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TRIzol Reagent is a complete, ready-to-use reagent for the isolation of high-quality total RNA or the simultaneous isolation of RNA, DNA, and protein from a variety of biological samples.
2013
Endothelial-Like Progenitor Cells Engineered to Produce Prostacyclin Rescue Monocrotaline-Induced Pulmonary Arterial Hypertension and Provide Right Ventricle Benefits
Authors: L Zhou, Z Chen, P Vanderslice, S-P So, K-H Ruan, JT Willerson, RAF Dixon
Intravenous prostacyclin is approved for treating pulmonary arterial hypertension (PAH), but it has a short half-life and must be delivered systemically via an indwelling intravenous catheter. We hypothesize that localized jugular vein delivery of prostacyclin-producing cells may provide sustained therapeutic effects without the limitations of systemic delivery.
2013
Authors: AB Mayfield, M-N Chen, P-J Meng, H-J Lin, C-S Chen, P-J Liu
Given the threat of climate change towards scleractinian corals, there is an urgent need to understand their physiological mechanisms of acclimation to increasing temperatures. To gain insight into this process, two mesocosm-based experiments were conducted in Southern Taiwan with the model reef-building coral Pocillopora damicornis.
2013
Characterization of β-casein gene in Indian riverine buffalo
Authors: PV Vinesh, B Brahma, R Kaur, TK Datta, SL Goswami, S De
Complete β-casein exon VII region analysis revealed two SSCP band patterns, with pattern-I representing predominant allele B (85%) present in homozygous (genotype BB) condition and pattern-II representing a rare allele A1 present in heterozygous condition (genotype A1B).
2012
Senescence is a cellular response preventing tumorigenesis. The Ras oncogene is frequently activated or mutated in human cancers, but Ras activation is insufficient to transform primary cells. In a search for cooperating oncogenes, we identify the lysine demethylase JMJD2A/KDM4A. We show that JMJD2A functions as a negative regulator of Ras-induced senescence and collaborates with oncogenic Ras to promote cellular transformation by negatively regulating the p53 pathway.
2012
Ablation of PRMT6 reveals a role as a negative transcriptional regulator of the p53 tumor suppressor
Authors: M Neault, FA Mallette, G Vogel, J Michaud-Levesque, S Richard
Arginine methylation of histones is a well-known regulator of gene expression. Protein arginine methyltransferase 6 (PRMT6) has been shown to function as a transcriptional repressor by methylating the histone H3 arginine 2 [H3R2(me2a)] repressive mark; however, few targets are known. To define the physiological role of PRMT6 and to identify its targets, we generated PRMT6−/− mouse embryo fibroblasts (MEFs).
2012
Authors: H Sun, X Huang, X Xu, H Lan, J Huang, H-S Zhang
2012
Authors: Hui Sun,Xi Huang,Xingjun Xu,Hongxia Lan,Ji Huang,Hong-Sheng Zhang
The plant-specific NAC (NAM, ATAF, and CUC)-domain proteins play important roles in plant development and stress responses. In this research, a full-length cDNA named ENAC1 (early NAC-domain protein induced by abiotic stress 1) was isolated from rice. ENAC1 possess one NAC domain in the N-terminus. Comparative time-course expression analysis indicated that ENAC1 expression, similar with OsDREB1A, was induced very quickly by various abiotic stresses including salt, drought, cold, and exogenous abscisic acid.
2012
MiR-135a functions as a selective killer of malignant glioma
Authors: S Wu, Y Lin, D Xu, J Chen, M Shu, Y Zhou, W Zhu, X Su, Y Zhou, P Qiu , G Yan
Glioma is the most common and fatal primary brain tumor. Thus far, therapeutic strategies to efficiently and specifically antagonize glioma are limited and poorly developed. Here we report that glia-enriched miR-135a, a microRNA that is dramatically downregulated in malignant glioma and correlated with the pathological grading, is capable of inducing mitochondria-dependent apoptosis of malignant glioma by regulating various genes including STAT6, SMAD5 and BMPR2, as well as affecting the signaling pathway downstream.
2012
Authors: G Tiana, X Wangd, F Zhanga, H Gengc, W Houc, L Chena, H Guoa, N Zhang
Phospholipids play an important role in mediating cell migration. In the present study, we investigated the role of cPLA2γ in chemotaxis of human breast cancer cells. Inhibition of cPLA2γ expression by small interference RNA severely inhibits EGF-induced chemotaxis in a dose-dependent manner in MDA-MB-231, MCF-7, T47D and ZR-75-30 cells.
2012
Authors: K Ranjan, A Surolia, C Pathak
Our previous studies have proven the adjuvanticity of chitosan in mice when administered with inactivated and subunit influenza vaccine. In this study, we investigated the adjuvant effect of chitosan on the immunogenicity and protective efficacy of a live attenuated influenza vaccine. Mice were inoculated intranasally with live attenuated influenza vaccine plus chitosan and then challenged with a high, lethal dose of homologous or heterologous virus. Antibody responses, secretion of IFN-γ by spleen cells, body weight loss, survival rates, and residual lung virus titers were tested.
2012
Authors: X Wang, W Zhang, F Liu et al
Our previous studies have proven the adjuvanticity of chitosan in mice when administered with inactivated and subunit influenza vaccine. In this study, we investigated the adjuvant effect of chitosan on the immunogenicity and protective efficacy of a live attenuated influenza vaccine. Mice were inoculated intranasally with live attenuated influenza vaccine plus chitosan and then challenged with a high, lethal dose of homologous or heterologous virus. Antibody responses, secretion of IFN-γ by spleen cells, body weight loss, survival rates, and residual lung virus titers were tested.
2012
Authors: D Liu, L Shi, C Han, J Yu, D Li, Y Zhang
Nicotiana benthamiana is the most widely-used experimental host in plant virology. The recent release of the draft genome sequence for N. benthamiana consolidates its role as a model for plant–pathogen interactions. Quantitative real-time PCR (qPCR) is commonly employed for quantitative gene expression analysis. For valid qPCR analysis, accurate normalisation of gene expression against an appropriate internal control is required.
2012
Authors: B-H Tzeng, Y-H Chen, C-H Huang, S-S Lin, K-R Lee, C-C Chen
Aims Restenosis is an undesirable consequence following percutaneous vascular interventions. However, the current strategy for preventing restenosis is inadequate. The aim of this study was to investigate the role of low-voltage gated T-type calcium channels in regulating vascular smooth cell (VSMC) proliferation during neointimal formation.
2012
Authors: D Kumar, P Singh, MA Yusuf, CP Upadhyaya, SD Roy, T Hohn, NB Sarin
We report the efficacy of an aldose reductase (ALDRXV4) enzyme from Xerophyta viscosa Baker in enhancing the prospects of plant’s survival under abiotic stress. Transgenic tobacco plants overexpressing ALDRXV4 cDNA showed alleviation of NaCl and mannitolinduced abiotic stress.
2012
Authors: H Xia, LL PJ Ooi, KM Hui
The down-regulation of miR-214 has previously been observed in human hepatocellular carcinoma (HCC). Here, we demonstrated the down-regulation of miR-214 is associated with cell invasion, stem-like traits and early recurrence of HCC. Firstly, we validated the suppression of miR-214 in human HCC by real-time quantitative RT-PCR (qRT-PCR) in 20 paired tumor and non-tumor liver tissues of HCC patients and 10 histologically normal liver tissues from colorectal cancer patients with liver metastases.
2012
Novel Pathways in the Pathobiology of Human Abdominal Aortic Aneurysms
Authors: I Hinterseher, R Erdman, JR Elmore, E Stahl, MC Pahl, K Derr, A Golden, JH Lillvis, MC Cindric, K Jackson, WD Bowen, CM Schworer, MA Chernousov, DP Franklin, JL Gray, RP Garvin, Z Gatalica, DJ Carey, G Tromp, H Kuivaniemi
Abdominal aortic aneurysm (AAA), a dilatation of the infrarenal aorta, typically affects males 1 65 years. The pathobiological mechanisms of human AAA are poorly understood. The goal of this study was to identify novel pathways involved in the development of AAAs. A custom-designed ‘AAA-chip’ was used to assay 43 of the differentially expressed genes identified in a previously published microarray study between AAA (n = 15) and control (n = 15) infrarenal abdominal aorta. Protein analyses were performed on selected genes.
2011
Authors: Jung-Chieh Hsua, Li-Ching Linb, Jason T.C. Tzena, Jyh-Yih Chen
The antimicrobial peptide, chrysophsin-1, exhibits antimicrobial activities with similar efficiencies for both gram-negative and gram-positive bacteria. In this study, we examined the antitumor activity and modulation of the inflammatory response of a synthetic chrysophsin-1 peptide. In vitro results showed that chrysophsin-1 had greater inhibitory effects against human fibrosarcoma (HT-1080), histiocytic lymphoma (U937), and epithelial carcinoma (HeLa) cells. LDH release by HeLa cells was comparable to that of an MTS assay after treatment with 1.5–3 μg/ml chrysophsin-1 for 24 h.
2011
Authors: RD Lin, YW Mao, SJ Leu, CY Huang, MH Lee
Many diseases occur when the immune system is weakened. Intracellular signals activate immuno-responsive cells to produce cytokines that modulate the immune response. Schisandra chinensis has been used traditionally to treat general fatigue, neurasthenia, and spontaneous sweating. In the present study, the effect of constituents of S. chinensis on cytokine release by human monocytic leukemia cells (THP-1) was tested using microparticle-based flow cytometric analysis.
2010
Characterizations of avian influenza virus H6N6 subtype isolated from domestic Muscovy duck
Authors: C Wan, G Fu, L Cheng, S Shi, H Chen, Y Huang
The full genome of A/Muscovy Duck/Fujian/FZ01/2008 (H6N6), which was first isolated from domestic Muscovy duck in Fujian Province in southern China at 2008, was cloned and sequenced by reverse transcription polymerase chain reaction (RT-PCR).
2010
Authors: RF Chen, HC Huang, CY Ou, TY Hsu, H Chuang, JC Chang, L Wang, HC Kuo, KD Yang
The prevalence of allergic diseases has increased in the past decades. It is unknown whether expression of certain microRNAs (miRNAs) in neonatal leucocytes is correlated to IgE production and/or allergic diseases. This study investigated the association of miRNA expression in neonatal leucocytes with cord blood IgE (CBIgE) elevation and development of allergic disease.
Single cell analysis has the potential to transform life science research. The standard practice of averaging gene expression resµl ts from many cells can mask subtle, important changes occurring within single cells. To further understand the complexity of biological systems, single cell analysis must be performed.
2008
Authors: AK Ganesan, H Ho, B Bodemann, S Petersen, J Aruri, S Koshy, Z Richardson, LQ Le, T Krasieva, MG Roth, P Farmer, MA White
Melanin protects the skin and eyes from the harmful effects of UV irradiation, protects neural cells from toxic insults, and is required for sound conduction in the inner ear. Aberrant regulation of melanogenesis underlies skin disorders (melasma and vitiligo), neurologic disorders (Parkinson's disease), auditory disorders (Waardenburg's syndrome), and ophthalmologic disorders (age related macular degeneration).
The Ambion MicroPoly(A)Purist Kit rapidly enriches for mRNA from total RNA or small amounts of cells or tissue. This robust method provides pure mRNA while minimizing ribosomal RNA contamination.
2013
Authors: HW Fescemyer, GV Sandoya, TA Gill, S Ozkan, JH Marden, DS Luthe
Understanding the molecular mechanisms underlying insect compensatory responses to plant defenses could lead to improved plant resistance to herbivores. The Mp708 inbred line of maize produces the maize insect resistant 1-cysteine protease (Mir1-CP) toxin.
The FirstChoice RLM-RACE Kit is designed to amplify cDNA only from full-length, capped mRNA, usually producing a single band after PCR. This kit is a major improvement over the basic rapid amplification of cDNA ends (RACE) protocol. The RLM-RACE procedure selects only full-length mRNA—no rRNA, tRNA or degraded RNA—and facilitates the cloning of sequences from the 5' ends of messages.
2013
Authors: G Ambigapathy, Z Zheng, W Li, J Keifer
Brain-derived neurotrophic factor (BDNF) has a diverse functional role and complex pattern of gene expression. Alternative splicing of mRNA transcripts leads to further diversity of mRNAs and protein isoforms. Here, we describe the regulation of BDNF mRNA transcripts in an in vitro model of eyeblink classical conditioning and a unique transcript that forms a functionally distinct truncated BDNF protein isoform.
The RNAqueous-96 Kit is used for high-throughput, phenol-free total RNA isolation from 100–2,000,000 cells or 0.1–1.5 mg of tissue using a guanidinium-based lysis/denaturant and glass fiber filter separation technology. The kit contains sufficient reagents for 192 (2 x 96) RNA purifications. The RNAqueous-96 Kit is ideal for the isolation of total RNA from multiple samples and very small samples.
2013
Authors: KB Szarama, N Gavara, RS Petralia, RS Chadwick, MW Kelley
Thyroid hormones regulate growth and development. However, the molecular mechanisms by which thyroid hormone regulates cell structural development are not fully understood. The mammalian cochlea is an intriguing system to examine these mechanisms, as cellular structure plays a key role in tissue development, and thyroid hormone is required for the maturation of the cochlea in the first postnatal week.
The Ambion RNAqueous-Micro Kit is used for phenol-free total RNA isolation from micro-sized samples such as 10–500,000 cultured cells, as few as 10 laser capture microdissected cells, or up to 10 mg tissue using a guanidinium-based lysis⁄;denaturant and glass fiber filter separation technology.
2013
Cadmium sulfate and CdTe-quantum dots alter DNA repair in zebrafish (Danio rerio) liver cells
Authors: S Tang, Q Cai, H Chibli, V Allagadda, JL Nadeaub, GD Mayer
Increasing use of quantum dots (QDs) makes it necessary to evaluate their toxicological impacts on aquatic organisms, since their contamination of surface water is inevitable. This study compares the genotoxic effects of ionic Cd versus CdTe nanocrystals in zebrafish hepatocytes. After 24 h of CdSO4 or CdTe QD exposure, zebrafish liver (ZFL) cells showed a decreased number of viable cells, an accumulation of Cd, an increased formation of reactive oxygen species (ROS), and an induction of DNA strand breaks. Measured levels of stress defense and DNA repair genes were elevated in both cases.
2013
Utilization of galactooligosaccharides by Bifidobacterium longum subsp. infantis isolates
Authors: D Garrido, S Ruiz-Moyano, R Jimenez-Espinoza, H-J Eom, DE Block, DA Mills
Prebiotics are non-digestible substrates that stimulate the growth of beneficial microbial populations in the intestine, especially Bifidobacterium species. Among them, fructo- and galacto-oligosaccharides are commonly used in the food industry, especially as a supplement for infant formulas. Mechanistic details on the enrichment of bifidobacteria by these prebiotics are important to understand the effects of these dietary interventions.
2012
A Sugar Gustatory Receptor Identified from the Foregut of Cotton Bollworm Helicoverpa armigera
Authors: Wei Xu,Hui-Jie Zhang,Alisha Anderson
Helicoverpa armigera (Hübner) is one of the most polyphagous and cosmopolitan pest species, the larvae of which feed on numerous important crops. The gustatory system is critical in guiding insect feeding behavior.
2012
Authors: R Chen, H Jiang, L Li, Q Zhai, L Qi, W Zhou, X Liu, H Li, W Zheng, J Sun, C Li
Transcriptional regulation plays a central role in plant hormone signaling. At the core of transcriptional regulation is the Mediator, an evolutionarily conserved, multisubunit complex that serves as a bridge between gene-specific transcription factors and the RNA polymerase machinery to regulate transcription.
2012
Structural analysis of oval-cell–mediated liver regeneration in rats
Authors: K Dezső, V Papp, E Bugyik, H Hegyesi, G Sáfrány, C Bödör, P Nagy, S Paku
We have analyzed the architectural aspects of progenitor-cell–driven regenerative growth in rat liver by applying the 2-acetaminofluorene/partial hepatectomy experimental model. The regeneration is initiated by the proliferation of so-called oval cells. The oval cells at the proximal tips of the ductules have a more differentiated phenotype and higher proliferative rate. This preferential growth results in the formation of a seemingly random collection of small hepatocytes, called foci.
2011
Lack of Angiogenesis in Experimental Brain Metastases
Authors: E Bugyik, K Dezső, L Reiniger, V László, J Tóvári, J Tímár, P Nagy, W Klepetko, B Döme, S Paku
Angiogenesis is believed to be essential for the growth of metastatic tumors in the brain. We analyzed the vascularization of tumors formed by 4 epithelial cell lines (C38, ZR75, HT25, and H1650) and a fibrosarcoma (HT1080) cell line injected into the brains of mice. No peritumoral angiogenesis was observed. Tumors apparently acquired their vasculature by incorporation of native vessels.
2006
Authors: TJ Klisch, J Souopgui, K Juergens, B Rust, T Pieler, KA Henningfeld
We have isolated and characterized Xenopus Mxi1, a member of the Myc/Max/Mad family of bHLHZip transcription factors. Xmxi1 transcripts are present during gastrulation and early neurula stages, earlier and in broader domains as compared to the neuronal determination factor neurogenin (X-ngnr-1). Consistent with an early role in neurogenesis, Xmxi1 is positively regulated by Sox3, SoxD, and proneural genes, as well as negatively by the Notch pathway. Loss-of-function experiments demonstrate an essential role for Xmxi1 in the establishment of a mature neural state that can be activated by factors that induce neuronal differentiation, such as SoxD and X-ngnr-1. Overexpression of Xmxi1 in Xenopus embryos results in ectopic activation of Sox3, an early pan-neural marker of proliferating neural precursor cells. Within the neural plate, the neuronal differentiation marker N-tubulin and cell cycle control genes such as XPak3 and p27(Xic1) are inhibited, but the expression of early determination and differentiation markers, including X-ngnr-1 and X-MyT1, is not affected. Inhibition of neuronal differentiation by Xmxi1 is only transient, and, at early tailbud stages, both endogenous and ectopic neurogenesis are observed. While Xmxi1 enhances cell proliferation and apoptosis in the early Xenopus embryo, both activities appear not to be required for the function of Xmxi1 in primary neurogenesis.
RecoverAll Total Nucleic Acid Isolation Kit for FFPE
The Ambion RecoverAll Total Nucleic Acid Isolation Kit is for the extraction of total nucleic acid from formalin- or paraformalin-fixed, paraffin-embedded (FFPE) tissues. Sufficient reagents are included for 40 purifications from up to four 20 µm sections, or up to 35 mg of unsectioned core samples each.
2012
Authors: YA Lussier, NN Khodarev, K Regan, K Corbin, H Li, S Ganai, SA Khan, J Gnerlich, TE Darga, H Fan, O Karpenko, PB Paty, MC Posner, SJ Chmura, S Hellman, MK Ferguson, RR Weichselbaum
Strategies to stage and treat cancer rely on a presumption of either localized or widespread metastatic disease. An intermediate state of metastasis termed oligometastasis(es) characterized by limited progression has been proposed. Oligometastases are amenable to treatment by surgical resection or radiotherapy.
2012
Authors: TY Seiwert, T Darga, D Haraf, EA Blair, K Stenson, EEW Cohen, JK Salama, V Villaflor, ME Witt, MW Lingen, RR Weichselbaum, EE Vokes
AdGV.EGR.TNF.11D (TNFerade™ Biologic) is a replication-deficient adenoviral vector expressing human tumor necrosis factor alpha (TNF-α) under the control of the chemoradiation-inducible EGR-1 promoter. TNF-α has been shown to function as a radiation sensitizer. We conducted a phase I dose escalation study to determine the maximum tolerated dose (MTD) and dose-limiting toxicity (DLT) of TNFerade™ Biologic, when added to chemoradiotherapy in poor prognosis patients with recurrent, previously irradiated head and neck cancer (HNC).
2012
Authors: C Weng, H Dong, G Chen, Y Zhai, R Bai, H Hu, L Lu, Z Xu
Although the expression of angiogenin (ANG), an angiogenic and tumorigenic factor, is elevated in various types of cancers, its regulation mechanism remains unclear. In the present study, in silico search predicted that miR-409-3p targeted to the 3′ untranslated region (3′UTR) of the ANG mRNA. Overexpression of miR-409-3p in fibrosarcoma HT1080 cells resulted in decreased steady-state level of ANG transcript and ANG production which were achieved through direct binding of this miRNA to the ANG 3′UTR.
Ambion ToTALLY RNA Total RNA Isolation Kit
The Ambion ToTALLY RNA Total RNA Isolation Kit is similar to the widely used guanidine thiocyanate, acid phenol:chloroform procedure of Chomczynski and Sacchi. All reagents needed to isolate, analyze, and store RNA (other than isopropanol) are included, making the kit an excellent value. The procedure has been modified to include an optional LiCl extraction step to reduce or eliminate DNA, carbohydrate, heme, and other contaminants that can be a problem with some guanidine-based methods.
2012
Serotonin 2c receptor RNA editing in major depression and suicide
Authors: R Lyddon, AJ Dwork, M Keddache, LJ Siever, SDracheva
mRNA for serotonin 2C receptor (5-HT2CR) undergoes editing which results in numerous isoforms. More highly edited isoforms exhibit decreased function. We recently found greater 5-HT2CR editing in suicide victims with prior bipolar disorder (BPD) or schizophrenia (SZ) compared with non-suicide patients and normal controls (NC).
The RiboPure-Blood Kit is for the isolation of high-quality RNA directly from whole blood. The kit combines two methods of RNA purification to efficiently remove blood components (protein, heme, genomic DNA, and RNases) that can compromise downstream procedures. The kit includes sufficient reagents for 40 RNA purifications from whole blood samples ranging from 0.3–0.5 mL each.
2012
Authors: R Ghassemifar, Forster, T Qadah, J Finlayson
In most references, the transcription initiation site for the α2- and α1-globin genes has been described to lie 37 bp upstream of the translation initiation codon, however, a review of data repositories such as GenBank and Ensembl showed a report of the α2-globin transcription initiation site occurring at position –66 relative to the initiation codon. To confirm the occurrence of these isoforms for both the α2- and α1-globin genes and to document their expression levels, we initiated our current investigation.
For the isolation of extremely high-quality RNA from yeast without the use of enzymatic pretreatments that may alter gene expression profiles. Each Ambion kit includes sufficient reagents for 50 purifications each from 107 to 108 yeast cells.
2011
Authors: AM Porman, K Alby, MP Hirakawa, RJ Bennett
Sexual reproduction can promote genetic diversity in eukaryotes, and yet many pathogenic fungi have been labeled as obligate asexual species. It is becoming increasingly clear, however, that cryptic sexual programs may exist in some species, and that efficient mating requires the necessary developmental switch to be triggered. In this study we investigate Candida tropicalis, an important human fungal pathogen that has been reported to be asexual. Significantly, we demonstrate that C. tropicalis uses a phenotypic switch to regulate a cryptic program of sexual mating. Thus, diploid a and α cells must undergo a developmental transition to the mating- competent form, and only then does efficient cell-cell conjugation take place resulting in the formation of stable a/α tetraploids. We show that both the phenotypic switch and sexual mating depend on the conserved transcriptional regulator Wor1, which is regulated by temperature in other fungal species.
The Ambion RiboPure-Bacteria Kit provides a rapid, robust, column-based method for isolating high quality RNA from bacteria. Total RNA can be isolated from the toughest Gram positive bacteria samples thanks to the kit's comprehensive protocol that uses zirconia beads to thoroughly disrupt bacterial cell walls. The RiboPure™-Bacteria Kit protocol also eliminates the need for harsh treatments or enzymatic digestion which may alter gene expression profile.
2013
The Novel Cis-Encoded Small RNA h2cR Is a Negative Regulator of hfq2 in Burkholderia cenocepacia
Authors: CG Ramos, PJP da Costa, G Döring, JH Leitão
Small non-coding regulatory RNAs (sRNAs) post-transcriptionally affect multiple phenotypes in prokaryotes and eukaryotes, yet most of the underlying regulatory mechanisms and the nature of the target mRNAs remain unclear.
ChargeSwitch Total RNA Cell kit
The ChargeSwitch Total RNA Cell Kit is ideal for the purification of up to 25 µg of total RNA from up to 1 x 106 cultured mammalian cells or from 1 ml overnight bacterial culture, including full-length RNA and small molecular weight RNA species.
2012
Regulation of the vapBC-1 Toxin-Antitoxin Locus in Nontypeable Haemophilus influenzae
Authors: SD Cline, S Saleem, DA Daines
Nontypeable Haemophilus influenzae (NTHi) are human-adapted commensal bacteria that can cause a number of chronic mucosal infections, including otitis media and bronchitis. One way for these organisms to survive antibiotic therapy and cause recurrent disease is to stop replicating, as most antimicrobials target essential biosynthetic pathways. Toxin-antitoxin (TA) gene pairs have been shown to facilitate entry into a reversible bacteriostatic state. Characteristically, these operons encode a protein toxin and an antitoxin that associate following translation to form a nontoxic complex, which then binds to and regulates the cognate TA promoter.
For the separation and isolation of bacterial RNA from mixed samples. The Ambion kit includes sufficient reagents for depleting 500 µg of host cell RNA (20 reactions x 25 µg RNA) from a complex host-bacterial RNA mixture.
2013
Authors: RK Gupta, J Alba, YQ Xiong, AS Bayer, CY Lee
Staphylococcus aureus produces numerous virulence factors but little is known about their in vivo regulation during an infection.
MICROBExpress Bacterial mRNA Enrichment Kit
This Ambion kit is for the purification of bacterial mRNA by removing rRNA from total RNA.
2010
Authors: Q Leroy, K Lebrigand, F Armougom, P Barbry, R Thiéry, D Raoult
Coxiella burnetii, the causative agent of the zoonotic disease Q fever, is mainly transmitted to humans through an aerosol route. A spore-like form allows C. burnetii to resist different environmental conditions. Because of this, analysis of the survival strategies used by this bacterium to adapt to new environmental conditions is critical for our understanding of C. burnetii pathogenicity. Here, we report the early transcriptional response of C. burnetii under temperature stresses. Our data show that C. burnetii exhibited minor changes in gene regulation under short exposure to heat or cold shock. While small differences were observed, C. burnetii seemed to respond similarly to cold and heat shock. The expression profiles obtained using microarrays produced in-house were confirmed by quantitative RT-PCR.
Acid Phenol:Chloroform:IAA (125:24:1) is premixed and supplied at pH 4.5 ± 0.2. Provided in one bottle of 100 mL. In RNA extraction procedures, Acid Phenol:Chloroform:IAA aids in the removal of DNA (it partitions into the organic phase), helps to stabilize the interface, and prevents foaming when mixing.
2008
Authors: S Ramanan, M Kooshkib, W Zhaob, F-C Hsud, ME Robbins
Whole-brain irradiation (WBI) can lead to cognitive impairment several months to years after irradiation. Studies on rodents have shown a rapid and sustained increase in activated microglia (brain macrophages) following brain irradiation, contributing to a chronic inflammatory response and a corresponding decrease in hippocampal neurogenesis. Thus, alleviating microglial activation following radiation represents a key strategy to minimize WBI-induced morbidity. We hypothesized that pretreatment with peroxisomal proliferator-activated receptor (PPAR)α agonists would ameliorate the proinflammatory responses seen in the microglia following in vitro radiation. Irradiating BV-2 cells (a murine microglial cell line) with single doses (2–10 Gy) of 137Cs γ-rays led to increases in (1) the gene expression of IL-1β and TNFα, (2) Cox-2 protein levels, and (3) intracellular ROS generation.
The Ambion MEGAclear Kit is designed for the quick cleanup of any large-scale transcription reaction. MEGAclear efficiently separates RNA from unincorporated NTPs, enzymes, and buffer components. Each kit includes sufficient reagents for 20 reactions.
2012
Highly Efficient and Specific Genome Editing in Silkworm Using Custom TALENs
Authors: S Ma, S Zhang, F Wang, Y Liu, Y Liu, H Xu, C Liu, Y Lin, P Zhao, Q Xia
Establishment of efficient genome editing tools is essential for fundamental research, genetic engineering, and gene therapy. Successful construction and application of transcription activator-like effector nucleases (TALENs) in several organisms herald an exciting new era for genome editing. We describe the production of two active TALENs and their successful application in the targeted mutagenesis of silkworm, Bombyx mori, whose genetic manipulation methods are parallel to those of Drosophila and other insects.
The Ambion GLOBINclear-Mouse⁄Rat Kit employs a novel, non-enzymatic technology that rapidly depletes >95% of the alpha and beta globin mRNA from total RNA preparations derived from whole blood. The kit includes sufficient reagents for 20 rxns.
2012
Novel roles for KLF1 in erythropoiesis revealed by mRNA-seq
Authors: MR Tallack, GW Magor, B Dartigues, et al.
KLF1 (formerly known as EKLF) regulates the development of erythroid cells from bi-potent progenitor cells via the transcriptional activation of a diverse set of genes. Mice lacking Klf1 die in utero prior to E15 from severe anemia due to the inadequate expression of genes controlling hemoglobin production, cell membrane and cytoskeletal integrity, and the cell cycle. We have recently described the full repertoire of KLF1 binding sites in vivo by performing KLF1 ChIP-seq in primary erythroid tissue (E14.5 fetal liver). Here we describe the KLF1-dependent erythroid transcriptome by comparing mRNA-seq from Klf1+/+ and Klf1-/-erythroid tissue. This has revealed novel target genes not previously obtainable by traditional microarray technology and provided novel insights into the function of KLF1 as a transcriptional activator. We define a cis regulatory module bound by KLF1, GATA1, TAL1 and Ep300 that co-ordinates a core set of erythroid genes. We also describe a novel set of erythroid specific promoters that drive high level expression of otherwise ubiquitously expressed genes in erythroid cells. Our study has identified two novel lncRNAs that are dynamically expressed during erythroid differentiation and discovered a role for KLF1 in directing apoptotic gene expression to drive the terminal stages of erythroid maturation.
MagMAX-96 Viral RNA Isolation Kit
Ambion's MagMAX Viral RNA isolation kits have been optimized for use with biological fluids and cell-free samples such as serum, plasma, swabs, and cell culture media.
2011
Authors: F Sun, PJ Ferro, B Lupiani, J Kahl, ME Morrow, JP Flanagan, C Estevez, A Clavijo
The Reticuloendotheliosis virus (REV) group of retroviruses infects a wide range of avian species, including chickens, turkeys, ducks, geese, quail, and prairie chickens. The objective of the present study was to develop a highly sensitive and specific diagnostic test for the detection of REV in whole blood samples. In order to increase the diagnostic sensitivity, a duplex real-time polymerase chain reaction (PCR) that detects both the envelope protein gene (env) and the long terminal repeat (LTR) region of REV was designed. This assay demonstrated greater analytical and diagnostic sensitivity than the gel-based PCR assay when using DNA extracted from whole blood by both phenol-chloroform and magnetic bead methods. In general, threshold cycle values in the duplex real-time PCR assay were lower from DNA extracted using the magnetic bead system compared to DNA extracted by the phenol-chloroform method. Data presented herein show the successful development of a rapid and accurate test procedure, with high-throughput capability, for the diagnosis of REV infection using avian blood samples.
The mirVana PARIS Kit is for the purification of both native protein and RNA (including small RNA) from the same sample. Each kit contains sufficient reagents and consumables for either 40 isolations of protein and total RNA (including small RNAs), or 20 isolation of protein and separate large and small RNA fractions.
2012
Authors: H Song, Q Wang, J Wen, S Liu, X Gao, J Cheng, D Zhang
Fibrodysplasia ossificans progressiva (FOP) is a rare congenital disorder of skeletal malformations and progressive extraskeletal ossification. There is still no effective treatment for FOP. All FOP individuals harbor conserved point mutations in ACVR1 gene that are thought to cause ACVR1 constitutive activation and activate BMP signal pathway. The constitutively active ACVR1 is also found to be able to cause endothelial-to-mesenchymal transition (EndMT) in endothelial cells, which may cause the formation of FOP lesions. MicroRNAs (miRNAs) play an essential role in regulating cell differentiation. Here, we verified that miR-148a directly targeted the 3' UTR of ACVR1 mRNA by reporter gene assays and mutational analysis at the miRNA binding sites, and inhibited ACVR1 both at the protein level and mRNA level. Further, we verified that miR-148a could inhibit the mRNA expression of the Inhibitor of DNA binding (Id) gene family thereby suppressing the BMP signaling pathway. This study suggests miR-148a is an important mediator of ACVR1, thus offering a new potential target for the development
of therapeutic agents against FOP.
2012
Authors: C Vidal, S Bermeo, W Li, D Huang, R Kremer, G Duque*
Interferon gamma (IFNγ) has been reported to induce osteoblastogenesis from mesenchymal stem cells (MSCs) both in vitro and in vivo. With ageing, adipocytes outnumber osteoblasts within the bone microenvironment leading to a decrease in bone formation. Since both osteoblasts and adipocytes are of mesenchymal origin, we hypothesized that IFNγ treatment might negatively affect adipogenesis while stimulating osteoblastogenesis in human MSC.
2010
Authors: GI Botchkina, ES Zuniga, M Das, Y Wang, H Wang, S Zhu, AG Savitt, RA Rowehl, Yan Leyfman, J Ju, K Shroyer, I Ojima
Growing evidence suggests that the majority of tumors are organized hierarchically, comprising a population of tumor-initiating, or cancer stem cells (CSCs) responsible for tumor development, maintenance and resistance to drugs. Previously
we have shown that the CD133 high/CD44 high fraction of colon cancer cells is different from their bulk counterparts at the functional, morphological and genomic levels.
The Ambion mirVana miRNA Detection Kit provides a fast and sensitive method for detecting small RNAs. The assay is 100–500 times more sensitive than Northern analysis, it is able to detect as little as 10 attomoles (10-17 mol) of target RNA. Each kit includes sufficient reagents for 100 reactions.
2007
MicroRNAs Play an Essential Role in the Development of Cardiac Hypertrophy
Authors: D Sayed, C Hong, I-Y Chen, J Lypowy, Ma Abdellatif
MicroRNAs are naturally existing, small, noncoding RNA molecules that downregulate posttranscriptional gene expression. Their expression pattern and function in the heart remain unknown.
The mirVana miRNA Isolation Kit uses a rapid procedure to isolate small RNAs from tissue and cells using an efficient glass fiber filter (GFF) – based method. The method isolates total RNA ranging in size from kilobases down to 10-mers.
2013
Organ-specific remodeling of the Arabidopsis transcriptome in response to spaceflight
Authors: A-L Paul, AK Zupanska, ER Schultz, RJ Fer
Spaceflight presents a novel environment that is outside the evolutionary experience of terrestrial organisms. Full activation of the International Space Station as a science platform complete with sophisticated plant growth chambers, laboratory benches, and procedures for effective sample return, has enabled a new level of research capability and hypothesis testing in this unique environment.
2013
Authors: MA Chaudry, RA Omaruddini, CD Brumbaugh, MA Tariq, N Pourmand
Gene regulation in cells exposed to ionizing radiation (IR) occurs at the transcriptional and post-transcriptional levels. Recent studies have suggested that micro-RNA (miRNA) play a significant role in post-transcriptional gene regulation in irradiated cells.
2013
Roles and Mechanism of miR-199a and miR-125b in Tumor Angiogenesis
Authors: J He, Y Jing, W Li, X Qian, Q Xu, F-S Li, L-Z Liu, B-H Jiang, Y Jiang
MicroRNAs (miRNAs) have been shown to be involved in different aspects of cancer biology including tumor angiogenesis. In this study, we identified that two miRNAs, miR-199a and miR-125b were downregulated in ovarian cancer tissues and cell lines.
2013
Authors: W Wei, J Hou, O Alder, X Ye, S Lee, R Cullum, A Chu, Y Zhao, SM Warner, DA Knight, D Yang, SJM Jones, MA Marra, PA Hoodless
MicroRNAs (miRNAs) are recently discovered small RNA molecules that regulate developmental processes, such as proliferation, differentiation, and apoptosis; however, the identity of miRNAs and their functions during liver development are largely unknown.
2013
miR-199a-5p Regulates Urothelial Permeability and May Play a Role in Bladder Pain Syndrome
Authors: K Monastyrskaya, V Sánchez-Freire, AH Gheinani, DJ Klumpp, EB Babiychuk, A Draeger, FC Burkhard
Defects in urothelial integrity resulting in leakage and activation of underlying sensory nerves are potential causative factors of bladder pain syndrome, a clinical syndrome of pelvic pain and urinary urgency/frequency in the absence of a specific cause. Herein, we identified the microRNA miR-199a-5p as an important regulator of intercellular junctions. On overexpression in urothelial cells, it impairs correct tight junction formation and leads to increased permeability.
2013
Varicella zoster virus infection of highly pure terminally differentiated human neurons
Authors: X Yu, S Seitz, T Pointon, JL Bowlin, RJ Cohrs, S Jonjić, J Haas, M Wellish, D Gilden
In vitro analyses of varicella zoster virus (VZV) reactivation from latency in human ganglia have been hampered by the inability to isolate virus by explantation or cocultivation techniques. Furthermore, attempts to study interaction of VZV with neurons in experimentally infected ganglion cells in vitro have been impaired by the presence of nonneuronal cells, which become productively infected and destroy the cultures.
2013
miR-199a-5p Regulates Urothelial Permeability and May Play a Role in Bladder Pain Syndrome
Authors: Katia Monastyrskaya,Verónica Sánchez-Freire,Ali Hashemi Gheinani,David J. Klumpp‡,Eduard B. Babiychuk,Annette Draeger,Fiona C. Burkhard
Defects in urothelial integrity resulting in leakage and activation of underlying sensory nerves are potential causative factors of bladder pain syndrome, a clinical syndrome of pelvic pain and urinary urgency/frequency in the absence of a specific cause. Herein, we identified the microRNA miR-199a-5p as an important regulator of intercellular junctions.
2013
MiR-206 inhibits gastric cancer proliferation in part by repressing CyclinD2
Authors: L Zhang, X Liu, H Jin et al
In this study, we detected miR-206 expression in gastric cancer (GC) and further investigated its effects on GC cell growth in vitro and in vivo. MiR-206 expression was found to be significantly decreased in 30 GC samples and GC cell lines by Real time-PCR.
2012
Alteration of colonic stem cell gene signatures during the regenerative response to injury
Authors: LA Davidson, JS Goldsby, ES Callaway, MS Shah, N Barker, RS Chapkin
Since aberrant wound healing and chronic inflammation can promote malignant transformation, we determined whether dietary bioactive fish oil (FO)-derived n − 3 polyunsaturated fatty acids (n − 3 PUFA) modulate stem cell kinetics in a colitis-wounding model.
2012
Underexpression of 4 Placenta-Associated MicroRNAs in Complete Hydatidiform Moles
Authors: Q Na, D Wang, W Song
Objective: Several placental microRNAs (miRNAs) have been identified as placenta-associated miRNAs with the potential of estimating the condition of the placenta. However, our understanding of these miRNAs is limited. The aim of this study was to determine the expression of 8 placenta-associated miRNAs (miR-512-3p, miR-517a, miR-517b, miR-518b, miR-519a, miR-1185, miR-1283, and miR-1323) in complete hydatidiform mole (CHM).
2012
Authors: C Liu, Z Peng, N Zhang, L Yu, S Han, D Li, J Li
We previously reported the involvement of conventional protein kinase C (cPKC) βII, γ, novel PKC (nPKC) ε and their interacting proteins in hypoxic pre-conditioning (HPC)-induced neuroprotection. In this study, the large-scale miRNA microarrays and bioinformatics analysis were used to determine the differentially expressed miRNAs and their PKC-isoform specific gene network in mouse brain after HPC and 6 h middle cerebral artery occlusion (MCAO).
2012
Authors: DW Lee, M Futami, M Carroll, Y Feng, Z Wang, M Fernandez, Z Whichard, Y Chen, S Kornblau, EJ Shpall, CE Bueso-Ramos, SJ Corey
The myelodysplastic syndromes (MDSs) comprise a group of disorders characterized by multistage progression from cytopenias to acute myeloid leukemia (AML). They display exaggerated apoptosis in early stages, but lose this behavior during evolution to AML. The molecular basis for loss of apoptosis is unknown. To investigate this critical event, we analyzed phosphatidylinositol (PI) 3′kinase signaling, implicated as a critical pathway of cell survival control in epithelial and hematological malignancies.
2012
Authors: J Bao, D Li, L Wang, J Wu, Y Hu, Z Wang, Y Chen, X Cao, C Jiang, W Yan, C Xu
MicroRNAs (miRNAs) mainly function as post-transcriptional regulators and are involved in a wide range of physiological and pathophysiological processes such as cell proliferation, differentiation, apoptosis, and tumorigenesis. Mouse testes express a large number of miRNAs. However, the physiological roles of these testicular miRNAs remain largely unknown.
2012
An atlas of DNA methylomes in porcine adipose and muscle tissues
Authors: M Li, H Wu, Z Luo, Y Xia et al
It is evident that epigenetic factors, especially DNA methylation, have essential roles in obesity development. Here, using pig as a model, we investigate the systematic association between DNA methylation and obesity. We sample eight variant adipose and two distinct skeletal muscle tissues from three pig breeds living within comparable environments but displaying distinct fat level.
2012
MicroRNA-409-3p regulates cell proliferation and apoptosis by targeting PHF10 in gastric cancer
Authors: C Li, H Nie, M Wang, L Su, J Li, B Yu, M Wei, J Ju, Y Yu, M Yan, Q Gu, Z Zhu, B Liu
Emerging evidence has indicated microRNAs are involved in tumor development and progression, acting as tumor suppressors or oncogenes. Here we report that miR-409-3p was significantly downregulated in gastric cancer (GC) cell lines and tissues. Overexpression of miR-409-3p in SGC-7901 gastric cancer cells dramatically suppressed cell proliferation and induced cell apoptosis both in vitro and in vivo. Furthermore, we demonstrate that the transcriptional regulator PHF10 was a target of miR-409-3p. Taken together, these findings suggest that miR-409-3p may function as a novel tumor suppressor in GC and its anti-oncogenic activity may involve the direct targeting and inhibition of PHF10.
2012
MiR-138 induces cell cycle arrest by targeting cyclin D3 in hepatocellular carcinoma
Authors: W Wang, L-J Zhao, Y-X Tan, H Ren, Z-T Qi
It has been reported that decreased Dicer expression leads to Alu RNAs accumulation in human retinal pigmented epithelium cells, and Dicer may process the endogenous SINE/B1 RNAs (the rodent equivalent of the primate Alu RNAs) into small interfering RNAs (siRNAs). In this study, we aimed to address whether Dicer can process Alu RNAs and their common ancestor, 7SL RNA. Using Solexa sequencing technology, we showed that Alu-derived small RNAs accounted for 0.6% of the total cellular small RNAs in HepG2.2.15 cells, and the abundance decreased when Dicer was knocked down.
2012
Authors: J Maj, A Jankowska-Konsur, E Plomer-Niezgoda, A Sadakierska-Chudy, A Reich
Data about genetic alterations in mycosis fungoides (MF) are limited and their significance not fully elucidated. The aim of the study was to explore the expression of various oncogenes in MF and to assess their influence on the disease course.
2012
Pri-miR-17-92a transcript folds into a tertiary structure and autoregulates its processing
Authors: S Chakraborty, S Mehtab, A Patwardhan, Y Krishnan
MicroRNAs control gene expression either by RNA transcript degradation or translational repression. Expressions of miRNAs are highly regulated in tissues, disruption of which leads to disease. How this regulation is achieved and maintained is still largely unknown.
2012
Novel Pathways in the Pathobiology of Human Abdominal Aortic Aneurysms
Authors: I Hinterseher, R Erdman, JR Elmore, E Stahl, MC Pahl, K Derr, A Golden, JH Lillvis, MC Cindric, K Jackson, WD Bowen, CM Schworer, MA Chernousov, DP Franklin, JL Gray, RP Garvin, Z Gatalica, DJ Carey, G Tromp, H Kuivaniemi
Abdominal aortic aneurysm (AAA), a dilatation of the infrarenal aorta, typically affects males 1 65 years. The pathobiological mechanisms of human AAA are poorly understood. The goal of this study was to identify novel pathways involved in the development of AAAs. A custom-designed ‘AAA-chip’ was used to assay 43 of the differentially expressed genes identified in a previously published microarray study between AAA (n = 15) and control (n = 15) infrarenal abdominal aorta. Protein analyses were performed on selected genes.
2012
Authors: J Maj, A Jankowska-Konsur, E Plomer-Niezgoda, A Sadakierska-Chudy, A Reich
Data about genetic alterations in mycosis fungoides (MF) are limited and their significance not fully elucidated. The aim of the study was to explore the expression of various oncogenes in MF and to assess their influence on the disease course
2012
Csy4 relies on an unusual catalytic dyad to position and cleave CRISPR RNA
Authors: RE Haurwitz, SH Sternberg, JA Doudna
CRISPR-Cas adaptive immune systems protect prokaryotes against foreign genetic elements. crRNAs derived from CRISPR loci base pair with complementary nucleic acids, leading to their destruction. In Pseudomonas aeruginosa, crRNA biogenesis requires the endoribonuclease Csy4, which binds and cleaves the repetitive sequence of the CRISPR transcript. Biochemical assays and three co-crystal structures of wild-type and mutant Csy4/RNA complexes reveal a substrate positioning and cleavage mechanism in which a histidine deprotonates the ribosyl 2'-hydroxyl pinned in place by a serine, leading to nucleophilic attack on the scissile phosphate.
2011
Repertoire of Porcine MicroRNAs in Adult Ovary and Testis by Deep Sequencing
Authors: M Li, Y Liu, T Wang et al
MicroRNAs (miRNAs)M-MLV Reverse Transcriptase, a large family of short endogenous RNAs known to post-transcriptionally repress gene expression, participate in the regulation of almost every cellular process. Changes in miRNA expression are associated with many pathologies. Ovarian folliculogenesis and testicular spermatogenesis are complex and coordinated biological processes, in which tightly regulated expression and interaction of a multitude of genes could be regulated by these miRNAs. Identification and preliminary characterization of gonad-specific miRNAs would be a prerequisite for a thorough understanding of the role that miRNA-mediated posttranscriptional gene regulation plays in mammalian reproduction.
2011
Circulating microRNAs in hepatitis B virus–infected patients
Authors: F Ji, B Yang, X Peng, H Ding, H You, P Tien
MicroRNAs (miRNAs) are stably present in human serum. The relationship between circulating miRNAs and hepatitis B virus (HBV) infected liver disease has not been previously reported. Applied Biosystems array-based miRNA expression profiling was performed on pooled sera obtained from identified groups of chronic asymptomatic carriers (ASC), patients with chronic hepatitis B (CHB) and HBV-associated acute-on-chronic liver failure (ACLF), as well as healthy controls (HC).
2011
Authors: JA López, LM Alvarez-Salas
MicroRNAs (miRNA) regulate expression of several genes associated with human cancer. Here, we analyzed the function of miR-34c, an effector of p53, in cervical carcinoma cells. Expression of either miR-34c-3p or miR-34c-5p mimics caused inhibition of cell proliferation in the HPV-containing SiHa cells but not in other cervical cells irrespective of tumorigenicity and HPV content.
2010
Authors: H Wei, C Wang, C Zhang, P Li, F Wang, Z Zhang
Neural stem cells’ transplantation has been proposed as a future therapy for spinal cord injury. The challenge is how to make proportionally more neural stem cells differentiate into spinal motor neurons. Recent reports reveal that microRNAs play an important role in regulating stem cell self-renewal and differentiation.
2010
Authors: N Bhatnagar, X Li, SKR Padi, Q Zhang, M-s Tang, B Guo
Advanced prostate cancers are known to acquire not only invasive capabilities but also significant resistance to chemotherapy-induced apoptosis. To understand how microRNAs (miRNAs) may contribute to prostate cancer resistance to apoptosis, we compared microRNA expression profiles of a benign prostate cancer cell line WPE1-NA22 and a highly malignant WPE1-NB26 cell line (derived from a common lineage). We found that miR-205 and miR-31 are significantly downregulated in WPE1-NB26 cells, as well as in other cell lines representing advanced-stage prostate cancers. Antiapoptotic genes BCL2L2 (encoding Bcl-w) and E2F6 are identified as the targets of miR-205 and miR-31, respectively. By downregulating Bcl-w and E2F6, miR-205 and miR-31 promote chemotherapeutic agents-induced apoptosis in prostate cancer cells.
For Research Use Only. Not for use in diagnostic procedures.