce the wear rate from 2.69×10^(-4) mm^(3)·(N·m)^(−1) at room temperature to 6.90×10^(-7) mm^(3)·(N·m)^(−1) at 600℃.These results indicate that the application of additive manufacturing to fabricate RHEAs with superior wear resistance at high temperatures paves the way for the development of functional coatings designed to withstand extreme conditions.展开更多
High intraocular pressure causes retinal ganglion cell injury in primary and secondary glaucoma diseases,yet the molecular landscape characteristics of retinal cells under high intraocular pressure remain unknown.Rat ...High intraocular pressure causes retinal ganglion cell injury in primary and secondary glaucoma diseases,yet the molecular landscape characteristics of retinal cells under high intraocular pressure remain unknown.Rat models of acute hypertension ocular pressure were established by injection of cross-linked hyaluronic acid hydrogel(Healaflow■).Single-cell RNA sequencing was then used to describe the cellular composition and molecular profile of the retina following high intraocular pressure.Our results identified a total of 12 cell types,namely retinal pigment epithelial cells,rod-photoreceptor cells,bipolar cells,Müller cells,microglia,cone-photoreceptor cells,retinal ganglion cells,endothelial cells,retinal progenitor cells,oligodendrocytes,pericytes,and fibroblasts.The single-cell RNA sequencing analysis of the retina under acute high intraocular pressure revealed obvious changes in the proportions of various retinal cells,with ganglion cells decreased by 23%.Hematoxylin and eosin staining and TUNEL staining confirmed the damage to retinal ganglion cells under high intraocular pressure.We extracted data from retinal ganglion cells and analyzed the retinal ganglion cell cluster with the most distinct expression.We found upregulation of the B3gat2 gene,which is associated with neuronal migration and adhesion,and downregulation of the Tsc22d gene,which participates in inhibition of inflammation.This study is the first to reveal molecular changes and intercellular interactions in the retina under high intraocular pressure.These data contribute to understanding of the molecular mechanism of retinal injury induced by high intraocular pressure and will benefit the development of novel therapies.展开更多
RNA sequencing is the use of hight hroughput next generation sequencing technology to survey, characterize, and quantify the transcriptome of a genome. RNA sequencing has been used to analyze the pathogenesis of sever...RNA sequencing is the use of hight hroughput next generation sequencing technology to survey, characterize, and quantify the transcriptome of a genome. RNA sequencing has been used to analyze the pathogenesis of several malignancies such melanoma, lung cancer, and colorectal cancer. RNA sequencing can identify differential expression of genes(DEG's), mutated genes, fusion genes, and gene isoforms in disease states. RNA sequencing has been used in the investigation of several colorectal diseases such as colorectal cancer, inflammatory bowel disease(ulcerative colitis and Crohn's disease), and irritable bowel syndrome.展开更多
Our aim is to study the roles of a new emerging group of non-coding RNAs, circRNAs, in tomato(Solanum lycopersicum L.) plants grown at the combination of drought and heat, two of the most usual stress conditions known...Our aim is to study the roles of a new emerging group of non-coding RNAs, circRNAs, in tomato(Solanum lycopersicum L.) plants grown at the combination of drought and heat, two of the most usual stress conditions known to frequently happen in field. Tomato seedlings from cultivar‘Jinling Meiyu’ were treated without stresses(control), at water shortage, high temperature and subjected the multiple stresses. In total, 467 circRNAs were identified with 87.82% from exon using high throughput sequencing technology. Among the circRNAs, 70 were from chr1 with the range from 23 to 49 from the other chromosomes. In detail, 156 circRNAs were shared in the four libraries, while 21, 17 and 36 circRNAs were only shown in drought, heat and multiple stresses libraries, respectively. Through a differential expression analysis, four, seven and nine circRNAs were differentially regulated in tomato at drought, heat and multiple stresses as compared with control. These circRNAs played roles on photosynthesis, starch and sucrose metabolism, RNA transport, RNA degradation, spliceosome, ribosome, etc. Our study underlined the potential role of circRNAs involved in the abiotic stress response in tomato, which might pave the way for studying biological roles of circRNAs responding to multiple stresses in plants.展开更多
In order to reveal the influence of different plant configurations on the microbial community structure and diversity in rhizosphere soil of Cotinus coggygria in Fragrant Hills park,the ITS+5.8S rDNA gene and 16S rDNA...In order to reveal the influence of different plant configurations on the microbial community structure and diversity in rhizosphere soil of Cotinus coggygria in Fragrant Hills park,the ITS+5.8S rDNA gene and 16S rDNA gene V3-V4 region sequencing analysis for fungi and bacteria,respectively,were conducted by high throughput sequencing(Illumina MiSeq).The results showed that the fungal diversity in the rhizosphere soil samples of C.coggygria in Fragrant Hills park in 2018 was significantly higher than that in 2016,and it was higher in the rhizosphere soil of healthy C.coggygria in Xunlupo than that in diseased ones in 2018.Verticillium dahliae,which is the causal agent of C.coggygria wilt,was detected in five soil samples.In 2018,the bacterial diversity in the rhizosphere soil of diseased C.coggygria in Xunlupo was the lowest,while it was the highest in the rhizosphere soil of healthy C.coggygria under Platycladus orientalis in Langfengting.展开更多
Torque teno virus(TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased seque...Torque teno virus(TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased sequencing to screen for viruses in the serum of a patient with persistent high fever who died of suspected viral infection and prolonged weakness, we identified the complete genome sequence of a TTV(isolate Hebei-1). The genome of TTV-Hebei-1 is 3649 bp in length, encoding four putative open reading frames, and it has a G+C content of 49%. Genomic comparison and a BLASTN search revealed that the assembled genome of TTV-Hebei-1 represented a novel isolate, with a genome sequence that was highly heterologous to the sequences of other reported TTV strains. A phylogenetic tree constructed using the complete genome sequence showed that TTV-Hebei-1 and an uncharacterized Taiwan Residents strain, TW53A37, constitute a new TTV genotype. The patient was strongly suspected of carrying a viral infection and died eventually without any other possible causes being apparent. No virus other than the novel TTV was identified in his serum sample. Although a direct causal link between the novel TTV genotype infection and the patient's disease could not be confirmed, the findings suggest that surveillance of this novel TTV genotype is necessary and that its role in disease deserves to be explored.展开更多
Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and h...Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.展开更多
This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（1...This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（10.7±0.6） years old）, were used for the rumen contents collection. Illumina MiSeq high-throughput sequencing technology was applied to examine the archaeal composition of rumen contents. A total of 92 901 high-quality archaeal sequences were analyzed, and these were assigned to 2 033 operational taxonomic units （OTUs）. Among these, 974 OTUs were unique to adult yaks while 846 OTUs were unique to elderly yaks; 213 OTUs were shared by both groups. At the phylum level, more than 99% of the obtained OTUs belonged to the Euryarchaeota phylum. At the genus level, the archaea could be divided into 7 archaeal genera. The 7 genera （i.e., Methanobrevibacter, Methanobacterium, Methanosphaera, Thermogymnomonas, Methanomicrobiu, Meth- animicrococcus and the unclassified genus） were shared by all yaks, and their total abundance accounted for 99% of the rumen archaea. The most abundant archaea in elderly and adult yaks were Methanobrevibacterand Thermogymnomonas, respectively. The abundance of Methanobacteria （class）, Methanobacteriales （order）, Methanobacteriaceae （family）, and Methanobrevibacter （genus） in elderly yaks was significantly higher than in adult yaks. In contrast, the abundance of Ther-mogymnomonas in elderly yaks was 34% lower than in adult yaks, though the difference was not statistically significant. The difference in abundance of other archaea was not significant between the two groups. These results suggested that the structure of archaea in the rumen of yaks changed with age. This is the first study to compare the phytogenetic differences of rumen archaeal structure and composition using the yak model.展开更多
Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has...Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has enabled the identification of RNA edits at unprecedented throughput and resolution. However, our knowledge of RNA editing in swine is still limited.Results: Here, we utilized RES-Scanner to identify RNA editing sites in the brain, subcutaneous fat, heart, liver,muscle, lung and ovary in three 180-day-old Large White gilts based on matched strand-specific RNA sequencing and whole-genome resequencing datasets. In total, we identified 74863 editing sites, and 92.1% of these sites caused adenosine-to-guanosine(A-to-G) conversion. Most A-to-G sites were located in noncoding regions and generally had low editing levels. In total, 151 A-to-G sites were detected in coding regions(CDS), including 94 sites that could lead to nonsynonymous amino acid changes. We provide further evidence supporting a previous observation that pig transcriptomes are highly editable at PRE-1 elements. The number of A-to-G editing sites ranged from 4155(muscle) to 25001(brain) across the seven tissues. The expression levels of the ADAR enzymes could explain some but not all of this variation across tissues. The functional analysis of the genes with tissuespecific editing sites in each tissue revealed that RNA editing might play important roles in tissue function.Specifically, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the muscle.Conclusions: This study identified a total of 74863 nonredundant RNA editing sites in seven tissues and revealed the potential importance of RNA editing in tissue function. Our findings largely extend the porcine editome and enhance our understanding of RNA editing in swine.展开更多
Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples fr...Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples from Huguangyan Maar Lake were investigated using a high-throughput sequencing method. We found significant differences between the microbial community compositions of the water and the sediment. The sediment samples contained more diverse Bacteria and Archaea than did the water samples. Actinobacteria, Betaproteobacteria, Cyanobacteria, and Deltaproteobacteria predominated in the water samples while Deltaproteobacteria, Anaerolineae, Nitrospira, and Dehalococcoidia were the major bacterial groups in the sediment. As for Archaea, Woesearchaeota (DHVEG-6), unclassified Archaea, and Deep Sea Euryarchaeotic Group were detected at higher abundances in the water, whereas the Miscellaneous Crenarchaeotic Group, Thermoplasmata, and Methanomicrobia were significantly more abundant in the sediment. Interactions between Bacteria and Archaea were common in both the water column and the sediment. The concentrations of major nutrients (NO^3-, PO4^3-, SiO3^2- and NH4^+) shaped the microbial population structures in the water. At the higher phylogenetic levels including phylum and class, many of the dominant groups were those that were also abundant in other lakes;however, novel microbial populations (unclassified) were often seen at the lower phylogenetic levels. Our study lays a foundation for examining microbial biogeochemical cycling in sequestered lakes or reservoirs.展开更多
The effect of high-strength ammonia nitrogen acclimation on sludge activity in sequencing batch reactor （SBR） was investigated. Two batch experiments, RUN1 and RUN2, were conducted with the influent ammonia nitrogen...The effect of high-strength ammonia nitrogen acclimation on sludge activity in sequencing batch reactor （SBR） was investigated. Two batch experiments, RUN1 and RUN2, were conducted with the influent ammonia nitrogen concentrations 60 and 500 mg/L, respectively. The sludges inoculated from RUN1 and RUN2 were used to treat a series of influent with ammonia nitrogen concentrations of 59, 232, 368, 604 and 1152 mg/L. It is found that the activated sludge acclimated to higher ammonia nitrogen concentrations revealed higher COD and NH 4 ＋ -N removal efficiencies, and slower DHA decrease. The results confirmed that the activities of the bacteria in activated sludge in SBR were inhibited by high-strength ammonia nitrogen, whereas the activated sludge acclimated to high-strength ammonia nitrogen showed substantial resistance to inhibition by influents containing high levels of ammonia nitrogen.展开更多
Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matc...Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matched paraneoplastic normal tissues, and to explore the intrinsic mechanism of OSCC development and progres- sion. We obtained the differentially expressed mRNA expression profiles in 10 pairs of fresh-frozen OSCC tissue specimens and matched paraneoplastic normal tissue specimens by high-throughput RNA sequencing. By using Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analyses, the functional significance of the differentially expressed genes were analyzed. We identified 1,120 sig- nificantly up-regulated mRNAs and 178 significantly down-regulated mRNAs in OSCC, compared to normal tissue. The differentially expressed mRNAs were involved in 20 biological processes and 68 signal pathways. Compared to adjacent normal tissue, the expression of MAGEAll was up-regulated; TCHH was down-regulated. These find- ings were verified by real-time PCR. These differentially expressed mRNAs may function as oncogenes or tumor suppressors in the development and progression of OSCC. This study provides novel insights into OSCC. However, further work is needed to determine if these differentially expressed mRNAs have potential roles as diagnostic bio- markers and candidate therapeutic targets for OSCC.展开更多
We used Illumina high-throughput sequencing of PCR-amplified V3-V4 16 S rRNA gene regions to characterize bacterial communities associated with the adductor muscles, gills, gonads and intestines of the Yesso scallop(P...We used Illumina high-throughput sequencing of PCR-amplified V3-V4 16 S rRNA gene regions to characterize bacterial communities associated with the adductor muscles, gills, gonads and intestines of the Yesso scallop(Patinopecten yessoensis) from waters around Zhangzidao, Dalian, China. Overall, 421,276 optimized reads were classified as 25 described bacterial phyla and 308 genera. Firmicutes, Proteobacteria, Tenericutes, Bacteroidetes, Chlamydiae and Spirochaetae accounted for > 97% of the total reads in the four organs. The bacterial 16 S rDNA sequences assigned to Firmicutes and Proteobacteria were abundant in the adductor muscles, gills and gonads; while reads from Tenericutes were dominant in the intestines, followed by those from Firmicutes, Chlamydiae, Proteobacteria and Bacteroidetes. At the genus level, the dominant genera in the adductor muscles, gills and gonads appeared to be Bacillus, Enterococcus and Lactococcus, whereas Mycoplasma was dominant in the intestines. The relative abundances of Bacillus, Enterococcus, Lactococcus, Alkaliphilus, Raoultella, Paenibacillus and Oceanobacillus were significantly lower in the intestine than in the other three organs. Cluster analysis and principal coordinates analysis of the operational taxonomy units profile revealed significant differences in the bacterial community structure between the intestine and the other three organs. Taken together, these results suggest that scallops have intestine-specific bacterial communities and the adductor muscles, gills and gonads harbor similar communities. The difference in the bacterial community between organs may relate to unique habitats, surroundings, diet and their respective physiological functions.展开更多
Multiple sclerosis（MS） is characterized by chronic inflammation in conjunction with neurodegeneration within the central nervous system. Most individuals with MS begin with a relapsing remitting course that later tr...Multiple sclerosis（MS） is characterized by chronic inflammation in conjunction with neurodegeneration within the central nervous system. Most individuals with MS begin with a relapsing remitting course that later transitions to secondary progressive MS. Currently available disease-modifying therapies（DMTs） for relapsing MS have been demonstrated to reduce disease activity, however most patients require a change in therapy over the course of their disease. Treatment goals include the prevention of relapses and disability accumulation and to achieve this objective requires careful planning. Sequencing of DMTs for individual patients should be designed in such a way to maximize disease control and minimize risk based on the mechanism of action, pharmacokinetic and pharmacodynamic properties of each therapy. This includes the DMT patients are being switched from to those they are being switched to. The reversibility of immune system effects should be a key consideration for DMT sequence selection. This feature varies across DMTs and should factor more prominently in decision making as newer treatments become available for the prevention of disability accumulation in patients with progressive MS. In this short review, we discuss the landscape of existing therapies with an eye to the future when planning for optimal DMT sequencing. While no cure exists for MS, efforts are being directed toward research in neuroregeneration with the hope for positive outcomes.展开更多
Delivery of safe and pathogen-free drinking water is crucial to public health.However,there exist challenges to the maintenance of the sterility of drinking water throughout the drinking water distribution systems（D...Delivery of safe and pathogen-free drinking water is crucial to public health.However,there exist challenges to the maintenance of the sterility of drinking water throughout the drinking water distribution systems（DWDS）.Microbial growth in DWDS,such as growth of opportunistic pathogenic microorganisms,can lead to severe health problems in consumers（Berry et al.,2006;Brettar and Hofle,2006;Lu et al.,2014;Zhang et al.,2015）.展开更多
Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequ...Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequisite step. In this study, 2 independent transgene soybean lines were selected(LB4-AtDCGS-1-20-5-2 and CGS-ZG11) as typical cases. Both lines contained expression cassette of At-DCGS that encoding a feedback-insensitive cystathionine gamma-synthase to produce higher level methionine(Met). LB4-AtDCGS-1-20-5-2 was whole genome sequenced with one paired-end 500 bp library and two mate-paired 1 kb and 2 kb libraries using Illumina HiSeq sequencing platform. CGS-ZG11 was sequenced with only one paired-end 500 bp library. Both genomes were assembled,and 2 scaffold sequences(1 for each line) were screened out by aligning with transgene.Then the transgene insertion and its flanking regions in soybean genome were further identified and confirmed by PCR cloning and Sanger sequencing. Results showed that these 2 transgene lines had single copy of inserted transgene. Their transgene insertion contents were identified, which facilitates further safety assessment. These results indicated that genome assembly using high throughput sequencing is a powerful tool for identifying transgene insertions, even with limited knowledge.展开更多
A longstanding discrepancy between theoretical predictions and experimental observations on the highpressurestructural transformations of lanthanum mononitride(LaN)has posed challenges for understandingthe behavior of...A longstanding discrepancy between theoretical predictions and experimental observations on the highpressurestructural transformations of lanthanum mononitride(LaN)has posed challenges for understandingthe behavior of heavy transition metal mononitrides.Here,we systematically investigate the structural evolutionof LaN under high pressure using first-principles calculations combined with angle-dispersive synchrotron X-raydiffraction,identifying the phase transition sequence and corresponding phase boundaries.Analyses of energetics,kinetic barriers,and lattice dynamics reveal distinct mechanisms driving these transitions.These results clarifythe structural stability of LaN and offer guidance for studying other heavy transition metal mononitrides withcomplex electronic behavior under extreme conditions.展开更多
miRNAs regulate a variety of biological processes through pairing-based regulation of gene expression at the 3＇ end of the noncoding region of the target miRNA, miRNAs were found to be abnormally expressed in ischemi...miRNAs regulate a variety of biological processes through pairing-based regulation of gene expression at the 3＇ end of the noncoding region of the target miRNA, miRNAs were found to be abnormally expressed in ischemia/reperfusion injury models. High-throughput sequencing is a recently developed method for sequencing miRNAs and has been widely used in the analysis of miRNAs. In this study, ischemia/reperfusion injury models were intracerebroventricularly injected with 50 pg/kg apelin-13. High-throughput sequencing showed that 357 known miRNAs were differentially expressed among rat models, among which 78 changed to 〉 2-fold or 〈 0.5-fold. Quantita- tive real-time polymerase chain reaction was selected to confirm the expression levels of four miRNAs that were differentially expressed, the results of which were consistent with the results of high-throughput sequencing. Gene Ontology analysis revealed that the predicted targets of the different miRNAs are particularly associated with cellular process, metabolic process, single-organism process, cell, and binding. Kyoto Encyclopedia of Gene and Genome analysis showed that the target genes are involved in metabolic pathways, mitogen-ac- tivated protein kinase signaling pathway, calcium signaling pathway, and nuclear factor-KB signaling pathway. Our findings suggest that differentially expressed miRNAs and their target genes play an important role in ischemia/reperfusion injury and neuroprotection by apelin-13.展开更多
Airborne particulate matter(PM),especially PM2.5,can be easily adsorbed by human respiratory system.Their roles in carrying pathogens for spreading epidemic diseases has attracted great concern.Herein,we developed a n...Airborne particulate matter(PM),especially PM2.5,can be easily adsorbed by human respiratory system.Their roles in carrying pathogens for spreading epidemic diseases has attracted great concern.Herein,we developed a novel gelatin filter-based and culture-independent method for investigation of the microbial diversity in PM samples during a haze episode in Tianjin,China.This method involves particle capture by gelatin filters,filter dissolution for DNA extraction,and high-throughput sequencing for analysis of the microbial diversity.A total of 584 operational taxonomic units(OTUs)of bacteria and 370 OTUs of fungi at the genus level were identified during hazy days.The results showed that both bacterial and fungal diversities could be evaluated by this method.This study provides a convenient strategy for investigation of microbial biodiversity in haze,facilitating accurate evaluation of airborne epidemic diseases.展开更多
基金National Natural Science Foundation of China(81904260)Scientific Research Project of Hunan Province Department of Education(22B0398)Scientific Research Project of Traditional Chinese Medicine of Hunan Province(D2022045).
文摘Objective To investigate the effects of Qingguang'anⅡFormula(QGAⅡ)on the gut micro-biota of mice with chronic high intraocular pressure(IOP)model,and explore its key micro-biota for protecting the optic nerve.Methods A total of 10 specific pathogen free(SPF)grade female DBA/2J mice were random-ly divided into model group and QGAⅡgroup(n=5 for each group),while additional 5 SPF-grade female C57BL/6J mice were assigned to control group.Mice presented spontaneous high IOP and showed elevated approximately at the age of seven months.The high IOP was maintained until week 38,when gavage was initiated.Mice in control group underwent the same intragastric treatment,while those in QGAⅡgroup were gavaged with QGAⅡ(9.67 g/kg),once a day for four weeks.Retinal morphology was examined using hematoxylin and eosin(HE)staining,with the number of retinal ganglion cells(RGCs)counted.The expression level of Brn3a protein,a specific marker for RGCs,was detected by immunofluorescence,with the mean optical density(OD)measured for quantitative analysis.In addition,16S rDNA se-quencing was leveraged to analyze changes in the diversity of gut microbiota,including theirα-diversity(Chao1,Shannon,Pielou’s evenness,and observed species index)andβ-diversity.Venn diagrams and linear discriminant analysis effect size(LEfSe)analysis was employed to investigate the number of amplicon sequence variants(ASVs),the abundance of differential gut microbiota species,and the classification of species at both the phylum and genus levels within the three groups of mice.Results HE staining revealed that compared with control group,model group showed signif-icant reduction in the number of RGCs(P<0.01),with intracellular vacuolar degeneration and nuclear pyknosis.After QGAⅡtreatment,the number of RGCs was significantly in-creased compared with model group(P<0.01),with notable improvements in intracellular vacuolar degeneration.Immunofluorescence analysis showed that the mean OD of Brn3a protein was significantly decreased in model group compared with control group(P<0.01),while QGAⅡtreatment significantly elevated its expression level(P<0.01).Analysis ofα-diversity showed that after QGAⅡintervention,the Chao1,Shannon,and Pielou’s evenness indices were significantly increased(P<0.01),and the observed species index was elevated(P<0.05).β-Diversity analysis demonstrated distinct clustering among the three groups,indicating relatively low similarity in bacterial community structures.ASV clustering identi-fied a total of 14061 ASVs across all groups,with 9514 ASVs shared between model and QGAⅡgroups.At the phylum level,the abundance of Bacteroidetes was significantly decreased in model group compared with control group(P<0.01),while Firmicutes and the Firmicutes/Bacteroidetes(F/B)ratio were significantly increased(P<0.01).QGAⅡtreatment significantly reduced both Firmicutes abundance and the F/B ratio(P<0.01).At the genus level,Lactobacillus was dominant across all groups,with its abundance significantly in-creased in model group(P<0.01)and subsequently decreased following QGAⅡintervention(P<0.05).Conclusion QGAⅡrestructured the gut microbiota of DBA/2J mice with chronic high IOP,bringing changes in their diversity and abundance of components.Firmicutes,Bacteroidetes,Lactobacillus,along with their associated microorganisms,are likely critical components of the gut microbiota that contribute to the optic neuroprotective effects of QGAⅡon chronic high IOP mice.
基金supported by Guangdong Major Project of Basic and Applied Basic Research,China(No.2019B030302010)the Joint Research Scheme sponsored by the Research Grants Council of the Hong Kong Special Administrative Region,China and National Natural Science Foundation of China(Nos.N_PolyU523/20 and 52061160483)+4 种基金the National Natural Science Foundation of China(Nos.52104362,52071222,52471179,52471180 and 52001221)the National Key R&D Program of China(No.2022YFA1603800)the National Key Research and Development Program of China(No.2021YFA0716302)Guangdong Provincial Quantum Science Strategic Initiative(No.GDZX2301001)Guangdong Basic and Applied Basic Research,China(No.2020B1515130007).
文摘To fulfill the demands of applications under severe operational conditions,alloys should possess outstanding wear resistance at elevated temperatures.A Ti-Hf-Nb-V based refractory high entropy alloy(RHEA)was successfully produced using the directed energy deposition(DED)technique,which avoided the formation of fatal defects and showcased well-performed mechanical properties across a broad temperature spectrum.Strategic design of the oxidation sequence enabled the early formation of oxide nanolayers,which can form a polycrystalline oxide nanocoating under a complex stress condition to drastically reduce the wear rate from 2.69×10^(-4) mm^(3)·(N·m)^(−1) at room temperature to 6.90×10^(-7) mm^(3)·(N·m)^(−1) at 600℃.These results indicate that the application of additive manufacturing to fabricate RHEAs with superior wear resistance at high temperatures paves the way for the development of functional coatings designed to withstand extreme conditions.
基金supported by the National Natural Science Foundation of China,No.82371051(to DW)the Natural Science Foundation of Beijing,No.7212092(to DW)+1 种基金the Capital’s Funds for Health Improvement and Research,No.2022-2-5041(to DW)the Fund of Science and Technology Development of Beijing Rehabilitation Hospital,Capital Medical University,No.2021R-001(to YL).
文摘High intraocular pressure causes retinal ganglion cell injury in primary and secondary glaucoma diseases,yet the molecular landscape characteristics of retinal cells under high intraocular pressure remain unknown.Rat models of acute hypertension ocular pressure were established by injection of cross-linked hyaluronic acid hydrogel(Healaflow■).Single-cell RNA sequencing was then used to describe the cellular composition and molecular profile of the retina following high intraocular pressure.Our results identified a total of 12 cell types,namely retinal pigment epithelial cells,rod-photoreceptor cells,bipolar cells,Müller cells,microglia,cone-photoreceptor cells,retinal ganglion cells,endothelial cells,retinal progenitor cells,oligodendrocytes,pericytes,and fibroblasts.The single-cell RNA sequencing analysis of the retina under acute high intraocular pressure revealed obvious changes in the proportions of various retinal cells,with ganglion cells decreased by 23%.Hematoxylin and eosin staining and TUNEL staining confirmed the damage to retinal ganglion cells under high intraocular pressure.We extracted data from retinal ganglion cells and analyzed the retinal ganglion cell cluster with the most distinct expression.We found upregulation of the B3gat2 gene,which is associated with neuronal migration and adhesion,and downregulation of the Tsc22d gene,which participates in inhibition of inflammation.This study is the first to reveal molecular changes and intercellular interactions in the retina under high intraocular pressure.These data contribute to understanding of the molecular mechanism of retinal injury induced by high intraocular pressure and will benefit the development of novel therapies.
文摘RNA sequencing is the use of hight hroughput next generation sequencing technology to survey, characterize, and quantify the transcriptome of a genome. RNA sequencing has been used to analyze the pathogenesis of several malignancies such melanoma, lung cancer, and colorectal cancer. RNA sequencing can identify differential expression of genes(DEG's), mutated genes, fusion genes, and gene isoforms in disease states. RNA sequencing has been used in the investigation of several colorectal diseases such as colorectal cancer, inflammatory bowel disease(ulcerative colitis and Crohn's disease), and irritable bowel syndrome.
基金funding from National Natural Science Foundation of China (Grant No. 31601745)Natural Science Foundation of Jiangsu Province (Grant No. BK20160579)Aarhus University Research Foundation (Grant No. 30379)
文摘Our aim is to study the roles of a new emerging group of non-coding RNAs, circRNAs, in tomato(Solanum lycopersicum L.) plants grown at the combination of drought and heat, two of the most usual stress conditions known to frequently happen in field. Tomato seedlings from cultivar‘Jinling Meiyu’ were treated without stresses(control), at water shortage, high temperature and subjected the multiple stresses. In total, 467 circRNAs were identified with 87.82% from exon using high throughput sequencing technology. Among the circRNAs, 70 were from chr1 with the range from 23 to 49 from the other chromosomes. In detail, 156 circRNAs were shared in the four libraries, while 21, 17 and 36 circRNAs were only shown in drought, heat and multiple stresses libraries, respectively. Through a differential expression analysis, four, seven and nine circRNAs were differentially regulated in tomato at drought, heat and multiple stresses as compared with control. These circRNAs played roles on photosynthesis, starch and sucrose metabolism, RNA transport, RNA degradation, spliceosome, ribosome, etc. Our study underlined the potential role of circRNAs involved in the abiotic stress response in tomato, which might pave the way for studying biological roles of circRNAs responding to multiple stresses in plants.
基金Supported by Science and Technology Project from the Beijing Municipal Administration Center of Parks(ZX2018016).
文摘In order to reveal the influence of different plant configurations on the microbial community structure and diversity in rhizosphere soil of Cotinus coggygria in Fragrant Hills park,the ITS+5.8S rDNA gene and 16S rDNA gene V3-V4 region sequencing analysis for fungi and bacteria,respectively,were conducted by high throughput sequencing(Illumina MiSeq).The results showed that the fungal diversity in the rhizosphere soil samples of C.coggygria in Fragrant Hills park in 2018 was significantly higher than that in 2016,and it was higher in the rhizosphere soil of healthy C.coggygria in Xunlupo than that in diseased ones in 2018.Verticillium dahliae,which is the causal agent of C.coggygria wilt,was detected in five soil samples.In 2018,the bacterial diversity in the rhizosphere soil of diseased C.coggygria in Xunlupo was the lowest,while it was the highest in the rhizosphere soil of healthy C.coggygria under Platycladus orientalis in Langfengting.
基金supported by a grant from the National Natural Science Foundation of China (No. 81072350)the National Hi-Tech Research and Development (863) Program of China (No. 2012AA022-003)+2 种基金the China Mega-Project on Major Drug Development (No. 2011ZX09401-023)the China Mega-Project on Infectious Disease Prevention (No. 2013ZX10004-605, No. 2013ZX10004-607, No. 2013ZX10004-217, and No. 2011ZX10004-001) the State Key Laboratory of Pathogen and BioSecurity Program (No. SKLPBS1113)
文摘Torque teno virus(TTV) has been found to be prevalent world-wide in healthy populations and in patients with various diseases, but its etiological role has not yet been determined. Using high-throughput unbiased sequencing to screen for viruses in the serum of a patient with persistent high fever who died of suspected viral infection and prolonged weakness, we identified the complete genome sequence of a TTV(isolate Hebei-1). The genome of TTV-Hebei-1 is 3649 bp in length, encoding four putative open reading frames, and it has a G+C content of 49%. Genomic comparison and a BLASTN search revealed that the assembled genome of TTV-Hebei-1 represented a novel isolate, with a genome sequence that was highly heterologous to the sequences of other reported TTV strains. A phylogenetic tree constructed using the complete genome sequence showed that TTV-Hebei-1 and an uncharacterized Taiwan Residents strain, TW53A37, constitute a new TTV genotype. The patient was strongly suspected of carrying a viral infection and died eventually without any other possible causes being apparent. No virus other than the novel TTV was identified in his serum sample. Although a direct causal link between the novel TTV genotype infection and the patient's disease could not be confirmed, the findings suggest that surveillance of this novel TTV genotype is necessary and that its role in disease deserves to be explored.
基金Supported by the National Natural Science Foundations of China(3127218631301791)
文摘Gene sequencing is a great way to interpret life, and high-throughput sequencing technology is a revolutionary technological innovation in gene sequencing researches. This technology is characterized by low cost and high-throughput data. Currently, high-throughput sequencing technology has been widely applied in multi-level researches on genomics, transcriptomics and epigenomics. And it has fundamentally changed the way we approach problems in basic and translational researches and created many new possibilities. This paper presented a general description of high-throughput sequencing technology and a comprehensive review of its application with plain, concisely and precisely. In order to help researchers finish their work faster and better, promote science amateurs and understand it easier and better.
基金the International Cooperation Project of the Ministry of Sciences and Technology of China(2014DFA32860)the National Natural Science Foundation of China(31402104)for their financial support
文摘This study was conducted to investigate the phylogenetic diversity of archaea in the rumen of adult and elderly yaks. Six domesticated female yaks, 3 adult yaks （（5.3±0.6） years old）, and 3 elderly yaks （（10.7±0.6） years old）, were used for the rumen contents collection. Illumina MiSeq high-throughput sequencing technology was applied to examine the archaeal composition of rumen contents. A total of 92 901 high-quality archaeal sequences were analyzed, and these were assigned to 2 033 operational taxonomic units （OTUs）. Among these, 974 OTUs were unique to adult yaks while 846 OTUs were unique to elderly yaks; 213 OTUs were shared by both groups. At the phylum level, more than 99% of the obtained OTUs belonged to the Euryarchaeota phylum. At the genus level, the archaea could be divided into 7 archaeal genera. The 7 genera （i.e., Methanobrevibacter, Methanobacterium, Methanosphaera, Thermogymnomonas, Methanomicrobiu, Meth- animicrococcus and the unclassified genus） were shared by all yaks, and their total abundance accounted for 99% of the rumen archaea. The most abundant archaea in elderly and adult yaks were Methanobrevibacterand Thermogymnomonas, respectively. The abundance of Methanobacteria （class）, Methanobacteriales （order）, Methanobacteriaceae （family）, and Methanobrevibacter （genus） in elderly yaks was significantly higher than in adult yaks. In contrast, the abundance of Ther-mogymnomonas in elderly yaks was 34% lower than in adult yaks, though the difference was not statistically significant. The difference in abundance of other archaea was not significant between the two groups. These results suggested that the structure of archaea in the rumen of yaks changed with age. This is the first study to compare the phytogenetic differences of rumen archaeal structure and composition using the yak model.
基金supported by the National Key Technology R&D Program of China(2015BAD03B02–2)Beijing Natural Science Foundation(6174047)+1 种基金earmarked fund for Modern Agro-industry Technology Research System(CARS-35)Agricultural Science and Technology Innovation Program(ASTIP-IAS02)
文摘Background: RNA editing is a co/posttranscriptional modification mechanism that increases the diversity of transcripts, with potential functional consequences. The advent of next-generation sequencing technologies has enabled the identification of RNA edits at unprecedented throughput and resolution. However, our knowledge of RNA editing in swine is still limited.Results: Here, we utilized RES-Scanner to identify RNA editing sites in the brain, subcutaneous fat, heart, liver,muscle, lung and ovary in three 180-day-old Large White gilts based on matched strand-specific RNA sequencing and whole-genome resequencing datasets. In total, we identified 74863 editing sites, and 92.1% of these sites caused adenosine-to-guanosine(A-to-G) conversion. Most A-to-G sites were located in noncoding regions and generally had low editing levels. In total, 151 A-to-G sites were detected in coding regions(CDS), including 94 sites that could lead to nonsynonymous amino acid changes. We provide further evidence supporting a previous observation that pig transcriptomes are highly editable at PRE-1 elements. The number of A-to-G editing sites ranged from 4155(muscle) to 25001(brain) across the seven tissues. The expression levels of the ADAR enzymes could explain some but not all of this variation across tissues. The functional analysis of the genes with tissuespecific editing sites in each tissue revealed that RNA editing might play important roles in tissue function.Specifically, more pathways showed significant enrichment in the fat and liver than in other tissues, while no pathway was enriched in the muscle.Conclusions: This study identified a total of 74863 nonredundant RNA editing sites in seven tissues and revealed the potential importance of RNA editing in tissue function. Our findings largely extend the porcine editome and enhance our understanding of RNA editing in swine.
基金Supported by the National Natural Science Foundation of China(Nos.41576123,41706129)the Guangdong Natural Science Foundation(Nos.2015A030313326,2016A030312004)+2 种基金the International Science and Technology Cooperation Project(No.GASI-IPOVI-04)the Project of Enhancing School with Innovation of Guangdong Ocean University(No.GDOU2016050243)the Program for Scientific Research Start-Up Funds of Guangdong Ocean University(No.E15030)
文摘Huguangyan Maar Lake is a typical maar lake in the southeast of China. It is well preserved and not disturbed by anthropogenic activities. In this study, microbial community structures in sediment and water samples from Huguangyan Maar Lake were investigated using a high-throughput sequencing method. We found significant differences between the microbial community compositions of the water and the sediment. The sediment samples contained more diverse Bacteria and Archaea than did the water samples. Actinobacteria, Betaproteobacteria, Cyanobacteria, and Deltaproteobacteria predominated in the water samples while Deltaproteobacteria, Anaerolineae, Nitrospira, and Dehalococcoidia were the major bacterial groups in the sediment. As for Archaea, Woesearchaeota (DHVEG-6), unclassified Archaea, and Deep Sea Euryarchaeotic Group were detected at higher abundances in the water, whereas the Miscellaneous Crenarchaeotic Group, Thermoplasmata, and Methanomicrobia were significantly more abundant in the sediment. Interactions between Bacteria and Archaea were common in both the water column and the sediment. The concentrations of major nutrients (NO^3-, PO4^3-, SiO3^2- and NH4^+) shaped the microbial population structures in the water. At the higher phylogenetic levels including phylum and class, many of the dominant groups were those that were also abundant in other lakes;however, novel microbial populations (unclassified) were often seen at the lower phylogenetic levels. Our study lays a foundation for examining microbial biogeochemical cycling in sequestered lakes or reservoirs.
基金supported by the Foundation of the Ministry of Education(No.WTWER0702)
文摘The effect of high-strength ammonia nitrogen acclimation on sludge activity in sequencing batch reactor （SBR） was investigated. Two batch experiments, RUN1 and RUN2, were conducted with the influent ammonia nitrogen concentrations 60 and 500 mg/L, respectively. The sludges inoculated from RUN1 and RUN2 were used to treat a series of influent with ammonia nitrogen concentrations of 59, 232, 368, 604 and 1152 mg/L. It is found that the activated sludge acclimated to higher ammonia nitrogen concentrations revealed higher COD and NH 4 ＋ -N removal efficiencies, and slower DHA decrease. The results confirmed that the activities of the bacteria in activated sludge in SBR were inhibited by high-strength ammonia nitrogen, whereas the activated sludge acclimated to high-strength ammonia nitrogen showed substantial resistance to inhibition by influents containing high levels of ammonia nitrogen.
基金supported by a project funded by the Priority Academic Program Development of Jiangsu Higher Education Institutions(PAPD,2014-37)
文摘Differentially expressed genes are thought to regulate the development and progression of oral squamous cell carcinomas （OSCC）. The purpose of this study was to screen differentially expressed mRNAs in OSCC and matched paraneoplastic normal tissues, and to explore the intrinsic mechanism of OSCC development and progres- sion. We obtained the differentially expressed mRNA expression profiles in 10 pairs of fresh-frozen OSCC tissue specimens and matched paraneoplastic normal tissue specimens by high-throughput RNA sequencing. By using Gene Ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes （KEGG） pathway enrichment analyses, the functional significance of the differentially expressed genes were analyzed. We identified 1,120 sig- nificantly up-regulated mRNAs and 178 significantly down-regulated mRNAs in OSCC, compared to normal tissue. The differentially expressed mRNAs were involved in 20 biological processes and 68 signal pathways. Compared to adjacent normal tissue, the expression of MAGEAll was up-regulated; TCHH was down-regulated. These find- ings were verified by real-time PCR. These differentially expressed mRNAs may function as oncogenes or tumor suppressors in the development and progression of OSCC. This study provides novel insights into OSCC. However, further work is needed to determine if these differentially expressed mRNAs have potential roles as diagnostic bio- markers and candidate therapeutic targets for OSCC.
基金financial support from Zhangzidao Group Company Limited for the project (No. 99801214)
文摘We used Illumina high-throughput sequencing of PCR-amplified V3-V4 16 S rRNA gene regions to characterize bacterial communities associated with the adductor muscles, gills, gonads and intestines of the Yesso scallop(Patinopecten yessoensis) from waters around Zhangzidao, Dalian, China. Overall, 421,276 optimized reads were classified as 25 described bacterial phyla and 308 genera. Firmicutes, Proteobacteria, Tenericutes, Bacteroidetes, Chlamydiae and Spirochaetae accounted for > 97% of the total reads in the four organs. The bacterial 16 S rDNA sequences assigned to Firmicutes and Proteobacteria were abundant in the adductor muscles, gills and gonads; while reads from Tenericutes were dominant in the intestines, followed by those from Firmicutes, Chlamydiae, Proteobacteria and Bacteroidetes. At the genus level, the dominant genera in the adductor muscles, gills and gonads appeared to be Bacillus, Enterococcus and Lactococcus, whereas Mycoplasma was dominant in the intestines. The relative abundances of Bacillus, Enterococcus, Lactococcus, Alkaliphilus, Raoultella, Paenibacillus and Oceanobacillus were significantly lower in the intestine than in the other three organs. Cluster analysis and principal coordinates analysis of the operational taxonomy units profile revealed significant differences in the bacterial community structure between the intestine and the other three organs. Taken together, these results suggest that scallops have intestine-specific bacterial communities and the adductor muscles, gills and gonads harbor similar communities. The difference in the bacterial community between organs may relate to unique habitats, surroundings, diet and their respective physiological functions.
文摘Multiple sclerosis（MS） is characterized by chronic inflammation in conjunction with neurodegeneration within the central nervous system. Most individuals with MS begin with a relapsing remitting course that later transitions to secondary progressive MS. Currently available disease-modifying therapies（DMTs） for relapsing MS have been demonstrated to reduce disease activity, however most patients require a change in therapy over the course of their disease. Treatment goals include the prevention of relapses and disability accumulation and to achieve this objective requires careful planning. Sequencing of DMTs for individual patients should be designed in such a way to maximize disease control and minimize risk based on the mechanism of action, pharmacokinetic and pharmacodynamic properties of each therapy. This includes the DMT patients are being switched from to those they are being switched to. The reversibility of immune system effects should be a key consideration for DMT sequence selection. This feature varies across DMTs and should factor more prominently in decision making as newer treatments become available for the prevention of disability accumulation in patients with progressive MS. In this short review, we discuss the landscape of existing therapies with an eye to the future when planning for optimal DMT sequencing. While no cure exists for MS, efforts are being directed toward research in neuroregeneration with the hope for positive outcomes.
文摘Delivery of safe and pathogen-free drinking water is crucial to public health.However,there exist challenges to the maintenance of the sterility of drinking water throughout the drinking water distribution systems（DWDS）.Microbial growth in DWDS,such as growth of opportunistic pathogenic microorganisms,can lead to severe health problems in consumers（Berry et al.,2006;Brettar and Hofle,2006;Lu et al.,2014;Zhang et al.,2015）.
基金supported by the Genetically Modified Organisms Breeding Major Projects of China (2016ZX08011-003)China Agriculture Research System (CARS-04)CAAS Agricultural Science and Technology Innovation Project
文摘Genetically modified(GM) organisms are widely adopted. However, their safety assessments and control are still of special concern to the public. Identifying and localizing transgene insertion is an essentially prerequisite step. In this study, 2 independent transgene soybean lines were selected(LB4-AtDCGS-1-20-5-2 and CGS-ZG11) as typical cases. Both lines contained expression cassette of At-DCGS that encoding a feedback-insensitive cystathionine gamma-synthase to produce higher level methionine(Met). LB4-AtDCGS-1-20-5-2 was whole genome sequenced with one paired-end 500 bp library and two mate-paired 1 kb and 2 kb libraries using Illumina HiSeq sequencing platform. CGS-ZG11 was sequenced with only one paired-end 500 bp library. Both genomes were assembled,and 2 scaffold sequences(1 for each line) were screened out by aligning with transgene.Then the transgene insertion and its flanking regions in soybean genome were further identified and confirmed by PCR cloning and Sanger sequencing. Results showed that these 2 transgene lines had single copy of inserted transgene. Their transgene insertion contents were identified, which facilitates further safety assessment. These results indicated that genome assembly using high throughput sequencing is a powerful tool for identifying transgene insertions, even with limited knowledge.
基金supported by the Natural Science Foundation of China(Grant Nos.T2325013,12474004,and 52288102)the National Key Research and Development Program of China(Grant No.2021YFA1400503)the Program for Jilin University Science and Technology Innovative Research Team。
文摘A longstanding discrepancy between theoretical predictions and experimental observations on the highpressurestructural transformations of lanthanum mononitride(LaN)has posed challenges for understandingthe behavior of heavy transition metal mononitrides.Here,we systematically investigate the structural evolutionof LaN under high pressure using first-principles calculations combined with angle-dispersive synchrotron X-raydiffraction,identifying the phase transition sequence and corresponding phase boundaries.Analyses of energetics,kinetic barriers,and lattice dynamics reveal distinct mechanisms driving these transitions.These results clarifythe structural stability of LaN and offer guidance for studying other heavy transition metal mononitrides withcomplex electronic behavior under extreme conditions.
基金supported by the National Natural Science Foundation of China,No.81501018 and 816712276the Natural Science Foundation of Shandong Province of China,No.ZR2013CQ031 and ZR2014HL040
文摘miRNAs regulate a variety of biological processes through pairing-based regulation of gene expression at the 3＇ end of the noncoding region of the target miRNA, miRNAs were found to be abnormally expressed in ischemia/reperfusion injury models. High-throughput sequencing is a recently developed method for sequencing miRNAs and has been widely used in the analysis of miRNAs. In this study, ischemia/reperfusion injury models were intracerebroventricularly injected with 50 pg/kg apelin-13. High-throughput sequencing showed that 357 known miRNAs were differentially expressed among rat models, among which 78 changed to 〉 2-fold or 〈 0.5-fold. Quantita- tive real-time polymerase chain reaction was selected to confirm the expression levels of four miRNAs that were differentially expressed, the results of which were consistent with the results of high-throughput sequencing. Gene Ontology analysis revealed that the predicted targets of the different miRNAs are particularly associated with cellular process, metabolic process, single-organism process, cell, and binding. Kyoto Encyclopedia of Gene and Genome analysis showed that the target genes are involved in metabolic pathways, mitogen-ac- tivated protein kinase signaling pathway, calcium signaling pathway, and nuclear factor-KB signaling pathway. Our findings suggest that differentially expressed miRNAs and their target genes play an important role in ischemia/reperfusion injury and neuroprotection by apelin-13.
基金supported by Project of Science and Technology Development in Wuqing District,Tianjin (No.WQKJ201614)Tianjin 131 innovative talent training project,Postdoctoral Science Foundation
文摘Airborne particulate matter(PM),especially PM2.5,can be easily adsorbed by human respiratory system.Their roles in carrying pathogens for spreading epidemic diseases has attracted great concern.Herein,we developed a novel gelatin filter-based and culture-independent method for investigation of the microbial diversity in PM samples during a haze episode in Tianjin,China.This method involves particle capture by gelatin filters,filter dissolution for DNA extraction,and high-throughput sequencing for analysis of the microbial diversity.A total of 584 operational taxonomic units(OTUs)of bacteria and 370 OTUs of fungi at the genus level were identified during hazy days.The results showed that both bacterial and fungal diversities could be evaluated by this method.This study provides a convenient strategy for investigation of microbial biodiversity in haze,facilitating accurate evaluation of airborne epidemic diseases.
