The protein expression landscape of the Arabidopsis root.
AuthorsPetricka JJ, Schauer MA, Megraw M, Breakfield NW, Thompson JW, Georgiev S, Soderblom EJ, Ohler U, Moseley MA, Grossniklaus U, Benfey PN,
JournalProc Natl Acad Sci U S A
PubMed ID22447775
Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins ... More
Post-training disruption of Arc protein expression in the anterior cingulate cortex impairs long-term memory for inhibitory avoidance training.
AuthorsHolloway CM, McIntyre CK,
JournalNeurobiol Learn Mem
PubMed ID21315825
'The activity-regulated-cytoskeletal-associated protein (Arc) has a well established role in memory consolidation and synaptic plasticity in the hippocampus and amygdala. However the role of Arc within the anterior cingulate cortex (ACC), an area of the brain involved in processing memory for pain, has yet to be examined. Here we sought ... More
Expression Analysis on Archival Material Revisited: Isolation and Quantification of RNA Extracted From FFPE Samples.
AuthorsDeben C, Zwaenepoel K, Boeckx C, Wouters A, Pauwels P, Peeters M, Lardon F, Baay M, Deschoolmeester V,
JournalDiagn Mol Pathol
PubMed ID23370428
'BACKGROUND:: Formalin-fixed paraffin-embedded (FFPE) tissue is the most readily available source of RNA for the gene expression studies. The main disadvantage is the poor quality of isolated RNA. Our group recently compared 5 commercially available RNA isolation kits and concluded that the RNeasy FFPE kit from Qiagen was the most ... More
A systematic evaluation of whole genome amplification of bisulfite-modified DNA.
'Studying DNA methylation profiles in detail should be the first step in epigenetic research. Although sodium bisulfite modification of genomic DNA is the gold standard method for DNA methylation analysis, this method results in the loss of the majority of the DNA material. Whole genome amplification (WGA) of bisulfite-modified DNA ... More
Investigation of the involvement of P-glycoprotein and multidrug resistance-associated protein 2 in the efflux of ximelagatran and its metabolites by using short hairpin RNA knockdown in Caco-2 cells.
AuthorsDarnell M, Karlsson JE, Owen A, Hidalgo IJ, Li J, Zhang W, Andersson TB,
JournalDrug Metab Dispos
PubMed ID20023051
'Liver and bile secretion can be an important first-pass and clearance route for drug compounds and also the site of several drug-drug interactions. In the clinical program for ximelagatran development, an unexpected effect of erythromycin on the pharmacokinetics of the direct thrombin inhibitor ximelagatran and its metabolites was detected. This ... More
Cell contact-dependent priming and Fc interaction with CD32+ immune cells contribute to the TGN1412-triggered cytokine response.
'Following inconspicuous preclinical testing, the superagonistic anti-CD28 mAb TGN1412 was applied to six study participants who all developed a devastating cytokine storm. We verified that TGN1412 treatment of fresh PBMCs induced only moderate responses, whereas restoration of tissue-like conditions by high-density preculture (HDC) allowed vigorous cytokine production. TGN1412 treatment of ... More
Systems-Level Analysis of Nitrogen Starvation-Induced Modifications of Carbon Metabolism in a Chlamydomonas reinhardtii Starchless Mutant.
AuthorsBlaby IK, Glaesener AG, Mettler T, Fitz-Gibbon ST, Gallaher SD, Liu B, Boyle NR, Kropat J, Stitt M, Johnson S, Benning C, Pellegrini M, Casero D, Merchant SS,
Journal
PubMed ID24280389
'To understand the molecular basis underlying increased triacylglycerol (TAG) accumulation in starchless (sta) Chlamydomonas reinhardtii mutants, we undertook comparative time-course transcriptomics of strains CC-4348 (sta6 mutant), CC-4349, a cell wall-deficient (cw) strain purported to represent the parental STA6 strain, and three independent STA6 strains generated by complementation of sta6 (CC-4565/STA6-C2, ... More
Synthesis and optimization of lectin functionalized nanoprobes for the selective recovery of glycoproteins from human body fluids.
'Biomedical sciences, and in particular biomarker research, demand efficient glycoprotein enrichment platforms. Herein magnetic nanoprobes (MNP), after being coated with three broad-spectrum lectins-concanavalin A (ConA), wheat germ agglutinin (WGA), and Maackia amurensis lectin (MA)-were utilized to selectively capture glycoproteins from human body fluids. Additionally, a new methodology, based on protection ... More
Active and total transforming growth factor-ß1 are differentially regulated by dopamine and estradiol in the pituitary.
'Dopamine, acting through the dopamine type 2 receptor (Drd2), is the main inhibitor of pituitary prolactin (PRL) secretion and lactotroph proliferation. TGF-ß1 is involved, at least in part, in mediating these actions. It was described that TGF-ß1 synthesis in rat pituitary lactotrophs is up-regulated by dopamine and down-regulated by estradiol. ... More
Silencing of NHE-1 blunts the slow force response to myocardial stretch.
AuthorsPérez NG, Nolly MB, Roldan MC, Villa-Abrille MC, Cingolani E, Portiansky EL, Alvarez BV, Ennis IL, Cingolani HE,
JournalJ Appl Physiol (1985)
PubMed ID21659487
'Myocardial stretch induces a biphasic force response: a first abrupt increase followed by a slow force response (SFR), believed to be the in vitro manifestation of the Anrep effect. The SFR is due to an increase in Ca²? transient of unclear mechanism. We proposed that Na?/H? exchanger (NHE-1) activation is ... More
[DNA extraction from coagulated human blood for application in genotyping techniques for human leukocyte antigen and immunoglobulin-like receptors].
'The objective of this study was to standardize a method for extracting high-quality DNA from samples of coagulated blood. Forty-eight samples of human coagulated blood were used for DNA extraction by means of the EZ-DNA commercial kit (Biological Industries, Beit Haemek, Israel), the Neoscience column kit (One Lambda Inc., San ... More
Triclosan-Induced Aminoglycoside-Tolerant Listeria monocytogenes Isolates Can Appear as Small-Colony Variants.
AuthorsKastbjerg VG, Hein-Kristensen L, Gram L,
Journal
PubMed ID24637686
'Exposure of the human food-borne pathogen Listeria monocytogenes to sublethal concentrations of triclosan can cause resistance to several aminoglycosides. Aminoglycoside-resistant isolates exhibit two colony morphologies: normal-size and pinpoint colonies. The purposes of the present study were to characterize the small colonies of L. monocytogenes and to determine if specific genetic ... More
Next-generation histopathologic diagnosis: a lesson from a hepatic carcinosarcoma.
AuthorsLuchini C, Capelli P, Fassan M, Simbolo M, Mafficini A, Pedica F, Ruzzenente A, Guglielmi A, Corbo V, Scarpa A,
Journal
PubMed ID24493719
'Hepatic carcinosarcoma is a malignant tumor with a poor prognosis that is composed of an intimate mixture of carcinomatous and sarcomatous elements.1,2 Because of its rarity and biphasic nature, both the histogenetic classification and the molecular genetic mechanisms that are involved remain unclear, and therapeutic approaches are left to subjective ... More
Potential role of multiple carbon fixation pathways during lipid accumulation in Phaeodactylum tricornutum.
'Phaeodactylum tricornutum is a unicellular diatom in the class Bacillariophyceae. The full genome has been sequenced (<30?Mb), and approximately 20 to 30% triacylglyceride (TAG) accumulation on a dry cell basis has been reported under different growth conditions. To elucidate P. tricornutum gene expression profiles during nutrient-deprivation and lipid-accumulation, cell cultures ... More
High-performance hydrogen production and oxidation electrodes with hydrogenase supported on metallic single-wall carbon nanotube networks.
'We studied the electrocatalytic activity of an [FeFe]-hydrogenase from Clostridium acetobutylicum (CaH2ase) immobilized on single-wall carbon nanotube (SWNT) networks. SWNT networks were prepared on carbon cloth by ultrasonic spraying of suspensions with predetermined ratios of metallic and semiconducting nanotubes. Current densities for both proton reduction and hydrogen oxidation electrocatalytic activities ... More
2,3-butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas.
AuthorsKöpke M, Mihalcea C, Liew F, Tizard JH, Ali MS, Conolly JJ, Al-Sinawi B, Simpson SD,
JournalAppl Environ Microbiol
PubMed ID21685168
'2,3-Butanediol (23BD) is a high-value chemical usually produced petrochemically but which can also be synthesized by some bacteria. To date, the best microbial 23BD production rates have been observed using pathogenic bacteria in fermentation systems that depend on sugars as the carbon and energy sources for product synthesis. Here we ... More
Phosphate-containing polyethylene glycol polymers prevent lethal sepsis by multidrug-resistant pathogens.
AuthorsZaborin A, Defazio JR, Kade M, Kaiser BL, Belogortseva N, Camp DG, Smith RD, Adkins JN, Kim SM, Alverdy A, Goldfeld D, Firestone MA, Collier JH, Jabri B, Tirrell M, Zaborina O, Alverdy JC,
Journal
PubMed ID24277029
'Antibiotic resistance among highly pathogenic strains of bacteria and fungi is a growing concern in the face of the ability to sustain life during critical illness with advancing medical interventions. The longer patients remain critically ill, the more likely they are to become colonized by multidrug-resistant (MDR) pathogens. The human ... More
Comparative expression analysis of rpf-like genes of Mycobacterium tuberculosis H37Rv under different physiological stress and growth conditions.
AuthorsGupta RK, Srivastava BS, Srivastava R,
JournalMicrobiology
PubMed ID20522500
'Mycobacterium tuberculosis H37Rv possesses five resuscitation-promoting factors, RpfA-E, which are required for the resuscitation of dormancy in mycobacteria induced by prolonged incubation of the culture in stationary phase. This study explores the transcriptional profile of all the rpf-like genes of M. tuberculosis H37Rv in the exponential phase, stationary phase, non-culturable ... More
LipidSeq: a next-generation clinical resequencing panel for monogenic dyslipidemias.
AuthorsJohansen CT, Dubé JB, Loyzer MN, MacDonald A, Carter DE, McIntyre AD, Cao H, Wang J, Robinson JF, Hegele RA,
Journal
PubMed ID24503134
'We report the design of a targeted resequencing panel for monogenic dyslipidemias, LipidSeq, for the purpose of replacing Sanger sequencing in the clinical detection of dyslipidemia-causing variants. We also evaluate the performance of the LipidSeq approach versus Sanger sequencing in 84 patients with a range of phenotypes including extreme blood ... More
Duplex PCR methods for the molecular detection of Escherichia fergusonii isolates from broiler chickens.
'Escherichia fergusonii is an emerging pathogen that has been isolated from a wide range of infections in animals and humans. Primers targeting specific genes, including yliE (encoding a conserved hypothetical protein of the cellulose synthase and regulator of cellulose synthase island), EFER_1569 (encoding a hypothetical protein, putative transcriptional activator for ... More
High-Throughput Genotyping of Green Algal Mutants Reveals Random Distribution of Mutagenic Insertion Sites and Endonucleolytic Cleavage of Transforming DNA.
AuthorsZhang R, Patena W, Armbruster U, Gang SS, Blum SR, Jonikas MC,
Journal
PubMed ID24706510
'A high-throughput genetic screening platform in a single-celled photosynthetic eukaryote would be a transformative addition to the plant biology toolbox. Here, we present ChlaMmeSeq (Chlamydomonas MmeI-based insertion site Sequencing), a tool for simultaneous mapping of tens of thousands of mutagenic insertion sites in the eukaryotic unicellular green alga Chlamydomonas reinhardtii. ... More
Growth, metabolic partitioning, and the size of microorganisms.
AuthorsKempes CP, Dutkiewicz S, Follows MJ,
JournalProc Natl Acad Sci U S A
PubMed ID22203990
'Population growth rate is a fundamental ecological and evolutionary characteristic of living organisms, but individuals must balance the metabolism devoted to biosynthesis and reproduction against the maintenance of existing structure and other functionality. Here we present a mathematical model that relates metabolic partitioning to the form of growth. The model ... More
Reduction in fecundity and shifts in cellular processes by a native virus on an invasive insect.
AuthorsCassone BJ, Michel AP, Stewart LR, Bansal R, Mian MA, Redinbaugh MG,
Journal
PubMed ID24682151
'Pathogens and their vectors have coevolutionary histories that are intricately intertwined with their ecologies, environments, and genetic interactions. The soybean aphid, Aphis glycines, is native to East Asia but has quickly become one of the most important aphid pests in soybean-growing regions of North America. In this study, we used ... More
Prevalence of Toxoplasma gondii infection in stray and household cats in regions of Seoul, Korea.
AuthorsLee SE, Kim JY, Kim YA, Cho SH, Ahn HJ, Woo HM, Lee WJ, Nam HW,
JournalKorean J Parasitol
PubMed ID20877509
'The principal objective of this study was to investigate the prevalence of toxoplasmosis in household and stray cats in Seoul, Republic of Korea. We collected blood samples from 72 stray and 80 household cats, and all samples were examined by ELISA and nested PCR. The overall positive rates of Toxoplasma ... More
Detection of autotrophic verrucomicrobial methanotrophs in a geothermal environment using stable isotope probing.
AuthorsSharp CE, Stott MB, Dunfield PF,
JournalFront Microbiol
PubMed ID22912630
Genomic analysis of the methanotrophic verrucomicrobium
Genome Sequence of Yersinia similis Y228T, a Member of the Yersinia pseudotuberculosis Complex.
AuthorsSprague LD, Neubauer H,
Journal
PubMed ID24675860
We report here on the genome sequence of Yersinia similis 228(T) isolated in Germany. The genome has a size of 4.9 Mb and a G+C content of 47% and is predicted to contain 4,135 coding sequences. Annotation of the 60,687-bp extrachromosomal element predicted 67 coding sequences and a G+C content ... More
Draft Genome Sequence of Photobacterium halotolerans S2753, Producer of Bioactive Secondary Metabolites.
AuthorsMachado H, Månsson M, Gram L,
Journal
PubMed ID24926051
We report here the whole draft genome sequence of marine isolate Photobacterium halotolerans S2753, which produces the known antibiotic holomycin and also ngercheumicins and solonamides A and B, which interfere with virulence of methicillin-resistant Staphylococcus aureus strains by interacting with the quorum-sensing system. ... More
De Novo Assembly of the Quorum-Sensing Pandoraea sp. Strain RB-44 Complete Genome Sequence Using PacBio Single-Molecule Real-Time Sequencing Technology.
AuthorsEe R, Lim YL, Yin WF, Chan KG,
Journal
PubMed ID24699956
We report the first complete genome sequence of Pandoraea sp. strain RB-44, which was found to possess quorum-sensing properties. To the best of our knowledge, this is the first documentation of both a complete genome sequence and quorum-sensing properties of a Pandoraea species. ... More
Draft Genome Sequences of Six Rhodobacter capsulatus Strains, YW1, YW2, B6, Y262, R121, and DE442.
AuthorsDing H, Moksa MM, Hirst M, Beatty JT,
Journal
PubMed ID24526637
Rhodobacter capsulatus is a model organism for studying a novel type of horizontal gene transfer mediated by a phage-like gene transfer agent (RcGTA). Here we report the draft genome sequences of six R. capsulatus strains that exhibit different RcGTA properties, including RcGTA overproducers, RcGTA nonproducers, and/or RcGTA nonreceivers. ... More
Competition for ammonia influences the structure of chemotrophic communities in geothermal springs.
AuthorsHamilton TL, Koonce E, Howells A, Havig JR, Jewell T, de la Torre JR, Peters JW, Boyd ES,
Journal
PubMed ID24242238
Source waters sampled from Perpetual Spouter hot spring (pH 7.03, 86.4°C), Yellowstone National Park, WY, have low concentrations of total ammonia, nitrite, and nitrate, suggesting nitrogen (N) limitation and/or tight coupling of N cycling processes. Dominant small-subunit rRNA sequences in Perpetual Spouter source sediments are closely affiliated with the ammonia-oxidizing ... More
Mutations in EZH2 cause Weaver syndrome.
AuthorsGibson WT, Hood RL, Zhan SH, Bulman DE, Fejes AP, Moore R, Mungall AJ, Eydoux P, Babul-Hirji R, An J, Marra MA, Chitayat D, Boycott KM, Weaver DD, Jones SJ,
JournalAm J Hum Genet
PubMed ID22177091
We used trio-based whole-exome sequencing to analyze two families affected by Weaver syndrome, including one of the original families reported in 1974. Filtering of rare variants in the affected probands against the parental variants identified two different de novo mutations in the enhancer of zeste homolog 2 (EZH2). Sanger sequencing ... More
Microbiota of human breast tissue.
AuthorsUrbaniak C, Cummins J, Brackstone M, Macklaim JM, Gloor GB, Baban CK, Scott L, O'Hanlon DM, Burton JP, Francis KP, Tangney M, Reid G,
Journal
PubMed ID24610844
In recent years, a greater appreciation for the microbes inhabiting human body sites has emerged. In the female mammary gland, milk has been shown to contain bacterial species, ostensibly reaching the ducts from the skin. We decided to investigate whether there is a microbiome within the mammary tissue. Using 16S ... More
Real-time whole-genome sequencing for routine typing, surveillance, and outbreak detection of verotoxigenic Escherichia coli.
Fast and accurate identification and typing of pathogens are essential for effective surveillance and outbreak detection. The current routine procedure is based on a variety of techniques, making the procedure laborious, time-consuming, and expensive. With whole-genome sequencing (WGS) becoming cheaper, it has huge potential in both diagnostics and routine surveillance. ... More
Emergence of the P2 phenotype in Pseudomonas aeruginosa PAO1 strains involves various mutations in mexT or mexF.
AuthorsLuong PM, Shogan BD, Zaborin A, Belogortseva N, Shrout JD, Zaborina O, Alverdy JC,
Journal
PubMed ID24244000
We recently demonstrated that Pseudomonas aeruginosa PAO1 undergoes a pronounced phenotypic change when introduced into the intestines of rats during surgical injury. Recovered strains displayed a specific phenotype (termed the P2 phenotype) characterized by altered pyocyanin production, high collagenase activity, high swarming motility, low resistance to chloramphenicol, and increased killing ... More
Genome-wide DNA methylation analysis of patients with imprinting disorders identifies differentially methylated regions associated with novel candidate imprinted genes.
AuthorsDocherty LE, Rezwan FI, Poole RL, Jagoe H, Lake H, Lockett GA, Arshad H, Wilson DI, Holloway JW, Temple IK, Mackay DJ,
Journal
PubMed ID24501229
Genomic imprinting is allelic restriction of gene expression potential depending on parent of origin, maintained by epigenetic mechanisms including parent of origin-specific DNA methylation. Among approximately 70 known imprinted genes are some causing disorders affecting growth, metabolism and cancer predisposition. Some imprinting disorder patients have hypomethylation of several imprinted loci ... More
PipX, the coactivator of NtcA, is a global regulator in cyanobacteria.
AuthorsEspinosa J, Rodríguez-Mateos F, Salinas P, Lanza VF, Dixon R, de la Cruz F, Contreras A,
Journal
PubMed ID24912181
To modulate the expression of genes involved in nitrogen assimilation, the cyanobacterial PII-interacting protein X (PipX) interacts with the global transcriptional regulator NtcA and the signal transduction protein PII, a protein found in all three domains of life as an integrator of signals of the nitrogen and carbon balance. PipX ... More
Sensitive deep-sequencing-based HIV-1 genotyping assay to simultaneously determine susceptibility to protease, reverse transcriptase, integrase, and maturation inhibitors, as well as HIV-1 coreceptor tropism.
AuthorsGibson RM, Meyer AM, Winner D, Archer J, Feyertag F, Ruiz-Mateos E, Leal M, Robertson DL, Schmotzer CL, Quiñones-Mateu ME,
Journal
PubMed ID24468782
With 29 individual antiretroviral drugs available from six classes that are approved for the treatment of HIV-1 infection, a combination of different phenotypic and genotypic tests is currently needed to monitor HIV-infected individuals. In this study, we developed a novel HIV-1 genotypic assay based on deep sequencing (DeepGen HIV) to ... More
Next-generation sequencing reveals how RNA catalysts evolve from random space.
AuthorsAmeta S, Winz ML, Previti C, Jäschke A,
Journal
PubMed ID24157838
Catalytic RNAs are attractive objects for studying molecular evolution. To understand how RNA libraries can evolve from randomness toward highly active catalysts, we analyze the original samples that led to the discovery of Diels-Alderase ribozymes by next-generation sequencing. Known structure-activity relationships are used to correlate abundance with catalytic performance. We ... More
Down-regulation of AUXIN RESPONSE FACTORS 6 and 8 by microRNA 167 leads to floral development defects and female sterility in tomato.
AuthorsLiu N, Wu S, Van Houten J, Wang Y, Ding B, Fei Z, Clarke TH, Reed JW, van der Knaap E,
Journal
PubMed ID24723401
Auxin regulates the expression of diverse genes that affect plant growth and development. This regulation requires AUXIN RESPONSE FACTORS (ARFs) that bind to the promoter regions of these genes. ARF6 and ARF8 in Arabidopsis thaliana are required to promote inflorescence stem elongation and late stages of petal, stamen, and gynoecium ... More
Aromatic residues in the catalytic center of chitinase A from Serratia marcescens affect processivity, enzyme activity, and biomass converting efficiency.
AuthorsZakariassen H, Aam BB, Horn SJ, Vårum KM, Sørlie M, Eijsink VG,
JournalJ Biol Chem
PubMed ID19244232
The processive Serratia marcescens chitinases A (ChiA) and B (ChiB) are thought to degrade chitin in the opposite directions. A recent study of ChiB suggested that processivity is governed by aromatic residues in the +1 and +2 (aglycon) subsites close to the catalytic center. To further investigate the roles of ... More
Giving drought the cold shoulder: a relationship between drought tolerance and fall dormancy in an agriculturally important crop.
AuthorsPembleton KG, Sathish P,
Journal
PubMed ID24790133
The growth of fall dormant/freezing tolerant plants often surpasses the growth of non-fall dormant/non-freezing tolerant types of the same species under water-limited conditions, while under irrigated conditions non-fall dormant types exhibit superior yield performance. To investigate the mechanism behind this phenomenon, we exposed seven diverse alfalfa (Medicago sativa) cultivars to ... More
A Limited Role for Carbonic Anhydrase in C4 Photosynthesis as Revealed by a ca1ca2 Double Mutant in Maize.
AuthorsStuder AJ, Gandin A, Kolbe AR, Wang L, Cousins AB, Brutnell TP,
Journal
PubMed ID24706552
Carbonic anhydrase (CA) catalyzes the first biochemical step of the carbon-concentrating mechanism of C4 plants, and in C4 monocots it has been suggested that CA activity is near limiting for photosynthesis. Here, we test this hypothesis through the characterization of transposon-induced mutant alleles of Ca1 and Ca2 in maize (Zea ... More
Multigene profiling to identify alternative treatment options for glioblastoma: a pilot study.
: Glioblastoma (GBM) is a highly aggressive malignancy and the most effective treatment regime has a high relapse rate. Increasingly, the development of therapies involves defining drug-diagnostic combinations where the presence of a molecular target or marker identifies patients who are most likely to respond to a specific therapy. Trials ... More
Network quantification of EGFR signaling unveils potential for targeted combination therapy.
AuthorsKlinger B, Sieber A, Fritsche-Guenther R, Witzel F, Berry L, Schumacher D, Yan Y, Durek P, Merchant M, Schäfer R, Sers C, Blüthgen N,
Journal
PubMed ID23752269
The epidermal growth factor receptor (EGFR) signaling network is activated in most solid tumors, and small-molecule drugs targeting this network are increasingly available. However, often only specific combinations of inhibitors are effective. Therefore, the prediction of potent combinatorial treatments is a major challenge in targeted cancer therapy. In this study, ... More
Characterization of silk fibroin modified surface: a proteomic view of cellular response proteins induced by biomaterials.
AuthorsYang MH, Yuan SS, Chung TW, Jong SB, Lu CY, Tsai WC, Chen WC, Lin PC, Chiang PW, Tyan YC,
Journal
PubMed ID24818131
The purpose of this study was to develop the pathway of silk fibroin (SF) biopolymer surface induced cell membrane protein activation. Fibroblasts were used as an experimental model to evaluate the responses of cellular proteins induced by biopolymer material using a mass spectrometry-based profiling system. The surface was covered by ... More
The phytosulfokine (PSK) receptor is capable of guanylate cyclase activity and enabling cyclic GMP-dependent signaling in plants.
AuthorsKwezi L, Ruzvidzo O, Wheeler JI, Govender K, Iacuone S, Thompson PE, Gehring C, Irving HR,
JournalJ Biol Chem
PubMed ID21504901
Phytosulfokines (PSKs) are sulfated pentapeptides that stimulate plant growth and differentiation mediated by the PSK receptor (PSKR1), which is a leucine-rich repeat receptor-like kinase. We identified a putative guanylate cyclase (GC) catalytic center in PSKR1 that is embedded within the kinase domain and hypothesized that the GC works in conjunction ... More
Molecular mechanism of signal perception and integration by the innate immune sensor retinoic acid-inducible gene-I (RIG-I).
AuthorsBinder M, Eberle F, Seitz S, Mücke N, Hüber CM, Kiani N, Kaderali L, Lohmann V, Dalpke A, Bartenschlager R,
JournalJ Biol Chem
PubMed ID21659521
RIG-I is a major innate immune sensor for viral infection, triggering an interferon (IFN)-mediated antiviral response upon cytosolic detection of viral RNA. Double-strandedness and 5'-terminal triphosphates were identified as motifs required to elicit optimal immunological signaling. However, very little is known about the response dynamics of the RIG-I pathway, which ... More
Neurofilament dot blot assays: novel means of assessing axon viability in culture.
AuthorsHares K, Kemp K, Gray E, Scolding N, Wilkins A,
JournalJ Neurosci Methods
PubMed ID21459112
Axonal structure and integrity are vital to overall neuronal maintenance and action potential propagation. Neurofilaments (NFs) are one of the main cytoskeletal components of axons and phosphorylation of NF subunits regulates speed of NF transport through axons and determines optimal axonal calibre required for signal propagation. Many previous studies of ... More
Global Proteomic Screening of Protein Allergens and Advanced Glycation Endproducts in Thermally Processed Peanuts.
AuthorsHebling CM, McFarland MA, Callahan JH, Ross MM,
JournalJ Agric Food Chem
PubMed ID23039025
Peanuts ( Arachis hypogaea ) are the cause of one of the most prevalent food allergies worldwide. Thermal processing (e.g., roasting) of peanuts and peanut-containing foods results in complex chemical reactions that alter structural conformations of peanut proteins, preventing accurate detection of allergens by most immunochemical and targeted screening methodologies. ... More
Bioreactor environment-sensitive sentinel genes as novel metrics for cell culture scale-down comparability.
AuthorsKondragunta B, Joshi BH, Han J, Brorson KA, Puri RK, Moreira AR, Rao G,
JournalBiotechnol Prog
PubMed ID22848039
Scale-down of bioreactors is currently done based on matching one or more measurable parameters such as k(L) a and P/V, which could result in insufficient process comparability. Currently, there is a lack of genomic translational studies in cell culture scale-down, which could help delineate measurable cellular attributes for improved scale-down. ... More
Differential neonatal testosterone imprinting of GH-dependent liver proteins and genes in female mice.
Abnormal exposure to steroid hormones within a critical developmental period elicits permanent alterations in female reproductive physiology in rodents, but the impact on the female GH axis and the underlying sexual differences in hepatic enzymes have not been described in detail. We have investigated the effect of neonatal androgenization of ... More
Simplifying and streamlining Escherichia coli-based cell-free protein synthesis.
AuthorsYang WC, Patel KG, Wong HE, Swartz JR,
JournalBiotechnol Prog
PubMed ID22275217
Escherichia coli cell-free protein synthesis (CFPS) uses E. coli extracts to make active proteins in vitro. The basic CFPS reaction mixture is comprised of four main reagent components: (1) energy source and CFPS chemicals, (2) DNA encoding the protein of interest, (3) T7 RNA Polymerase (RNAP) for transcription, and (4) ... More
Recombinant expression of two bacteriophage proteins that lyse clostridium perfringens and share identical sequences in the C-terminal cell wall binding domain of the molecules but are dissimilar in their N-terminal active domains.
AuthorsSimmons M, Donovan DM, Siragusa GR, Seal BS,
JournalJ Agric Food Chem
PubMed ID20825156
Clostridium perfringens is a Gram-positive anaerobic spore-forming bacterium capable of producing four major toxins that are responsible for disease symptoms and pathogenesis in a variety of animals, humans, and poultry. The organism is the third leading cause of human foodborne bacterial disease, and C. perfringens is the presumptive etiologic agent ... More
Automated extraction improves multiplex molecular detection of infection in septic patients.
AuthorsRegueiro BJ, Varela-Ledo E, Martinez-Lamas L, Rodriguez-Calviño J, Aguilera A, Santos A, Gomez-Tato A, Alvarez-Escudero J,
JournalPLoS One
PubMed ID20967222
Sepsis is one of the leading causes of morbidity and mortality in hospitalized patients worldwide. Molecular technologies for rapid detection of microorganisms in patients with sepsis have only recently become available. LightCycler SeptiFast test M(grade) (Roche Diagnostics GmbH) is a multiplex PCR analysis able to detect DNA of the 25 ... More
Development and validation of a SYBR-Green I real-time PCR protocol to detect hazelnut (Corylus avellana L.) in foods through calibration via plasmid reference standard.
AuthorsD'Andrea M, Coïsson JD, Travaglia F, Garino C, Arlorio M,
JournalJ Agric Food Chem
PubMed ID19891480
Many tree nuts are considered to be a serious problem in food safety, because of the presence of causative factors in IgE-mediated food allergies. Among these, hazelnut (Corylus avellana L.) seeds are largely used in a range of confectionery products and contain many well-characterized allergens. DNA-based methods and ELISA tests ... More
On-chip aptamer-based sandwich assay for thrombin detection employing magnetic beads and quantum dots.
AuthorsTennico YH, Hutanu D, Koesdjojo MT, Bartel CM, Remcho VT,
JournalAnal Chem
PubMed ID20545301
In this paper, we report the development of an on-chip aptamer-based fluorescence assay for protein detection and quantification based on sandwich ELISA principles. Thrombin was selected as a model analyte to validate the assay design, which involves two DNA thrombin aptamers recognizing two different epitopes of the protein. Aptamer-functionalized magnetic ... More
Memory-enhancing corticosterone treatment increases amygdala norepinephrine and Arc protein expression in hippocampal synaptic fractions.
Considerable evidence indicates that glucocorticoid hormones enhance the consolidation of memory for emotionally arousing events through interactions with the noradrenergic system of the basolateral complex of the amygdala (BLA). We previously reported that intra-BLA administration of a beta-adrenoceptor agonist immediately after inhibitory avoidance training enhanced memory consolidation and increased hippocampal ... More
Disruption of the dopamine d2 receptor impairs insulin secretion and causes glucose intolerance.
AuthorsGarcía-Tornadú I, Ornstein AM, Chamson-Reig A, Wheeler MB, Hill DJ, Arany E, Rubinstein M, Becu-Villalobos D,
JournalEndocrinology
PubMed ID20147524
The relationship between antidopaminergic drugs and glucose has not been extensively studied, even though chronic neuroleptic treatment causes hyperinsulinemia in normal subjects or is associated with diabetes in psychiatric patients. We sought to evaluate dopamine D2 receptor (D2R) participation in pancreatic function. Glucose homeostasis was studied in D2R knockout mice ... More
The alternative oxidase (AOX) gene in Vibrio fischeri is controlled by NsrR and upregulated in response to nitric oxide.
AuthorsDunn AK, Karr EA, Wang Y, Batton AR, Ruby EG, Stabb EV,
JournalMol Microbiol
PubMed ID20487270
Alternative oxidase (AOX) is a respiratory oxidase found in certain eukaryotes and bacteria; however, its role in bacterial physiology is unclear. Exploiting the genetic tractability of the bacterium Vibrio fischeri, we explore the regulation of aox expression and AOX function. Using quantitative PCR and reporter assays, we demonstrate that aox ... More
Exposure of DNA and Bacillus subtilis spores to simulated martian environments: use of quantitative PCR (qPCR) to measure inactivation rates of DNA to function as a template molecule.
Several NASA and ESA missions are planned for the next decade to investigate the possibility of present or past life on Mars. Evidence of extraterrestrial life will likely rely on the detection of biomolecules, which highlights the importance of preventing forward contamination not only with viable microorganisms but also with ... More
Differential expression of microRNAs between eutopic and ectopic endometrium in ovarian endometriosis.
AuthorsFiligheddu N, Gregnanin I, Porporato PE, Surico D, Perego B, Galli L, Patrignani C, Graziani A, Surico N,
JournalJ Biomed Biotechnol
PubMed ID20300586
Endometriosis, defined as the presence of endometrial tissue outside the uterus, is a common gynecological disease with poorly understood pathogenesis. MicroRNAs are members of a class of small noncoding RNA molecules that have a critical role in posttranscriptional regulation of gene expression by repression of target mRNAs translation. We assessed ... More
Concomitant administration of nitric oxide and glucocorticoids improves protection against bronchoconstriction in a murine model of asthma.
AuthorsJonasson S, Hedenstierna G, Hjoberg J,
JournalJ Appl Physiol
PubMed ID20538845
Glucocorticoids (GC) remain the first choice of treatment in asthma, but GC therapy is not always effective and is associated with side effects. In a porcine study in our laboratory, simultaneous administration of GC and nitric oxide (NO) attenuated the endotoxin-induced inflammatory response and made GC treatment more effective than ... More
Isolation of a novel lipase from a metagenomic library derived from mangrove sediment from the south Brazilian coast.
A novel gene coding for a LipA-like lipase with 283 amino acids and a molecular mass of 32 kDa was isolated and characterized from a metagenomic library prepared from mangrove sediment from the south Brazilian coast. LipA was 52% identical to a lipolytic enzyme from an uncultured bacterium and shared ... More
Targeted quantitation of overexpressed and endogenous cystic fibrosis transmembrane conductance regulator using multiple reaction monitoring tandem mass spectrometry and oxygen stable isotope dilution.
AuthorsJiang H, Ramos AA, Yao X,
JournalAnal Chem
PubMed ID19947594
Cystic fibrosis transmembrane conductance regulator (CFTR) functions as an ion channel in the apical plasma membrane of epithelial cells. Mutations in the gene coding for CFTR cause cystic fibrosis (CF). A major cellular dysfunction is insufficient apical plasma membrane expression of the protein. Its correction is important for developing new ... More
DNA qualification workflow for next generation sequencing of histopathological samples.
AuthorsSimbolo M, Gottardi M, Corbo V, Fassan M, Mafficini A, Malpeli G, Lawlor RT, Scarpa A,
Journal
PubMed ID23762227
Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the ... More