Identification of genes specifying proline biosynthesis in marine bacteriumAlteromonas haloplanktis

Summary A gene bank of total DNA of a marine bacterium,Alteromonas haloplanktis, was constructed on pBR322. Two hybrid plasmids pUS2010 and pUS2011 carrying inserts of 8.2 and 5.7 kb, respectively, were isolated that complemented theproBA deletion inE.coli CSH26. Restriction map of the inserts showed that both plasmids in common carried a 5.7 kb fragment. This restriction fragment thus contains both the genes involved in proline biosynthesis inA.haloplanktis and could be expressed inE.coli.     

Resistance of bacterial film to contamination during use as inoculum in repeated batch fermentation

Summary AnEscherichia coli strain constitutive for -galactosidase was immobilized onto cotton cloth. The resultingE.coli film was used as a resident inoculum in repeated batch fermentations for 30 days in the presence ofBrevibacterium ammoniagenes added as a contaminant. Analysis of -galactosidase production shows that contamination did not decrease the capacity of the film to generateE.coli cells, or decrease theE.coli population on the film.     

Thermostable tryptophan synthase ofBacillus stearothermophilus expressed inEscherichia coli

Summary The tryptophan synthase genes,trpA andtrpB, from a moderate thermophile,Bacillus stearothermophilus IFO13737, were expressed efficiently inEscherichia coli. The recombinant tryptophan synthase amounted to 22% of the soluble cellular protein, and was purified to homogeneity by three steps. The enzyme is more thermostable thanE.coli tryptophan synthase, especially the subunit. The enzyme is also more resistant to sodium dodecylsulfate and methanol thanE.coli enzyme.     

High level extracellular secretion of thermostable α-amylase ofBacillus stearothermophilus inEscherichia coli

Summary Bacillus stearothermophilus BR135 (ATCC 29609)amy gene was cloned in pBR322 from its plasmid DNA and was subcloned in a vector useful both forB. subtilis andE. coli.E.coli HB101 harboring the plasmid pSS099 when grown in L medium in presence of 5. g/ml chloramphenicol produces 70 units/ml of extracellular -amylase. This is nearly twice that ofE.coli cells harboring pSSO76, a plasmid havingamy ofB.stearothermophilus BR135 atHindIII site of pBR322. Characteristically the protein was a 58 kd protein and cross reacted with antiserum developed against purified -amylase of BR135.     

Genome sequence analyses of two isolates from the recent <Emphasis Type="Italic">Escherichia coli</Emphasis> outbreak in Germany reveal the emergence of a new pathotype: Entero-Aggregative-Haemorrhagic <Emphasis Type="Italic">Escherichia coli</Emphasis> (EAHEC)

The genome sequences of two Escherichia coli O104:H4 strains derived from two different patients of the 2011 German E. coli outbreak were determined. The two analyzed strains were designated E. coli GOS1 and GOS2 (German outbreak strain). Both isolates comprise one chromosome of approximately 5.31 Mbp and two putative plasmids. Comparisons of the 5,217 (GOS1) and 5,224 (GOS2) predicted protein-encoding genes with various E. coli strains, and a multilocus sequence typing analysis revealed that the isolates were most similar to the entero-aggregative E. coli (EAEC) strain 55989. In addition, one of the putative plasmids of the outbreak strain is similar to pAA-type plasmids of EAEC strains, which contain aggregative adhesion fimbrial operons. The second putative plasmid harbors genes for extended-spectrum β-lactamases. This type of plasmid is widely distributed in pathogenic E. coli strains. A significant difference of the E. coli GOS1 and GOS2 genomes to those of EAEC strains is the presence of a prophage encoding the Shiga toxin, which is characteristic for enterohemorrhagic E. coli (EHEC) strains. The unique combination of genomic features of the German outbreak strain, containing characteristics from pathotypes EAEC and EHEC, suggested that it represents a new pathotype Entero-Aggregative-Haemorrhagic E scherichia c oli (EAHEC).     

Rationale and design of a prospective study: Cervical Dystonia Patient Registry for Observation of OnaBotulinumtoxinA Efficacy (CD PROBE)

Background  

A registry of patients with cervical dystonia (Cervical Dystonia Patient Registry for Observation of onaBotulinumtoxinA Efficacy [CD PROBE]) was initiated to capture data regarding physician practices and patient outcomes with onabotulinumtoxinA (BOTOX^?, Allergan, Inc., Irvine, CA, USA). Methods and baseline demographics from an interim analysis are provided.     

Ovulation induction in rhesus monkeys by treatment with gonadotropins and prostaglandins

In rhesus monkeys (Macaca mulatta), superovulation has been successfully induced using a combined regimen of PMS, HCG and PG E₁ or E₂. The ovulation was confirmed by a number of ova recovered either from the tubes or from the uterine flushings at various intervals after ovulation. The time of ovulation in this study under the conditions cited appears to be around 60 hrs after HCG, 36 hrs after PG administration.     

Transgenic antibiotic resistance may be differentially silenced in germinating pollen grains

Transgenic tobacco (Nicotiana tabacum L.) plants, carrying the neomycin phosphotransferase (NPT II) gene from E. coli, are resistant to kanamycin when grown from seeds on kanamycin containing medium. Tissue and cell cultures derived from those transformants also express resistance and regenerate complete plantlets in the presence of the antibiotic. This unspecific response to the selective condition has led to the belief that the foreign gene is continuously active or uniformly inducible in all cells of the transgenic plant. However, our experiments show that this view is not true for pollen grains during in vitro germination. Pollen grains isolated from kanamycin resistant tobacco plants carry and transmit the foreign gene but do not express resistance when germinating in vitro. This data presents evidence for differential silencing of a foreign gene in a mature gamete. On the other hand, immature pollen grains (microspores) appear to express resistance. The point of the downregulation of the neomycin transferase gene during pollen maturation is discussed.Abbreviations kan kanamycin sulfate - NPT II neomycin phosphotransferase II - sr streptomycin sulfate     

RIKEN tandem mass spectral database (ReSpect) for phytochemicals: A plant-specific MS/MS-based data resource and database

The fragment pattern analysis of tandem mass spectrometry (MS/MS) has long been used for the structural characterization of metabolites. The construction of a plant-specific MS/MS data resource and database will enable complex phytochemical structures to be narrowed down to candidate structures. Therefore, a web-based database of MS/MS data pertaining to phytochemicals was developed and named ReSpect (RIKEN tandem mass spectral database). Of the 3595 metabolites in ReSpect, 76% were derived from 163 literature reports, whereas the rest was obtained from authentic standards. As a main web application of ReSpect, a fragment search was established based on only the m/z values of query data and records. The confidence levels of the annotations were managed using the MS/MS fragmentation association rule, which is an algorithm for discovering common fragmentations in MS/MS data. Using this data resource and database, a case study was conducted for the annotation of untargeted MS/MS data that were selected after quantitative trait locus analysis of the accessions (Gifu and Miyakojima) of a model legume Lotus japonicus. In the case study, unknown metabolites were successfully narrowed down to putative structures in the website.     

Construction of aClostridium acetobutylicum-Escherichia coli shuttle vector

Summary A 4.1-kb cryptic plasmid, designated pCA134, has been isolated fromClostridium species. In order to develop a vector suitable for transforming saccharolytic clostridia three hybrid plasmids were constructed by inserting pCA134 into pHV32 withEcoRI, orBglII andBamHI. The newly constructed plasmids were propagated inEscherichia coli and were used to transformBacillus subtilis andClostridium acetobutylicum. One of them, pCAB32 (10.1 kb), which contains chloramphenicol acetyltransferase gene and an origin of replication derived from pCA134 was introduced intoB.subtilis andC.acetobutylicum as well asE.coli.     

The Screening of RNA Aptamers Specific for Carbonic Anhydrase I Using the Systematic Evolution of Ligands by an Exponential Enrichment Method (SELEX)

Carbonic anhydrases (CA) or carbonate dehydratases are a family of enzymes that catalyze the rapid interconversion of carbon dioxide and water to bicarbonate. CA I is the most abundant protein in the cytosol and has been reported to the partially associated with a number of fatal diseases. A newly established Systematic Evolution of Ligands by EXponential enrichment (SELEX) method referred to as Protein-SELEX was used to select RNA aptamers against the human erythrocyte CA I (CA I) protein. After five rounds of selection and counter selection the specific binding of the 6th cycle in vitro transcribed RNA library to CA I was detected by an Electrophoretic Mobility Shift Assay (EMSA). Three Specific sequences were identified as binding candidates after cloning and sequence analysis and one of the selected CA I specific RNA aptamers, CAapt1, was used to confirm specific binding and the Kd values were determined using an EMSA. The CAapt1 RNA aptamer showed no affinity towards any other protein and in comparison to the “0” cycle library, a significant enrichment was obtained. This methodology permitted us to successfully investigate the ssRNA aptamer CAapt1 for CA I protein.     

Glycogen Synthase Kinase-3 regulates IGFBP-1 gene transcription through the Thymine-rich Insulin Response Element

Background  

Hepatic expression of several gene products involved in glucose metabolism, including phosphoenolpyruvate carboxykinase (PEPCK), glucose-6-phosphatase (G6Pase) and insulin-like growth factor binding protein-1 (IGFBP-1), is rapidly and completely inhibited by insulin. This inhibition is mediated through the regulation of a DNA element present in each of these gene promoters, that we call the Thymine-rich Insulin Response Element (TIRE). The insulin signalling pathway that results in the inhibition of these gene promoters requires the activation of phosphatidylinositol 3-kinase (PI 3-kinase). However, the molecules that connect PI 3-kinase to these gene promoters are not yet fully defined. Glycogen Synthase Kinase 3 (GSK-3) is inhibited following activation of PI 3-kinase. We have shown previously that inhibitors of GSK-3 reduce the activity of two TIRE-containing gene promoters (PEPCK and G6Pase), whose products are required for gluconeogenesis.     

Industrial-scale production and purification of a heterologous protein in <Emphasis Type="Italic">Lactococcus lactis</Emphasis> using the nisin-controlled gene expression system NICE: The case of lysostaphin

Background  

The NIsin-Controlled gene Expression system NICE of Lactococcus lactis is one of the most widespread used expression systems of Gram-positive bacteria. It is used in more than 100 laboratories for laboratory-scale gene expression experiments. However, L. lactis is also a micro-organism with a large biotechnological potential. Therefore, the aim of this study was to test whether protein production in L. lactis using the NICE system can also effectively be performed at the industrial-scale of fermentation.     

Synthesis of prostaglandin by reproductive tissue of the male house cricket, acheta domesticus

Whole reproductive tracts of male house crickets, Acheta domesticus, incubated with arachidonic acid and glutathione yielded an average of 17 ug of prostaglandin (PG) E₂/g of tissue. Biosynthesized PGE₂ was identified by mass spectroscopy. A compound with thin layer and gas chromatographic properties identical to PGE₁ was isolated from spermatophores of house crickets. This appears to be the first report of the occurrence of a PG in an insect species. The possible role of PG in insect reproduction is discussed.     

The STAR RNA binding proteins GLD-1, QKI, SAM68 and SLM-2 bind bipartite RNA motifs

Background  

SAM68, SAM68-like mammalian protein 1 (SLM-1) and 2 (SLM-2) are members of the K homology (KH) and STAR (signal transduction activator of RNA metabolism) protein family. The function of these RNA binding proteins has been difficult to elucidate mainly because of lack of genetic data providing insights about their physiological RNA targets. In comparison, genetic studies in mice and C. elegans have provided evidence as to the physiological mRNA targets of QUAKING and GLD-1 proteins, two other members of the STAR protein family. The GLD-1 binding site is defined as a hexanucleotide sequence (NACUCA) that is found in many, but not all, physiological GLD-1 mRNA targets. Previously by using Systematic Evolution of Ligands by EXponential enrichment (SELEX), we defined the QUAKING binding site as a hexanucleotide sequence with an additional half-site (UAAY). This sequence was identified in QKI mRNA targets including the mRNAs for myelin basic proteins.     

Transformation ofClostridium thermohydrosulfuricum DSM 568 with plasmid DNA

A method was developed for the transformation of the ethanol-producing thermophilic bacteriumClostridium thermohydrosulfuricum DSM 568 without protoplast formation. Competence for DNA uptake was induced by treatment ofCl. thermohydrosulfuricum cells with 50 mM Tris-HCl pH 8. 3. In the presence of polyethylene glycol (PEG 6000) the Tris-treated cells were transformed with the antibiotic resistance plasmids pUB110 (Km^R) and pGS13 (Km^R Cm^R) at frequencies of 4×10^–6 per viable cell. This transformation method will be useful for the development of genetic exchange systems in thermophilic clostridia of biotechnological interest.     

A serum factor cross-reactive with antibodies to a determinant of rabbit encephalitogenic sequence 65–74 of myelin basic protein

A serum factor. cross-reactive with antibodies to a defined determinant of myelin basic protein (residues 66–71), has been found in the sera of nine mammalian species where it may function as a specific neuroautotolerogen. In equilibrium competitive inhibition radioimmunoassays the factor appears to be completely competitive with synthetic peptide S24 (TTHYGSLPQKG) at high affinity and is therefore termed MBP-SF-24 (myelin basic protein serum factor of the S24 type). The bulk of the activity can be recovered by ammonium sulfate fractionation at 61.1% saturated ammonium sulfate (SAS), pH 7, (fractionE) after removal by precipitation at pH 7 of the 37.5, 42.6, 47.5, and 51.4% SAS fractions (fractionsA-D), including the immunoglobulins, and before removal by precipitation at pH 5 of the albumin fraction (fractionF). The factor, by its retention on XM300 during ultrafiltration of fractionE, can be purified 20-fold from serum proteins without much loss through a combination of SAS fractionation and ultrafiltration. The yield of MBP-SF-S24 in fractionE may range from a low 26 pmol S24 equivalents from 10 ml in sheep serum to a high 1.7 nmoles from 10 ml rat serum. The serum factor is reactive at high affinity with each of two populations of S24-reactive antibodies in one rabbit reagent antiserum and with one of two populations of S24-reactive antibodies in another. It appears to express a determinant involving residues THYGSL (66–71) of myelin basic protein with the same conformation as found in intact S24.This work was supported at Duke University Medical Center by Research Grant NS-10237 from the National Institutes of Health of the U. S. Public Health Service and the Medical Scientist Training Program Grant #5-T32-OMO-7171-08; at St. Luke's Hospital Center by RG-1197-B-6 from the National Multiple Sclerosis Society and by a grant from the M.T. Biddle Foundation; and at Northwestern University by Research Grant NS-06262 from the National Institutes of Health of the U.S. Public Health Service.     

MET-IDEA version 2.06; improved efficiency and additional functions for mass spectrometry-based metabolomics data processing

Metabolomics Ion-based Data Extraction Algorithm (MET-IDEA) is a computer program for processing large-scale metabolomics data. MET-IDEA utilizes network Common Data Form (netCDF) data files available from a diversity of chromatographically coupled mass spectrometry (MS) systems, utilizes the sensitivity and selectivity associated with selected ion quantification, and greatly reduces the time and effort necessary to obtain large-scale organized data. This article reports on recent improvements to MET-IDEA which include new visualization of peak integrations, display of mass spectra associated with integrated peaks, and optional manual peak integration. The computational performance of MET-IDEA has also been improved to avoid memory overflow during the processing of large data sets and the software made compatible with 64 bit CPUs and operating systems. These new functions improve the performance of MET-IDEA, and they allow users to visualize peak integrations and curate the results through manual integration if desired. The improved version of MET-IDEA better facilitates the quantitative analysis of complex MS-based metabolomics data. MET-IDEA is freely available for academic and non commercial use at (http://bioinfo.noble.org/gateway/index.php?option=com_wrapper&;Itemid=57). Commercial use is available via licensing agreement.

     

Physiological constraints in increasing biomass concentration ofEscherichia coli B in fed-batch culture

Summary Fed-batch culture ofE.coli B was carried out to obtain high concentration of biomass. After requirement of oxygen was met by sparging the pure oxygen, physiological constraints were delineated. High partial pressure of CO₂ caused the decrease of the maximum specific growth rate, whereas fermentative byproducts caused the decrease of biomass yield as well as the maximum specific growth rate.