scholarly journals A successful use of a new shuttle cloning vector pA13 for the cloning of the bacteriocins BacSJ and acidocin 8912

2010 ◽  
Vol 62 (2) ◽  
pp. 231-243 ◽  
Author(s):  
Milan Kojic ◽  
Jelena Lozo ◽  
B. Jovcic ◽  
Ivana Strahinic ◽  
D. Fira ◽  
...  
Keyword(s):  
In Silico Analysis ◽  
Functional Expression ◽  
Open Reading Frames ◽  
Cloning Vector ◽  
The Novel ◽  
Genetic Manipulations ◽  
Genes Encoding ◽  
Editorial Decision ◽  
Terminal Amino

The aim of this paper was to research the molecular cloning of genes encoding the novel bacteriocin BacSJ from Lactobacillus paracasei subsp. paracasei BGSJ2-8 by using a newly constructed shuttle cloning vector pA13. A new shuttle-cloning vector, pA13, was constructed and successfully introduced into Escherichia coli, Lactobacillus and Lactococcus strains, showing a high segregational and structural stability in all three hosts. The natural plasmid pSJ2-8 from L. paracasei subsp. paracasei BGSJ2-8 was cloned in the pA13 using BamHI, obtaining the construct pB5. Sequencing and in silico analysis of the pB5 revealed 15 open reading frames (ORF). Plasmid pSJ2-8 harbors the genes encoding the production of two bacteriocins, BacSJ and acidocin 8912. The combined N-terminal amino acid sequencing of BacSJ in combination with DNA sequencing of the bacSJ2-8 gene enabled the determination of the primary structure of a bacteriocin BacSJ. The production and functional expression of BacSJ in homologous and heterologous hosts suggest that bacSJ2-8 and bacSJ2-8i together with the genes encoding the ABC transporter and accessory protein are the minimal requirement for the production of BacSJ. Biochemical and genetic analyses showed that BacSJ belongs to the class II bacteriocins. The shuttle cloning vector pA13 could be used as a tool for genetic manipulations in lactobacilli and lactococci. <br><br><b><font color="red">withdrawn; due to a printing error. Link to the Editorial Decision <u><a href="http://dx.doi.org/10.2298/ABS1004251U">10.2298/ABS1004251U</a></u></font></b><br>

scholarly journals Cloning and characterization of novel human SLC4A8 gene products encoding Na+-driven Cl−/HCO3− exchanger variants NDCBE-A, -C, and -D

2008 ◽  
Vol 34 (3) ◽  
pp. 265-276 ◽  
Author(s):  
Mark D. Parker ◽  
Patrice Bouyer ◽  
Christopher M. Daly ◽  
Walter F. Boron
Keyword(s):  
In Silico Analysis ◽  
Functional Expression ◽  
Inhibitory Effect ◽  
Functional Difference ◽  
The Novel ◽  
Equivalent Position ◽  
Rapid Amplification ◽  
Novel Exon ◽  
Silico Analysis

The reported sequences of the human and mouse Na+-driven Cl−/HCO3− exchangers (NDCBEs) differ greatly in their extreme cytosolic COOH termini (Ct). In human NDCBE (NDCBE-B), a 17-amino acid (aa) sequence replaces 66 aa at the equivalent position in mouse NDCBE (NDCBE-A). We performed 5′- and 3′-rapid amplification of cDNA ends (RACE) on human brain cDNA, followed by PCR of full-length cDNAs to determine whether the human SLC4A8 gene was capable of producing the mouselike Ct sequence. Our study confirmed the presence in human cDNA of mouse NDCBE-like transcripts (human NDCBE-A) and also disclosed the existence of three further novel NDCBE transcripts that we have called NDCBE-C, NDCBE-D, and NDCBE-D′. The novel NDCBE-C/D/D′ transcripts initiate at a novel “exon 0” positioned ∼35 kb upstream of the first exon of NDCBE-A/B. NDCBE-C/D/D′ protein products are predicted to be truncated by 54 aa in the cytosolic NH2 terminus (Nt) compared with NDCBE-A/B. Our data, combined with a new in silico analysis of partial transcripts reported by others in the region of the human SLC4A8 gene, increase the known extent of the SLC4A8 gene by 49 kb, to 124 kb. A functional comparison of NDCBE-A/B/C/D expressed in Xenopus oocytes demonstrates that the Nt variation does not affect the basal functional expression of NDCBE, but those with the shorter Ct have a 25–50% reduced functional expression compared with those with the longer Ct. By comparison with an artificially truncated NDCBE that contains neither 17-aa nor 66-aa Ct cassette, we determined that the functional difference is unrelated to the 66-aa cassette of NDCBE-A/C, but is instead due to an inhibitory effect of the 17-aa cassette of NDCBE-B/D.

scholarly journals Genetic and Biochemical Characterization of a Novel Monoterpene ɛ-Lactone Hydrolase from Rhodococcus erythropolis DCL14

2001 ◽  
Vol 67 (2) ◽  
pp. 733-741 ◽  
Author(s):  
Cécile J. B van der Vlugt-Bergmans ◽  
Mariët J. van der Werf
Keyword(s):  
Ring Opening ◽  
Biochemical Characterization ◽  
Rhodococcus Erythropolis ◽  
Open Reading Frames ◽  
Apparent Homogeneity ◽  
Terminal Amino ◽  
Acyl Coenzyme A ◽  
Reading Frames

ABSTRACT A monoterpene ɛ-lactone hydrolase (MLH) from Rhodococcus erythropolis DCL14, catalyzing the ring opening of lactones which are formed during degradation of several monocyclic monoterpenes, including carvone and menthol, was purified to apparent homogeneity. It is a monomeric enzyme of 31 kDa that is active with (4R)-4-isopropenyl-7-methyl-2-oxo-oxepanone and (6R)-6-isopropenyl-3-methyl-2-oxo-oxepanone, lactones derived from (4R)-dihydrocarvone, and 7-isopropyl-4-methyl-2-oxo-oxepanone, the lactone derived from menthone. Both enantiomers of 4-, 5-, 6-, and 7-methyl-2-oxo-oxepanone were converted at equal rates, suggesting that the enzyme is not stereoselective. Maximal enzyme activity was measured at pH 9.5 and 30°C. Determination of the N-terminal amino acid sequence of purified MLH enabled cloning of the corresponding gene by a combination of PCR and colony screening. The gene, designated mlhB(monoterpene lactone hydrolysis), showed up to 43% similarity to members of the GDXG family of lipolytic enzymes. Sequencing of the adjacent regions revealed two other open reading frames, one encoding a protein with similarity to the short-chain dehydrogenase reductase family and the second encoding a protein with similarity to acyl coenzyme A dehydrogenases. Both enzymes are possibly also involved in the monoterpene degradation pathways of this microorganism.

A novel method for the determination of linting propensity of paper

TAPPI Journal ◽  
2012 ◽  
Vol 11 (10) ◽  
pp. 9-17
Author(s):  
ALESSANDRA GERLI ◽  
LEENDERT C. EIGENBROOD
Keyword(s):  
Ash Content ◽  
The Novel ◽  
Offset Printing ◽  
Excellent Correlation ◽  
End Conditions ◽  
Bottom Side ◽  
Novel Method ◽  
Total Fraction

A novel method was developed for the determination of linting propensity of paper based on printing with an IGT printability tester and image analysis of the printed strips. On average, the total fraction of the surface removed as lint during printing is 0.01%-0.1%. This value is lower than those reported in most laboratory printing tests, and more representative of commercial offset printing applications. Newsprint paper produced on a roll/blade former machine was evaluated for linting propensity using the novel method and also printed on a commercial coldset offset press. Laboratory and commercial printing results matched well, showing that linting was higher for the bottom side of paper than for the top side, and that linting could be reduced on both sides by application of a dry-strength additive. In a second case study, varying wet-end conditions were used on a hybrid former machine to produce four paper reels, with the goal of matching the low linting propensity of the paper produced on a machine with gap former configuration. We found that the retention program, by improving fiber fines retention, substantially reduced the linting propensity of the paper produced on the hybrid former machine. The papers were also printed on a commercial coldset offset press. An excellent correlation was found between the total lint area removed from the bottom side of the paper samples during laboratory printing and lint collected on halftone areas of the first upper printing unit after 45000 copies. Finally, the method was applied to determine the linting propensity of highly filled supercalendered paper produced on a hybrid former machine. In this case, the linting propensity of the bottom side of paper correlated with its ash content.

Characterization of Glycoprotein Fraction from Carp Pituitaries Isolated Using Concanavalin A as the Affinity Ligand

1998 ◽  
Vol 63 (3) ◽  
pp. 434-440 ◽  
Author(s):  
Irena Hulová ◽  
Jana Barthová ◽  
Helena Ryšlavá ◽  
Václav Kašička
Keyword(s):  
Concanavalin A ◽  
Reversed Phase ◽  
Amino Acid Sequences ◽  
Gel Chromatography ◽  
Affinity Ligand ◽  
Sds Page ◽  
Terminal Amino ◽  
Α And Β Subunits

Glycoproteins that have affinity to Concanavalin A were isolated from the acetone-dried pituitaries of common carp (Cyprinus carpio L.). Two fractions of glycoproteins were separated using gel chromatography on Superdex 75HR. The fraction with lower molecular weight (30 000) corresponding to the carp gonadotropin cGtH II was composed of two subunits as determined using SDS-PAGE. This protein fraction was further divided into four components using reversed-phase HPLC. Two fractions were pure α and β subunits of cGtH II as follows from immunodetection and from determination of N-terminal amino acid sequences. The other two were a mixture of α and β subunits as was also revealed by N-terminal analysis. Capillary electrophoresis was also used for characterization of isolated glycoproteins.

scholarly journals Fine-tuning the performance of ddRAD-seq in the peach genome

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Maximiliano Martín Aballay ◽  
Natalia Cristina Aguirre ◽  
Carla Valeria Filippi ◽  
Gabriel Hugo Valentini ◽  
Gerardo Sánchez
Keyword(s):  
Germplasm Collection ◽  
In Silico Analysis ◽  
Genotyping By Sequencing ◽  
Fine Tuning ◽  
The Novel ◽  
Peach Genome ◽  
Genome Complexity ◽  
Next Generation Sequencing Ngs ◽  
Sample Set ◽  
Silico Analysis

AbstractThe advance of Next Generation Sequencing (NGS) technologies allows high-throughput genotyping at a reasonable cost, although, in the case of peach, this technology has been scarcely developed. To date, only a standard Genotyping by Sequencing approach (GBS), based on a single restriction with ApeKI to reduce genome complexity, has been applied in peach. In this work, we assessed the performance of the double-digest RADseq approach (ddRADseq), by testing 6 double restrictions with the restriction profile generated with ApeKI. The enzyme pair PstI/MboI retained the highest number of loci in concordance with the in silico analysis. Under this condition, the analysis of a diverse germplasm collection (191 peach genotypes) yielded 200,759,000 paired-end (2 × 250 bp) reads that allowed the identification of 113,411 SNP, 13,661 InDel and 2133 SSR. We take advantage of a wide sample set to describe technical scope of the platform. The novel platform presented here represents a useful tool for genomic-based breeding for peach.

scholarly journals Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 27
Author(s):  
Jun Kwon ◽  
Sang Guen Kim ◽  
Hyoun Joong Kim ◽  
Sib Sankar Giri ◽  
Sang Wha Kim ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Open Reading Frames ◽  
Genome Comparison ◽  
The Novel ◽  
Promising Alternative ◽  
Isolation And Characterization ◽  
Global Issue ◽  
Reading Frames ◽  
Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

Comparative Study for the Assay of Plant Derived Chemicals in Pharmaceutical Formulation Using Methods Dependent on Factorized Spectra

2021 ◽  
Author(s):  
Nesma M Fahmy ◽  
Adel M Michael
Keyword(s):  
Pharmaceutical Formulations ◽  
Pharmaceutical Formulation ◽  
Ternary Mixtures ◽  
Ratio Method ◽  
The Novel ◽  
Naturally Occurring ◽  
Accuracy And Precision ◽  
Validation Parameters ◽  
Significant Difference

Abstract Background Modern built-in spectrophotometer software supporting mathematical processes provided a solution for increasing selectivity for multicomponent mixtures. Objective Simultaneous spectrophotometric determination of the three naturally occurring antioxidants—rutin(RUT), hesperidin(HES), and ascorbic acid(ASC)—in bulk forms and combined pharmaceutical formulation. Method This was achieved by factorized zero order method (FZM), factorized derivative method (FD1M), and factorized derivative ratio method (FDRM), coupled with spectrum subtraction(SS). Results Mathematical filtration techniques allowed each component to be obtained separately in either its zero, first, or derivative ratio form, allowing the resolution of spectra typical to the pure components present in Vitamin C Forte® tablets. The proposed methods were applied over a concentration range of 2–50, 2–30, and 10–100 µg/mL for RUT, HES, and ASC, respectively. Conclusions Recent methods for the analysis of binary mixtures, FZM and FD1M, were successfully applied for the analysis of ternary mixtures and compared to the novel FDRM. All were revealed to be specific and sensitive with successful application on pharmaceutical formulations. Validation parameters were evaluated in accordance with the International Conference on Harmonization guidelines. Statistical results were satisfactory, revealing no significant difference regarding accuracy and precision. Highlights Factorized methods enabled the resolution of spectra identical to those of pure drugs present in mixtures. Overlapped spectra of ternary mixtures could be resolved by spectrum subtraction coupled FDRM (SS-FDRM) or by successive application of FZM and FD1M.

scholarly journals Phylogenetic Core Groups: a promising concept in search of a consistent methodological framework

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Author(s):  
Alberto Pascual-García
Keyword(s):  
Microbial Communities ◽  
Microbial Ecology ◽  
Environmental Conditions ◽  
The Novel ◽  
Methodological Framework ◽  
Operational Taxonomic Units ◽  
Traditional Classification ◽  
Taxonomical Classification ◽  
Novel Concept

AbstractIn this comment, we analyse the conceptual framework proposed by Aguirre de Cárcer (Microbiome 7:142, 2019), introducing the novel concept of Phylogenetic Core Groups (PCGs). This notion aims to complement the traditional classification in operational taxonomic units (OTUs), widely used in microbial ecology, to provide a more intrinsic taxonomical classification which avoids the use of pre-determined thresholds. However, to introduce this concept, the author frames his proposal in a wider theoretical framework based on a conceptualization of selection that we argue is a tautology. This blurs the subsequent formulation of an assembly principle for microbial communities, favouring that some contradictory examples introduced to support the framework appear aligned in their conclusions. And more importantly, under this framework and its derived methodology, it is not possible to infer PCGs from data in a consistent way. We reanalyse the proposal to identify its logical and methodological flaws and, through the analysis of synthetic scenarios, we propose a number of methodological refinements to contribute towards the determination of PCGs in a consistent way. We hope our analysis will promote the exploration of PCGs as a potentially valuable tool, helping to bridge the gap between environmental conditions and community composition in microbial ecology.

scholarly journals Reaktive E=C(p–p)π Systeme, XXXIV Addition von Alkoholen oder primären Aminen an Phosphaalkene F3CP=C(F)OR. Neue Trifluormethylphosphane und -phosphaalkene/Reactive E = C( p – p ) π-Systems, XXXIV Addition of Alcohols or Primary Amines to Phosphaalkenes F3CP= C(F)OR . Novel Trifluoromethylphosphanes and Phosphaalkenes

1993 ◽  
Vol 48 (1) ◽  
pp. 58-67 ◽  
Author(s):  
Joseph Grobe ◽  
Duc Le Van ◽  
Gudrun Lange
Keyword(s):  
High Resolution Mass Spectrometry ◽  
Molar Ratio ◽  
Primary Amines ◽  
The Novel ◽  
Experimental Conditions ◽  
Pull System ◽  
Fragment Ions ◽  
New Compounds ◽  
C Nmr

The course of the reactions o f fluorophosphaalkenes F3CP = C (F)OR [R = Me (1), Et (2)] with methanol or ethanol strongly depends on the experimental conditions. Thus at 70 °C a mixture of the 2-phosphapropionic acid ester F3CP (H )CO2R [R = Me (3), Et (4)] and trifluoromethylphosphane H2PCF3 is formed [molar ratio: 3 or 4 /H2 CF3 ≈1/1]. If the precursors F3CP (H )CO2R [R = Me (3), Et) are used as starting materials, the reaction with ROH under the same conditions affords 3 and 4, respectively, (90 to 95% yield) with only traces of H2PCF 3. In the presence o f iPr2NH these precursors react with R′OH to give the novel trifluoromethylphosphaalkenes F3CP = C (OR )OR [R /R′: Me/Me (6); E t/E t (7); Me/Et (8)]. With Et2NH , 3 undergoes an addition/elimination process yielding the interesting push/pull system Et2N(F)C = P-CO2Me (5). 1 and 2 react with primary amines R′NH2 (R′= tBu, Me) with stereoselective formation of the fairly labile phosphaalkenes F3CP = C(OR)NHR′ [R /R′: Me/tBu (9), Et/tBu(10), Me/Me (11)] with trans-positions for CF3 and NHR′.The new compounds 3 -11 were characterized by spectroscopic investigations (1H , 19F, 31P, 13C NMR ; IR, MS) and determination of M+ or typical fragment ions [M+ -OR ] by high resolution mass spectrometry.

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