When he left his uncle in Nor-bu Linka, the Dalai Lama’s summer palace in Lhasa, on the evening of March 10,1959, Qiampa Getsang never expected one day he would do the same job as his late uncle did to manage the pal...When he left his uncle in Nor-bu Linka, the Dalai Lama’s summer palace in Lhasa, on the evening of March 10,1959, Qiampa Getsang never expected one day he would do the same job as his late uncle did to manage the palace of the Dalai Lama.展开更多
AIM:To investigate the stability of the seven housekeeping genes:beta-actin(ActB),glyceraldehyde-3-phosphate dehydrogenase(GAPDH),18s ribosomal unit 5(18s),cyclophilin A(CycA),hypoxanthine-guanine phosphoribosyl trans...AIM:To investigate the stability of the seven housekeeping genes:beta-actin(ActB),glyceraldehyde-3-phosphate dehydrogenase(GAPDH),18s ribosomal unit 5(18s),cyclophilin A(CycA),hypoxanthine-guanine phosphoribosyl transferase(HPRT),ribosomal protein large P0(36B4)and terminal uridylyl transferase 1(U6)in the diabetic retinal tissue of rat model.METHODS:The expression of these seven genes in rat retinal tissues was determined using real-time quantitative reverse transcription polymerase chain reaction(RT-qPCR)in two groups;normal control rats and streptozotocininduced diabetic rats.The stability analysis of gene expression was investigated using geNorm,NormFinder,BestKeeper,and comparative delta-Ct(ΔCt)algorithms.RESULTS:The 36B4 gene was stably expressed in the retinal tissues of normal control animals;however,it was less stable in diabetic retinas.The 18s gene was expressed consistently in both normal control and diabetic rats’retinal tissue.That this gene was the best reference for data normalisation in RT-qPCR studies that used the retinal tissue of streptozotocin-induced diabetic rats.Furthermore,there was no ideal gene stably expressed for use in all experimental settings.CONCLUSION:Identifying relevant genes is a need for achieving RT-qPCR validity and reliability and must be appropriately achieved based on a specific experimental setting.展开更多
Rhizobia, crucial for nitrogen fixation in leguminous plants, play a vital role in soybean cultivation. This study, conducted in Mexico, a major soybean importer, aimed to identify bacteria from nodules of five soybea...Rhizobia, crucial for nitrogen fixation in leguminous plants, play a vital role in soybean cultivation. This study, conducted in Mexico, a major soybean importer, aimed to identify bacteria from nodules of five soybean varieties in high-production regions. Multilocus sequence analysis (MLSA) was employed for enhanced species resolution. The study identified six Bradyrhizobium species: Bradyrhizobium japonicum USDA 110, Bradyrhizobium japonicum USDA 6, Bradyrhizobium elkanii USDA 76, Bradyrhizobium neotropicale, Bradyrhizobium lablabi, and Bradyrhizobium icense. Bradyrhizobium japonicum USDA 110 predominated in the soils, displaying symbiotic preference for the Huasteca 400 variety. However, phylogenetic analysis didn't reveal a clear association between strains, soil, and soybean variety. This research sheds light on the diversity of rhizobia in Mexican soybean cultivation, contributing to the understanding of symbiotic relationships in soybean production systems.展开更多
It is not easy to associate apetite, easy-going younglady with some prestigiousproperty developments inBeijing. Kuang Yijun, alsoknown as Sally Kwong, isthe new "Shopping MallTailor" of China Ping AnTrust an...It is not easy to associate apetite, easy-going younglady with some prestigiousproperty developments inBeijing. Kuang Yijun, alsoknown as Sally Kwong, isthe new "Shopping MallTailor" of China Ping AnTrust and Investment Co.Ltd., a subsidiary of a China-展开更多
BACKGROUND Sleep breathing,one of the basic human needs,is a physiological need that affects cardiac functions,body temperature,daily vitality,muscle tone,hormone secretion,blood pressure,and many more.In the internat...BACKGROUND Sleep breathing,one of the basic human needs,is a physiological need that affects cardiac functions,body temperature,daily vitality,muscle tone,hormone secretion,blood pressure,and many more.In the international literature,studies reported that patients have had sleep problems in the hospital since the 1990s,but no measurement tool has been developed to determine the causes of hospitalacquired insomnia in individuals.These findings suggest that sleep remains in the background compared to activities such as nutrition and breathing.Although patients generally experience hospital-acquired sleep problems,there is no measurement tool to determine hospital-acquired sleep problems.These features show the originality of the research.AIM To develop a measurement tool to determine the sleep problems experienced by patients in the hospital.METHODS A personal information form,hospital-acquired insomnia scale(HAIS),and insomnia severity index(ISI)were used to collect research data.The study population consisted of patients hospitalized in the internal and surgical clinics of a research hospital in Turkey between December 2021 and March 2022.The sample consisted of 64 patients in the pilot application stage and 223 patients in the main application stage.Exploratory factor analysis and confirmatory factor analysis(CFA)analyses were performed using the SPSS 20 package program and the analysis of moment structure(AMOS)package program.Equivalent forms method used.RESULTS The HAIS consisted of 18 items and 5 subscales.The Cronbach alpha values of the subscales ranged between 0.672 and 0.842 and the Cronbach alpha value of the overall scale was 0.783.The scale explained 58.269%of the total variance.The items that constitute the factors were examined in terms of content integrity and named as physical environmental,psychological,safety,socioeconomic,and nutritional factors.CFA analysis of the 5-factor structure was performed in the AMOS package program.The fit indices of the obtained structure were examined.It was determined that the values obtained from the fit indices were sufficient.A significant correlation was determined between the HAIS and the ISI,which was used for the equivalent form method.CONCLUSION The HAIS is a valid and reliable measurement tool for determining patients’level of hospitalacquired insomnia.It is recommended to use this measurement tool to determine the insomnia problems of patients and to adapt it in other countries.展开更多
Background: Expression levels for genes of interest must be normalized with an appropriate reference, or housekeeping gene, to make accurate comparisons of quantitative real-time PCR results. The purpose of this stud...Background: Expression levels for genes of interest must be normalized with an appropriate reference, or housekeeping gene, to make accurate comparisons of quantitative real-time PCR results. The purpose of this study was to identify the most stable housekeeping genes in porcine articular cartilage subjected to a mechanical injury from a panel of 10 candidate genes. Results: Ten candidate housekeeping genes were evaluated in three different treatment groups of mechanically impacted porcine articular cartilage. The genes evaluated were: beta actin, beta-2-microglobulin, glyceraldehyde-3-phosphate dehydrogenase, hydroxymethylbilane synthase, hypoxanthine phosphoribosyl transferase, peptidylprolyl isomerase A (cyclophilin A), ribosomal protein L4, succinate dehydrogenase flavoprotein subunit A, TATA box binding protein, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein--zeta polypeptide The stability of the genes was measured using geNorm, BestKeeper, and NormFinder software. The four most stable genes measured via geNorm were (most to least stable) succinate dehydrogenase flavoprotein, subunit A, peptidylprolyl isomerase A, glyceraldehyde-3-phosphate dehydrogenase, beta actin; the four most stable genes measured via BestKeeper were glyceraldehyde-3-phosphate dehydrogenase, peptidylprolyl isomerase A, beta actin, succinate dehydrogenase flavoprotein, subunit A; and the four most stable genes measured via NormFinder were peptidylprolyl isomerase A, sucdnate dehydrogenase flavoprotein, subunit A, glyceraldehyde-3-phosphate dehydrogenase, beta actin. Conclusions: BestKeeper, geNorm, and NormFinder all generated similar results for the most stable genes in porcine articular cartilage. The use of these appropriate reference genes will facilitate accurate gene expression studies of porcine articular cartilage and suggest appropriate housekeeping genes for articular cartilage studies in other species.展开更多
The normalization of quantitative real-time PCR (qPCR) is important to obtain accurate gene expression data, and the most common method for qPCR normalization is to use reference genes. However, reference genes can ...The normalization of quantitative real-time PCR (qPCR) is important to obtain accurate gene expression data, and the most common method for qPCR normalization is to use reference genes. However, reference genes can be regulated under different conditions, qPCR has recently been used for gene expression study in Laodelphax striatellus, but there is no study on validation of the reference genes. In this study, five new housekeeping genes (LstrTUB1, LstrTUB2, LstrTUB3, LstrARF and LstrRPL9) in L. striatellus were cloned and deposited in the GenBank with accession numbers of JF728809, JF728810, JF728811, JF728807 and JF728806, respectively. Furthermore, mRNA expressions of the five genes and β-actin were measured by qPCR with insect samples of different instar at nymph stage, and the expression stabilities were determined by the software geNorm and NormFinder. As a result, ARF and RPL9 were consistently more stable than β-actin, while three TUB genes were less stable than β-actin. To determine the optimal number of reference genes used in qPCR, a pairwise variations analysis by geNorm indicated that two references ARF and RPL9 were required to obtain the accurate quantification. These results were fiarther confirmed by the validation qPCR experiment with chitinase gene as the target gene, in which the standard error of the mRNA quantification by using binary reference ARF-RPL9 was much lower than those by ARF, RPL9 or β-actin alone. Taken together, our study suggested that the combination of ARF-RPL9 could replace β-actin as the reference genes for qPCR in L. striatellus.展开更多
Trachinotus blochii is one of the important commercial fish species.In this study,we aim to confirm the reliability reference genes in T.blochii during different bacterial challenge through quantitative real-time PCR(...Trachinotus blochii is one of the important commercial fish species.In this study,we aim to confirm the reliability reference genes in T.blochii during different bacterial challenge through quantitative real-time PCR(qRT-PCR).The expression of the seven selected genes in four immune organs(i.e.,spleen,kidney,intestine,and gill)stimulated with Vibrio harveyi,Edwardsiella tarda,and Streptococcus agalactiae were determined by qRT-PCR.The PCR data was analyzed using the geNorm and NormFinder algorithms.The results showed the selection of the internal controls should be tissue specific when studying gene expression in response to bacterial stimulation.After 48 h of stimulation with V.harveyi,geNorm ranked EF1 A/Actin,18 S rRNA/B2M,UBCE/B2M,and 18 S rRNA/B2M,as the most stably expressed genes in spleen,kidney,intestine,and gill,respectively.After 48 h of stimulation with E.tarda,geNorm ranked 18 S rRNA/EF1 A,18 S rRNA/B2M,B2M/RPL13,and 18 S rRNA/EF1 A,as the most stably expressed genes in spleen,kidney,intestine,and gill,respectively.After 48 h of stimulation with S.agalactiae,18 S rRNA/EF1 A,18 S rRNA/B2 M,B2 M/Actin,and 18 S rRNA/B2M were ranked as the most stably expressed genes in spleen,kidney,intestine,and gill,respectively.Compared to the results analyzed by geNorm,reference genes received similar rankings when using NormFinder software.The results showed that the reference genes appeared to be not only tissue specific,but also specific to the infecting species of bacteria.If one gene is preferred when T.blochii were infected by bacteria,18 S rRNA,B2M,B2M,18 S rRNA may be used in spleen,kidney,intestine,and gill,respectively.展开更多
Bacillus coagulans can help ameliorate or prevent gastrointestinal diseases, but the genetic relationships among B. coagulans isolates are not well studied. Multilocus sequence typing analysis was conducted on 57 isol...Bacillus coagulans can help ameliorate or prevent gastrointestinal diseases, but the genetic relationships among B. coagulans isolates are not well studied. Multilocus sequence typing analysis was conducted on 57 isolates of B. coagulans from 22 provinces or autonomous regions in China. B. coagulans isolates were highly diverse and a total of 33(sequence typings) STs were found. These isolates had a weak clonal population structure and strong indications of intraspecies recombination. The evolution direction of B. coagulans was not correlated with geography or isolation source. Fifteen strains were selected for further analysis based on proximity relationships from the phylogenetic tree. Five isolates(B. coagulans-1, B. coagulans-10, B. coagulans-39, B. coagulans-70 and B. coagulans-71) with good spore-forming ability relative to the rest of the isolates were evaluated for constipation relief. B. coagulans-39 significantly relieved constipation symptoms in mice by regulating intestinal flora, increasing the production of short-chain fatty acids and restoring the level of gastrointestinal regulatory peptides. Comparative genomic analysis showed the beneficial effects of B. coagulans-39 might be associated with specific functional genes that are involved in the utilization of various carbohydrates as primary substrates and short-chain fatty acid production.展开更多
Real time quantitative PCR (RT-qPCR) requires a method to normalize the expression of target genes against an en- dogenous reference gene. It is known that commonly used housekeeping genes (HKGs) vary tremendously in ...Real time quantitative PCR (RT-qPCR) requires a method to normalize the expression of target genes against an en- dogenous reference gene. It is known that commonly used housekeeping genes (HKGs) vary tremendously in inflam- matory conditions;however information about the stability and expression of HKGs in chronic inflammatory joint dis- ease such as rheumatoid arthritis (RA) is scarce. The expressional stability of 10 commonly used HKGs was analyzed in the neuronal (spinal cord, dorsal root ganglia) and in the musculoskeletal tissues (tendon, muscle, epiphysis, capsule, periosteum and ankle joint) using RT-qPCR in the rat model of RA. In individual tissues, suitable HKGs were selected by | △Ct| (│Ct control-Ct arthritis│) and further analyzed by using software programs;geNorm and normfinder. We found hypoxanthine-guanine phosphoribosyl tranferase (HPRT) as the most stable gene except ankle joint while glyce-raldehyde-3-phosphate dehydrogenase (GAPDH) was found as the least stable gene in musculoskeletal tissues. In in-flamed ankle joint where no reference gene was found to be stably expressed, an inflammatory cell marker CD3 was used to normalize peptidylprolyl isomerase B (PPIB), the most homogenous HKG identified among the 10 HKGs. The normalized PPIB was then used to analyze the gene expression of neurokinin 1 (NK1), receptor of substance P, a potent pro-inflammatory mediator. We observed a 3.5 fold increase (p = 0.009) in NK1 expression in inflamed ankle joint compared to control. Our results indicate that reference genes stability should be evaluated before using them as refer- ence during inflammatory conditions. In tissues with intense inflammatory cell infiltration, an inflammatory cell marker should be used to normalize the selected reference gene to avoid erroneous results.展开更多
Purpose: The aim of this study was to isolate and identify potentially pathogenic airborne fungi from Hospital das Clínicas Samuel Libanio in the city of Pouso Alegre-MG and evaluate their susceptibility to natur...Purpose: The aim of this study was to isolate and identify potentially pathogenic airborne fungi from Hospital das Clínicas Samuel Libanio in the city of Pouso Alegre-MG and evaluate their susceptibility to natural and industrial products. Methods: The air collection was performed by passive sedimentation in the morning during the autumn and winter seasons. Petri dishes were open as the location of air conditioning. The isolates were subjected to pathogenicity test. The identification of the fungi was performed according to the macroscopic evaluation and micromorphology. Potentially pathogenic isolates were susceptibility tested by disc diffusion method. The agents used were insecticides and industrial cleaning products and essential oils of citronella plants, lemon grass, eucalyptus and Melaleuca extracted by steam distillation method. Results: We obtained a total of 356 fungal isolates. The inside door environments were 126 (35.39%) and the outside environments were 230 (64.6%) isolates. The 22 (6.18%) isolates from the inside and 25 (6.18%) outside the hospital showed pathogenic potential. This isolates were identified as Acremonium spp., A. niger, A. terreus, A. versicolor, Curvularia sp., Penicillium sp. and Scopulariopsis sp. Susceptibility testing it was observed that most of the isolates were susceptible to the principle product containing sodium hypochlorite. Citronella oil showed enormous potential inhibition against all isolates. Already lemon grass oil was effective only against isolates of Penicillium spp. Conclusions: All genres identified are significant allergens, which can cause respiratory disease in both immunocompromised individuals such as asthmatics and people with any immune deficit. The monitoring of environmental sources should be performed, especially in special areas with immunocompromised patients. Despite efforts to try to reduce fungal infections hospital there are still flaws in the strategies employed.展开更多
Clostridium difficile is a Gram positive rod-shaped bacterium that produces two major toxins, A and B. The detection of the organism and its toxins has been widely carried out using specialized Enzyme-Linked Immunosor...Clostridium difficile is a Gram positive rod-shaped bacterium that produces two major toxins, A and B. The detection of the organism and its toxins has been widely carried out using specialized Enzyme-Linked Immunosorbent Assay (ELISA) kits;however these generally have been unsuccessful in identifying all Clostridium difficile positive samples. In this study, fifteen clinically symptomatic patients from three of the five major regional hospitals in Trinidad were investigated for Clostridium difficile infections. Stool samples were assessed by ELISA and cultured isolates were characterized using agar dilution antibiotic sensitivity assays, conventional Polymerase Chain Reaction (PCR), DNA sequencing and phylogenetic analysis of toxin A and B genes. All 15 patient stool samples and isolates were positive for toxigenic Clostridium difficile via ELISA and PCR respectively. All isolates were positive for the housekeeping tpi and Toxin B genes by PCR but only three of these were positive for the Toxin A gene. The Toxin B gene sequences showed 100% similarity levels among isolates while the Toxin A gene sequences showed 99% similarity among isolates. Phylogenetic analysis showed that the strains isolated in Trinidad most likely belonged to the same strain/group. Agar dilution sensitivity tests showed highest susceptibility to Pipercillin/Tazobactam and Meropenem (87%) and the highest resistance was seen with Cefotaxime in 93%. These results indicate that similar virulent strains of C. difficile are present in the Trinidad population and that pathogenic strains are more likely to be susceptible to Pipercillin/Tazobactam and Meropenem.展开更多
BACKGROUND Validation of the reference gene(RG)stability during experimental analyses is essential for correct quantitative real-time polymerase chain reaction(RT-qPCR)data normalisation.Commonly,in an unreliable way,...BACKGROUND Validation of the reference gene(RG)stability during experimental analyses is essential for correct quantitative real-time polymerase chain reaction(RT-qPCR)data normalisation.Commonly,in an unreliable way,several studies use genes involved in essential cellular functions[glyceraldehyde-3-phosphate dehydro-genase(GAPDH),18S rRNA,andβ-actin]without paying attention to whether they are suitable for such experimental conditions or the reason for choosing such genes.Furthermore,such studies use only one gene when Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines recom-mend two or more genes.It impacts the credibility of these studies and causes dis-tortions in the gene expression findings.For tissue engineering,the accuracy of gene expression drives the best experimental or therapeutical approaches.We cultivated DPSCs under two conditions:Undifferentiated and osteogenic dif-ferentiation,both for 35 d.We evaluated the gene expression of 10 candidates for RGs[ribosomal protein,large,P0(RPLP0),TATA-binding protein(TBP),GAPDH,actin beta(ACTB),tubulin(TUB),aminolevulinic acid synthase 1(ALAS1),tyro-sine 3-monooxygenase/tryptophan 5-monooxygenase activation protein,zeta(YWHAZ),eukaryotic translational elongation factor 1 alpha(EF1a),succinate dehydrogenase complex,subunit A,flavoprotein(SDHA),and beta-2-micro-globulin(B2M)]every 7 d(1,7,14,21,28,and 35 d)by RT-qPCR.The data were analysed by the four main algorithms,ΔCt method,geNorm,NormFinder,and BestKeeper and ranked by the RefFinder method.We subdivided the samples into eight subgroups.RESULTS All of the data sets from clonogenic and osteogenic samples were analysed using the RefFinder algorithm.The final ranking showed RPLP0/TBP as the two most stable RGs and TUB/B2M as the two least stable RGs.Either theΔCt method or NormFinder analysis showed TBP/RPLP0 as the two most stable genes.However,geNorm analysis showed RPLP0/EF1αin the first place.These algorithms’two least stable RGs were B2M/GAPDH.For BestKeeper,ALAS1 was ranked as the most stable RG,and SDHA as the least stable RG.The pair RPLP0/TBP was detected in most subgroups as the most stable RGs,following the RefFinfer ranking.CONCLUSION For the first time,we show that RPLP0/TBP are the most stable RGs,whereas TUB/B2M are unstable RGs for long-term osteogenic differentiation of human DPSCs in traditional monolayers.展开更多
Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for uncovering the regulatory codes of the human genome and understanding the molecular mechanisms of human disease...Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for uncovering the regulatory codes of the human genome and understanding the molecular mechanisms of human diseases.Ubiquitously expressed genes(UEGs)refer to the genes expressed across a majority of,if not all,phenotypic and physiological conditions of an organism.It is known that many human genes are broadly expressed across tissues.However,most previous UEG studies have only focused on providing a list of UEGs without capturing their global expression patterns,thus limiting the potential use of UEG information.In this study,we proposed a novel data-driven framework to leverage the extensive collection of40,000 human transcriptomes to derive a list of UEGs and their corresponding global expression patterns,which offers a valuable resource to further characterize human transcriptome.Our results suggest that about half(12,234;49.01%)of the human genes are expressed in at least 80%of human transcriptomes,and the median size of the human transcriptome is 16,342 genes(65.44%).Through gene clustering,we identified a set of UEGs,named LoVarUEGs,which have stable expression across human transcriptomes and can be used as internal reference genes for expression measurement.To further demonstrate the usefulness of this resource,we evaluated the global expression patterns for 16 previously predicted disallowed genes in islet beta cells and found that seven of these genes showed relatively more varied expression patterns,suggesting that the repression of these genes may not be unique to islet beta cells.展开更多
Blood-based mieroRNA (miRNA) signatures as biomarkers have been reported for various pathologies, including cancer, neurological disorders, cardiovascular diseases, and also infections. The regulatory mechanism behi...Blood-based mieroRNA (miRNA) signatures as biomarkers have been reported for various pathologies, including cancer, neurological disorders, cardiovascular diseases, and also infections. The regulatory mechanism behind respective miRNA patterns is only partially understood. Moreover, "preserved" miRNAs, i.e., miRNAs that are not dysregulated in any disease, and their biological impact have been explored to a very limited extent. We set out to systematically determine their role in regulatory networks by defining groups of highly-dysregulated miRNAs that contribute to a disease signature as opposed to preserved housekeeping miRNAs. We further determined preferential targets and pathways of both dysregulated and preserved miRNAs by computing multi-layer networks, which were compared between housekeeping and dysregulated miRNAs. Of 848 miRNAs examined across 1049 blood samples, 8 potential housekeepers showed very limited expression variations, while 20 miRNAs showed highly-dysregulated expression throughout the investigated blood samples. Our approach provides important insights into miRNAs and their role in regulatory networks. The methodology can be applied to systematically investigate the differences in target genes and pathways of arbitrary miRNA sets.展开更多
A bstract The tawny crazy ant(Nylanderia fulva)is a new invasive pest in the United States.At present,its management mainly relies on the use of synthetic insecticides,which are generally ineffective at producing last...A bstract The tawny crazy ant(Nylanderia fulva)is a new invasive pest in the United States.At present,its management mainly relies on the use of synthetic insecticides,which are generally ineffective at producing lasting control of the pest,necessitating alternative environmentally friendly measures.In this study,we evaluated the feasibility of gene silencing to control this ant species.Six housekeeping genes encoding actin(NfActin),coatomer subunit β (NfCOPP),arginine kinase(NfArgK),and V-type proton ATPase subunits A(NfvATPaseA),B(NfvATPaseB)and E(NfvATPaseE)were cloned.Phylogenetic analysis revealed high sequence similarity to homologs from other ant species,particularly the Florida carpenter ant(Camponotus floridanus).To silence these genes,vector L4440 was used to generate six specific RNAi constructs for bacterial expression.Heat-inactivated,dsRNA-expressing Escherichia coli were incorporated into artificial diet.Worker ants exhibited reduced endogenous gene expression after feeding on such diet for 9 d.However,only ingestion of dsRNAs of NfCOPfi(a gene involved in protein trafficking)and NfArgK(a cellular energy reserve regulatory gene in invertebrates)caused modest but significantly higher ant mortality than the control.These results suggest that bacterially expressed dsRNA can be orally delivered to ant cells as a mean to target its vulnerabilities.Improved efficacy is necessary for the RNAi-based approach to be useful in tawny crazy ant management.展开更多
Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED(Rice Expression Database;http://expression.ic4r.org),an integrated dat...Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED(Rice Expression Database;http://expression.ic4r.org),an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.展开更多
Rhizobial diversity is affected by interactions between soil features, fertilization strategy, and cropping system. However, interactions among the rhizobial community, chemical-organic manure fertilization, and plant...Rhizobial diversity is affected by interactions between soil features, fertilization strategy, and cropping system. However, interactions among the rhizobial community, chemical-organic manure fertilization, and plant production have not been well documented in Mollisols from long-term experiments. Aimed at maintaining and recovering the productivity of Chinese Mollisols, a long-term fertilization experiment had been carried out for 29 years under a wheat-maize-soybean rotation system, involving the application of recycled organic manure (ROM), chemical fertilizers (N, P, and/or K), or ROM plus N, P, and/or K. In the present study, the effects of different treatments were evaluated by determining soil physicochemical features, soybean production, and soybean rhizobial diversity. The results showed that application of ROM plus NPK maintained or increased soil fertility, which was accompanied by higher production and higher diversity of rhizobia, as compared with the other treatments. The negative association of Bradyrhizobium japonicum with N fertilizer, positive association of B. diazoefficiens with soil pH, and alleviation of N-inhibition on the diversity of Bradyrhizobium by the addition of ROM were recorded as new findings. Therefore, application of ROM or ROM plus NPK could be a feasible strategy for maintaining and recovering the fertility of Chinese Mollisols, whereas rhizobial diversity could be an indicator of soil fertility.展开更多
Internal standards are critical for quantitative RNA analyses.Housekeeping genes are often used as internal standards with the assumption that their express-ion levels remain relatively constant in different experi-me...Internal standards are critical for quantitative RNA analyses.Housekeeping genes are often used as internal standards with the assumption that their express-ion levels remain relatively constant in different experi-mental conditions.In this study,four commonly used housekeeping genes,Glyceraldehyde-3-phosphate dehy-drogenase(GAPDH),β-actin,28S rRNA and 18S rRNA were selected to test whether this assumption is tenable under hypoxic conditions.We tested the RNA expression level of these four genes in different hypoxic conditions.Rats subjected to acute hypoxia for 2 hours were used for tissue detection.Primary cultured neural stem cells from E13 fetal rats were treated with 3%O_(2) or 10%O_(2) for 24 hours for in vitro experiments.In both experiments,expression levels of 28S rRNA and 18S rRNA were constant,independent of hypoxia types.However,expression levels of GAPDH and b-actin were all changed in all kinds of hypoxic conditions.In particu-lar,the mRNA expression level of GAPDH was increased by 43.4%under 3%O_(2) hypoxic conditions.These results suggest that 18S rRNA and 28S rRNA are reliable internal controls for comparative analyses of transcrip-tion under hypoxia.GAPDH appears particularly unfa-vorable for this purpose in hypoxic conditions.展开更多
Surfeit 4(Surf 4), one of the identified housekeeping genes, was previously thought to encode a transmembrane protein that acts as a cargo receptor to maintain basic cellular functions. In recent years, Surf 4 gene is...Surfeit 4(Surf 4), one of the identified housekeeping genes, was previously thought to encode a transmembrane protein that acts as a cargo receptor to maintain basic cellular functions. In recent years, Surf 4 gene is overexpressed in some types of cancer, involved in the exosome signaling pathway in gastrointestinal stromal tumors, and played the role of an oncogene in ovarian cancer stem cells. In this paper,we review the characteristics and protein localization of Surf 4 gene, as well as its possible physiological functions and pathogenesis in various diseases and cancers,expecting to discuss its clinical application value.展开更多
文摘When he left his uncle in Nor-bu Linka, the Dalai Lama’s summer palace in Lhasa, on the evening of March 10,1959, Qiampa Getsang never expected one day he would do the same job as his late uncle did to manage the palace of the Dalai Lama.
基金Supported by grant from Fundamental Research Grant Scheme by Ministry of Higher Education(MoHE)600-IRMI/FRGS 5/3(101/2019).
文摘AIM:To investigate the stability of the seven housekeeping genes:beta-actin(ActB),glyceraldehyde-3-phosphate dehydrogenase(GAPDH),18s ribosomal unit 5(18s),cyclophilin A(CycA),hypoxanthine-guanine phosphoribosyl transferase(HPRT),ribosomal protein large P0(36B4)and terminal uridylyl transferase 1(U6)in the diabetic retinal tissue of rat model.METHODS:The expression of these seven genes in rat retinal tissues was determined using real-time quantitative reverse transcription polymerase chain reaction(RT-qPCR)in two groups;normal control rats and streptozotocininduced diabetic rats.The stability analysis of gene expression was investigated using geNorm,NormFinder,BestKeeper,and comparative delta-Ct(ΔCt)algorithms.RESULTS:The 36B4 gene was stably expressed in the retinal tissues of normal control animals;however,it was less stable in diabetic retinas.The 18s gene was expressed consistently in both normal control and diabetic rats’retinal tissue.That this gene was the best reference for data normalisation in RT-qPCR studies that used the retinal tissue of streptozotocin-induced diabetic rats.Furthermore,there was no ideal gene stably expressed for use in all experimental settings.CONCLUSION:Identifying relevant genes is a need for achieving RT-qPCR validity and reliability and must be appropriately achieved based on a specific experimental setting.
文摘Rhizobia, crucial for nitrogen fixation in leguminous plants, play a vital role in soybean cultivation. This study, conducted in Mexico, a major soybean importer, aimed to identify bacteria from nodules of five soybean varieties in high-production regions. Multilocus sequence analysis (MLSA) was employed for enhanced species resolution. The study identified six Bradyrhizobium species: Bradyrhizobium japonicum USDA 110, Bradyrhizobium japonicum USDA 6, Bradyrhizobium elkanii USDA 76, Bradyrhizobium neotropicale, Bradyrhizobium lablabi, and Bradyrhizobium icense. Bradyrhizobium japonicum USDA 110 predominated in the soils, displaying symbiotic preference for the Huasteca 400 variety. However, phylogenetic analysis didn't reveal a clear association between strains, soil, and soybean variety. This research sheds light on the diversity of rhizobia in Mexican soybean cultivation, contributing to the understanding of symbiotic relationships in soybean production systems.
文摘It is not easy to associate apetite, easy-going younglady with some prestigiousproperty developments inBeijing. Kuang Yijun, alsoknown as Sally Kwong, isthe new "Shopping MallTailor" of China Ping AnTrust and Investment Co.Ltd., a subsidiary of a China-
文摘BACKGROUND Sleep breathing,one of the basic human needs,is a physiological need that affects cardiac functions,body temperature,daily vitality,muscle tone,hormone secretion,blood pressure,and many more.In the international literature,studies reported that patients have had sleep problems in the hospital since the 1990s,but no measurement tool has been developed to determine the causes of hospitalacquired insomnia in individuals.These findings suggest that sleep remains in the background compared to activities such as nutrition and breathing.Although patients generally experience hospital-acquired sleep problems,there is no measurement tool to determine hospital-acquired sleep problems.These features show the originality of the research.AIM To develop a measurement tool to determine the sleep problems experienced by patients in the hospital.METHODS A personal information form,hospital-acquired insomnia scale(HAIS),and insomnia severity index(ISI)were used to collect research data.The study population consisted of patients hospitalized in the internal and surgical clinics of a research hospital in Turkey between December 2021 and March 2022.The sample consisted of 64 patients in the pilot application stage and 223 patients in the main application stage.Exploratory factor analysis and confirmatory factor analysis(CFA)analyses were performed using the SPSS 20 package program and the analysis of moment structure(AMOS)package program.Equivalent forms method used.RESULTS The HAIS consisted of 18 items and 5 subscales.The Cronbach alpha values of the subscales ranged between 0.672 and 0.842 and the Cronbach alpha value of the overall scale was 0.783.The scale explained 58.269%of the total variance.The items that constitute the factors were examined in terms of content integrity and named as physical environmental,psychological,safety,socioeconomic,and nutritional factors.CFA analysis of the 5-factor structure was performed in the AMOS package program.The fit indices of the obtained structure were examined.It was determined that the values obtained from the fit indices were sufficient.A significant correlation was determined between the HAIS and the ISI,which was used for the equivalent form method.CONCLUSION The HAIS is a valid and reliable measurement tool for determining patients’level of hospitalacquired insomnia.It is recommended to use this measurement tool to determine the insomnia problems of patients and to adapt it in other countries.
文摘Background: Expression levels for genes of interest must be normalized with an appropriate reference, or housekeeping gene, to make accurate comparisons of quantitative real-time PCR results. The purpose of this study was to identify the most stable housekeeping genes in porcine articular cartilage subjected to a mechanical injury from a panel of 10 candidate genes. Results: Ten candidate housekeeping genes were evaluated in three different treatment groups of mechanically impacted porcine articular cartilage. The genes evaluated were: beta actin, beta-2-microglobulin, glyceraldehyde-3-phosphate dehydrogenase, hydroxymethylbilane synthase, hypoxanthine phosphoribosyl transferase, peptidylprolyl isomerase A (cyclophilin A), ribosomal protein L4, succinate dehydrogenase flavoprotein subunit A, TATA box binding protein, and tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein--zeta polypeptide The stability of the genes was measured using geNorm, BestKeeper, and NormFinder software. The four most stable genes measured via geNorm were (most to least stable) succinate dehydrogenase flavoprotein, subunit A, peptidylprolyl isomerase A, glyceraldehyde-3-phosphate dehydrogenase, beta actin; the four most stable genes measured via BestKeeper were glyceraldehyde-3-phosphate dehydrogenase, peptidylprolyl isomerase A, beta actin, succinate dehydrogenase flavoprotein, subunit A; and the four most stable genes measured via NormFinder were peptidylprolyl isomerase A, sucdnate dehydrogenase flavoprotein, subunit A, glyceraldehyde-3-phosphate dehydrogenase, beta actin. Conclusions: BestKeeper, geNorm, and NormFinder all generated similar results for the most stable genes in porcine articular cartilage. The use of these appropriate reference genes will facilitate accurate gene expression studies of porcine articular cartilage and suggest appropriate housekeeping genes for articular cartilage studies in other species.
基金the National 973 Program of China(2010CB126200)the Genetically Modified Organism Breeding Project,Ministry of Agriculture,China(2009ZX08001-002B)
文摘The normalization of quantitative real-time PCR (qPCR) is important to obtain accurate gene expression data, and the most common method for qPCR normalization is to use reference genes. However, reference genes can be regulated under different conditions, qPCR has recently been used for gene expression study in Laodelphax striatellus, but there is no study on validation of the reference genes. In this study, five new housekeeping genes (LstrTUB1, LstrTUB2, LstrTUB3, LstrARF and LstrRPL9) in L. striatellus were cloned and deposited in the GenBank with accession numbers of JF728809, JF728810, JF728811, JF728807 and JF728806, respectively. Furthermore, mRNA expressions of the five genes and β-actin were measured by qPCR with insect samples of different instar at nymph stage, and the expression stabilities were determined by the software geNorm and NormFinder. As a result, ARF and RPL9 were consistently more stable than β-actin, while three TUB genes were less stable than β-actin. To determine the optimal number of reference genes used in qPCR, a pairwise variations analysis by geNorm indicated that two references ARF and RPL9 were required to obtain the accurate quantification. These results were fiarther confirmed by the validation qPCR experiment with chitinase gene as the target gene, in which the standard error of the mRNA quantification by using binary reference ARF-RPL9 was much lower than those by ARF, RPL9 or β-actin alone. Taken together, our study suggested that the combination of ARF-RPL9 could replace β-actin as the reference genes for qPCR in L. striatellus.
基金Supported by the National Natural Science Foundation of China(No.41666006,31702379)the Nanhai Famous Youth Project
文摘Trachinotus blochii is one of the important commercial fish species.In this study,we aim to confirm the reliability reference genes in T.blochii during different bacterial challenge through quantitative real-time PCR(qRT-PCR).The expression of the seven selected genes in four immune organs(i.e.,spleen,kidney,intestine,and gill)stimulated with Vibrio harveyi,Edwardsiella tarda,and Streptococcus agalactiae were determined by qRT-PCR.The PCR data was analyzed using the geNorm and NormFinder algorithms.The results showed the selection of the internal controls should be tissue specific when studying gene expression in response to bacterial stimulation.After 48 h of stimulation with V.harveyi,geNorm ranked EF1 A/Actin,18 S rRNA/B2M,UBCE/B2M,and 18 S rRNA/B2M,as the most stably expressed genes in spleen,kidney,intestine,and gill,respectively.After 48 h of stimulation with E.tarda,geNorm ranked 18 S rRNA/EF1 A,18 S rRNA/B2M,B2M/RPL13,and 18 S rRNA/EF1 A,as the most stably expressed genes in spleen,kidney,intestine,and gill,respectively.After 48 h of stimulation with S.agalactiae,18 S rRNA/EF1 A,18 S rRNA/B2 M,B2 M/Actin,and 18 S rRNA/B2M were ranked as the most stably expressed genes in spleen,kidney,intestine,and gill,respectively.Compared to the results analyzed by geNorm,reference genes received similar rankings when using NormFinder software.The results showed that the reference genes appeared to be not only tissue specific,but also specific to the infecting species of bacteria.If one gene is preferred when T.blochii were infected by bacteria,18 S rRNA,B2M,B2M,18 S rRNA may be used in spleen,kidney,intestine,and gill,respectively.
基金supported by the National Natural Science Foundation of China Program[No.31871773 and No.31820103010]Projects of Innovation and Development Pillar Program for Key Industries in Southern Xinjiang of Xinjiang Production and Construction Corps[2018DB002]+2 种基金National First-Class Discipline Program of Food Science and Technology[JUFSTR20180102]the BBSRC Newton Fund Joint Centre AwardCollaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province。
文摘Bacillus coagulans can help ameliorate or prevent gastrointestinal diseases, but the genetic relationships among B. coagulans isolates are not well studied. Multilocus sequence typing analysis was conducted on 57 isolates of B. coagulans from 22 provinces or autonomous regions in China. B. coagulans isolates were highly diverse and a total of 33(sequence typings) STs were found. These isolates had a weak clonal population structure and strong indications of intraspecies recombination. The evolution direction of B. coagulans was not correlated with geography or isolation source. Fifteen strains were selected for further analysis based on proximity relationships from the phylogenetic tree. Five isolates(B. coagulans-1, B. coagulans-10, B. coagulans-39, B. coagulans-70 and B. coagulans-71) with good spore-forming ability relative to the rest of the isolates were evaluated for constipation relief. B. coagulans-39 significantly relieved constipation symptoms in mice by regulating intestinal flora, increasing the production of short-chain fatty acids and restoring the level of gastrointestinal regulatory peptides. Comparative genomic analysis showed the beneficial effects of B. coagulans-39 might be associated with specific functional genes that are involved in the utilization of various carbohydrates as primary substrates and short-chain fatty acid production.
文摘Real time quantitative PCR (RT-qPCR) requires a method to normalize the expression of target genes against an en- dogenous reference gene. It is known that commonly used housekeeping genes (HKGs) vary tremendously in inflam- matory conditions;however information about the stability and expression of HKGs in chronic inflammatory joint dis- ease such as rheumatoid arthritis (RA) is scarce. The expressional stability of 10 commonly used HKGs was analyzed in the neuronal (spinal cord, dorsal root ganglia) and in the musculoskeletal tissues (tendon, muscle, epiphysis, capsule, periosteum and ankle joint) using RT-qPCR in the rat model of RA. In individual tissues, suitable HKGs were selected by | △Ct| (│Ct control-Ct arthritis│) and further analyzed by using software programs;geNorm and normfinder. We found hypoxanthine-guanine phosphoribosyl tranferase (HPRT) as the most stable gene except ankle joint while glyce-raldehyde-3-phosphate dehydrogenase (GAPDH) was found as the least stable gene in musculoskeletal tissues. In in-flamed ankle joint where no reference gene was found to be stably expressed, an inflammatory cell marker CD3 was used to normalize peptidylprolyl isomerase B (PPIB), the most homogenous HKG identified among the 10 HKGs. The normalized PPIB was then used to analyze the gene expression of neurokinin 1 (NK1), receptor of substance P, a potent pro-inflammatory mediator. We observed a 3.5 fold increase (p = 0.009) in NK1 expression in inflamed ankle joint compared to control. Our results indicate that reference genes stability should be evaluated before using them as refer- ence during inflammatory conditions. In tissues with intense inflammatory cell infiltration, an inflammatory cell marker should be used to normalize the selected reference gene to avoid erroneous results.
文摘Purpose: The aim of this study was to isolate and identify potentially pathogenic airborne fungi from Hospital das Clínicas Samuel Libanio in the city of Pouso Alegre-MG and evaluate their susceptibility to natural and industrial products. Methods: The air collection was performed by passive sedimentation in the morning during the autumn and winter seasons. Petri dishes were open as the location of air conditioning. The isolates were subjected to pathogenicity test. The identification of the fungi was performed according to the macroscopic evaluation and micromorphology. Potentially pathogenic isolates were susceptibility tested by disc diffusion method. The agents used were insecticides and industrial cleaning products and essential oils of citronella plants, lemon grass, eucalyptus and Melaleuca extracted by steam distillation method. Results: We obtained a total of 356 fungal isolates. The inside door environments were 126 (35.39%) and the outside environments were 230 (64.6%) isolates. The 22 (6.18%) isolates from the inside and 25 (6.18%) outside the hospital showed pathogenic potential. This isolates were identified as Acremonium spp., A. niger, A. terreus, A. versicolor, Curvularia sp., Penicillium sp. and Scopulariopsis sp. Susceptibility testing it was observed that most of the isolates were susceptible to the principle product containing sodium hypochlorite. Citronella oil showed enormous potential inhibition against all isolates. Already lemon grass oil was effective only against isolates of Penicillium spp. Conclusions: All genres identified are significant allergens, which can cause respiratory disease in both immunocompromised individuals such as asthmatics and people with any immune deficit. The monitoring of environmental sources should be performed, especially in special areas with immunocompromised patients. Despite efforts to try to reduce fungal infections hospital there are still flaws in the strategies employed.
文摘Clostridium difficile is a Gram positive rod-shaped bacterium that produces two major toxins, A and B. The detection of the organism and its toxins has been widely carried out using specialized Enzyme-Linked Immunosorbent Assay (ELISA) kits;however these generally have been unsuccessful in identifying all Clostridium difficile positive samples. In this study, fifteen clinically symptomatic patients from three of the five major regional hospitals in Trinidad were investigated for Clostridium difficile infections. Stool samples were assessed by ELISA and cultured isolates were characterized using agar dilution antibiotic sensitivity assays, conventional Polymerase Chain Reaction (PCR), DNA sequencing and phylogenetic analysis of toxin A and B genes. All 15 patient stool samples and isolates were positive for toxigenic Clostridium difficile via ELISA and PCR respectively. All isolates were positive for the housekeeping tpi and Toxin B genes by PCR but only three of these were positive for the Toxin A gene. The Toxin B gene sequences showed 100% similarity levels among isolates while the Toxin A gene sequences showed 99% similarity among isolates. Phylogenetic analysis showed that the strains isolated in Trinidad most likely belonged to the same strain/group. Agar dilution sensitivity tests showed highest susceptibility to Pipercillin/Tazobactam and Meropenem (87%) and the highest resistance was seen with Cefotaxime in 93%. These results indicate that similar virulent strains of C. difficile are present in the Trinidad population and that pathogenic strains are more likely to be susceptible to Pipercillin/Tazobactam and Meropenem.
基金Supported by São Paulo Research Foundation(FAPESP),No.2010/08918-9 and 2020/11564-6the KBSP Young Investigator Fellowship,No.2011/00204-0+2 种基金the DBF Fellowship,No.2019/27492-7the LMG Fellowship,No.2014/01395-1the CFB Fellowship,No.2014/14278-3.
文摘BACKGROUND Validation of the reference gene(RG)stability during experimental analyses is essential for correct quantitative real-time polymerase chain reaction(RT-qPCR)data normalisation.Commonly,in an unreliable way,several studies use genes involved in essential cellular functions[glyceraldehyde-3-phosphate dehydro-genase(GAPDH),18S rRNA,andβ-actin]without paying attention to whether they are suitable for such experimental conditions or the reason for choosing such genes.Furthermore,such studies use only one gene when Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines recom-mend two or more genes.It impacts the credibility of these studies and causes dis-tortions in the gene expression findings.For tissue engineering,the accuracy of gene expression drives the best experimental or therapeutical approaches.We cultivated DPSCs under two conditions:Undifferentiated and osteogenic dif-ferentiation,both for 35 d.We evaluated the gene expression of 10 candidates for RGs[ribosomal protein,large,P0(RPLP0),TATA-binding protein(TBP),GAPDH,actin beta(ACTB),tubulin(TUB),aminolevulinic acid synthase 1(ALAS1),tyro-sine 3-monooxygenase/tryptophan 5-monooxygenase activation protein,zeta(YWHAZ),eukaryotic translational elongation factor 1 alpha(EF1a),succinate dehydrogenase complex,subunit A,flavoprotein(SDHA),and beta-2-micro-globulin(B2M)]every 7 d(1,7,14,21,28,and 35 d)by RT-qPCR.The data were analysed by the four main algorithms,ΔCt method,geNorm,NormFinder,and BestKeeper and ranked by the RefFinder method.We subdivided the samples into eight subgroups.RESULTS All of the data sets from clonogenic and osteogenic samples were analysed using the RefFinder algorithm.The final ranking showed RPLP0/TBP as the two most stable RGs and TUB/B2M as the two least stable RGs.Either theΔCt method or NormFinder analysis showed TBP/RPLP0 as the two most stable genes.However,geNorm analysis showed RPLP0/EF1αin the first place.These algorithms’two least stable RGs were B2M/GAPDH.For BestKeeper,ALAS1 was ranked as the most stable RG,and SDHA as the least stable RG.The pair RPLP0/TBP was detected in most subgroups as the most stable RGs,following the RefFinfer ranking.CONCLUSION For the first time,we show that RPLP0/TBP are the most stable RGs,whereas TUB/B2M are unstable RGs for long-term osteogenic differentiation of human DPSCs in traditional monolayers.
基金We thank Dr.Yongkun Wang from the Network and Information Center at Shanghai Jiao Tong University(SJTU)for his support in high-performance computing.We thank Ph.D.Candidate Wei Liu from Yale University for her support in the acquisition of physiological trait-related genes.HL is supported by the National Key R&D Program of China(Grant No.2018YFC0910500)JG and JD are supported by the SJTU-Yale Collaborative Research Seed Fund and Neil Shen’s SJTU Medical Research Fund,China.JG and HL are partially supported by the Shanghai Municipal Commission of Health and Family Planning,China(Grant No.2018ZHYL0223)the Science and Technology Commission of Shanghai Municipality(STCSM),China(Grant No.17DZ2251200).
文摘Comprehensive characterization of spatial and temporal gene expression patterns in humans is critical for uncovering the regulatory codes of the human genome and understanding the molecular mechanisms of human diseases.Ubiquitously expressed genes(UEGs)refer to the genes expressed across a majority of,if not all,phenotypic and physiological conditions of an organism.It is known that many human genes are broadly expressed across tissues.However,most previous UEG studies have only focused on providing a list of UEGs without capturing their global expression patterns,thus limiting the potential use of UEG information.In this study,we proposed a novel data-driven framework to leverage the extensive collection of40,000 human transcriptomes to derive a list of UEGs and their corresponding global expression patterns,which offers a valuable resource to further characterize human transcriptome.Our results suggest that about half(12,234;49.01%)of the human genes are expressed in at least 80%of human transcriptomes,and the median size of the human transcriptome is 16,342 genes(65.44%).Through gene clustering,we identified a set of UEGs,named LoVarUEGs,which have stable expression across human transcriptomes and can be used as internal reference genes for expression measurement.To further demonstrate the usefulness of this resource,we evaluated the global expression patterns for 16 previously predicted disallowed genes in islet beta cells and found that seven of these genes showed relatively more varied expression patterns,suggesting that the repression of these genes may not be unique to islet beta cells.
基金funded by the European Union (FP7 Best Ageing,6031)Saarland University,Medical Faculty.Authors acknowledge the contribution of Comprehensive Biomarker Center (CBC),Heidelberg,in funding the study
文摘Blood-based mieroRNA (miRNA) signatures as biomarkers have been reported for various pathologies, including cancer, neurological disorders, cardiovascular diseases, and also infections. The regulatory mechanism behind respective miRNA patterns is only partially understood. Moreover, "preserved" miRNAs, i.e., miRNAs that are not dysregulated in any disease, and their biological impact have been explored to a very limited extent. We set out to systematically determine their role in regulatory networks by defining groups of highly-dysregulated miRNAs that contribute to a disease signature as opposed to preserved housekeeping miRNAs. We further determined preferential targets and pathways of both dysregulated and preserved miRNAs by computing multi-layer networks, which were compared between housekeeping and dysregulated miRNAs. Of 848 miRNAs examined across 1049 blood samples, 8 potential housekeepers showed very limited expression variations, while 20 miRNAs showed highly-dysregulated expression throughout the investigated blood samples. Our approach provides important insights into miRNAs and their role in regulatory networks. The methodology can be applied to systematically investigate the differences in target genes and pathways of arbitrary miRNA sets.
基金supported by the AgriLife Research Invasive Ant Research and Management Project and by China Scholarship Council.
文摘A bstract The tawny crazy ant(Nylanderia fulva)is a new invasive pest in the United States.At present,its management mainly relies on the use of synthetic insecticides,which are generally ineffective at producing lasting control of the pest,necessitating alternative environmentally friendly measures.In this study,we evaluated the feasibility of gene silencing to control this ant species.Six housekeeping genes encoding actin(NfActin),coatomer subunit β (NfCOPP),arginine kinase(NfArgK),and V-type proton ATPase subunits A(NfvATPaseA),B(NfvATPaseB)and E(NfvATPaseE)were cloned.Phylogenetic analysis revealed high sequence similarity to homologs from other ant species,particularly the Florida carpenter ant(Camponotus floridanus).To silence these genes,vector L4440 was used to generate six specific RNAi constructs for bacterial expression.Heat-inactivated,dsRNA-expressing Escherichia coli were incorporated into artificial diet.Worker ants exhibited reduced endogenous gene expression after feeding on such diet for 9 d.However,only ingestion of dsRNAs of NfCOPfi(a gene involved in protein trafficking)and NfArgK(a cellular energy reserve regulatory gene in invertebrates)caused modest but significantly higher ant mortality than the control.These results suggest that bacterially expressed dsRNA can be orally delivered to ant cells as a mean to target its vulnerabilities.Improved efficacy is necessary for the RNAi-based approach to be useful in tawny crazy ant management.
基金supported by grants from Strategic Priority Research Program of the Chinese Academy of Sciences(No. XDA08020102 to Z.Z.and S.H.)International Partnership Program of the Chinese Academy of Sciences(No.153F11KYSB20160008)+3 种基金National Programs for High Technology Research and Development (863 ProgramNo.2015AA020108 to Z.Z.)National Natural Science Foundation of China(No.31100915 to LH.)the 100-Talent Program of Chinese Academy of Sciences(awarded to Z.Z.)
文摘Rice is one of the most important stable food as well as a monocotyledonous model organism for the plant research community.Here,we present RED(Rice Expression Database;http://expression.ic4r.org),an integrated database of rice gene expression profiles derived entirely from RNA-Seq data.RED features a comprehensive collection of 284 high-quality RNA-Seq experiments,integrates a large number of gene expression profiles and covers a wide range of rice growth stages as well as various treatments.Based on massive expression profiles,RED provides a list of housekeeping and tissue-specific genes and dynamically constructs co-expression networks for gene(s) of interest.Besides,it provides user-friendly web interfaces for querying,browsing and visualizing expression profiles of concerned genes.Together,as a core resource in BIG Data Center,RED bears great utility for characterizing the function of rice genes and better understanding important biological processes and mechanisms underlying complex agronomic traits in rice.
基金financially supported by the National Key Research and Development Program of China(No.2018YFD1000905)the Applied Technology Research and Development Program of Heilongjiang Province,China(Nos.GA19B101,GA19B105,and GY-2017ZB006)
文摘Rhizobial diversity is affected by interactions between soil features, fertilization strategy, and cropping system. However, interactions among the rhizobial community, chemical-organic manure fertilization, and plant production have not been well documented in Mollisols from long-term experiments. Aimed at maintaining and recovering the productivity of Chinese Mollisols, a long-term fertilization experiment had been carried out for 29 years under a wheat-maize-soybean rotation system, involving the application of recycled organic manure (ROM), chemical fertilizers (N, P, and/or K), or ROM plus N, P, and/or K. In the present study, the effects of different treatments were evaluated by determining soil physicochemical features, soybean production, and soybean rhizobial diversity. The results showed that application of ROM plus NPK maintained or increased soil fertility, which was accompanied by higher production and higher diversity of rhizobia, as compared with the other treatments. The negative association of Bradyrhizobium japonicum with N fertilizer, positive association of B. diazoefficiens with soil pH, and alleviation of N-inhibition on the diversity of Bradyrhizobium by the addition of ROM were recorded as new findings. Therefore, application of ROM or ROM plus NPK could be a feasible strategy for maintaining and recovering the fertility of Chinese Mollisols, whereas rhizobial diversity could be an indicator of soil fertility.
基金supported by National Basic Research Program of China(973 program)(No.2006CB504100)the National Natural Science Foundation of China(Grant Nos.30393133 and 30260034).
文摘Internal standards are critical for quantitative RNA analyses.Housekeeping genes are often used as internal standards with the assumption that their express-ion levels remain relatively constant in different experi-mental conditions.In this study,four commonly used housekeeping genes,Glyceraldehyde-3-phosphate dehy-drogenase(GAPDH),β-actin,28S rRNA and 18S rRNA were selected to test whether this assumption is tenable under hypoxic conditions.We tested the RNA expression level of these four genes in different hypoxic conditions.Rats subjected to acute hypoxia for 2 hours were used for tissue detection.Primary cultured neural stem cells from E13 fetal rats were treated with 3%O_(2) or 10%O_(2) for 24 hours for in vitro experiments.In both experiments,expression levels of 28S rRNA and 18S rRNA were constant,independent of hypoxia types.However,expression levels of GAPDH and b-actin were all changed in all kinds of hypoxic conditions.In particu-lar,the mRNA expression level of GAPDH was increased by 43.4%under 3%O_(2) hypoxic conditions.These results suggest that 18S rRNA and 28S rRNA are reliable internal controls for comparative analyses of transcrip-tion under hypoxia.GAPDH appears particularly unfa-vorable for this purpose in hypoxic conditions.
基金The Scientific Research Fund of Jiangsu Provincial Department of Healthgrant number:H2017075+1 种基金Taizhou People’s Hospital Innovation Team Fundgrant number:CXTDB201904。
文摘Surfeit 4(Surf 4), one of the identified housekeeping genes, was previously thought to encode a transmembrane protein that acts as a cargo receptor to maintain basic cellular functions. In recent years, Surf 4 gene is overexpressed in some types of cancer, involved in the exosome signaling pathway in gastrointestinal stromal tumors, and played the role of an oncogene in ovarian cancer stem cells. In this paper,we review the characteristics and protein localization of Surf 4 gene, as well as its possible physiological functions and pathogenesis in various diseases and cancers,expecting to discuss its clinical application value.