Gel Isolation Research Articles

Preparation, purification, and biochemical of fat-degrading bacterial enzymes from pig carcass compost and its application

BackgroundA lot of kitchen waste oil is produced every day worldwide, leading to serious environmental pollution. As one of the environmental protection methods, microorganisms are widely used treating of various wastes. Lipase, as one of the cleaning agents can effectively degrade kitchen waste oil. The composting process of pig carcasses produces many lipase producing microorganisms, rendering compost products an excellent source for isolating lipase producing microorganisms. To our knowledge, there are no reports isolating of lipase producing strains from the high temperature phase of pig carcass compost.MethodologyLipase producing strains were isolated using a triglyceride medium and identified by 16S rRNA gene sequencing. The optimal fermentation conditions for maximum lipase yield were gradually optimized by single-factor tests. The extracellular lipase was purified by ammonium sulfate precipitation and Sephadex G-75 gel isolation chromatography. Amino acid sequence analysis, structure prediction, and molecular docking of the purified protein were performed. The pure lipase's enzymatic properties and application potential were evaluated by characterizing its biochemical properties.ResultsIn this study, a lipase producing strain of Bacillus sp. ZF2 was isolated from pig carcass compost products, the optimal fermentation conditions of lipase: sucrose 3 g/L, ammonium sulfate 7 g/L, Mn2+ 1.0 mmol/L, initial pH 6, inoculum 5%, temperature 25 ℃, and fermentation time 48 h. After purification, the specific activity of the purified lipase reached 317.59 U/mg, a 9.78-fold improvement. Lipase had the highest similarity to the GH family 46 chitosanase and molecular docking showed that lipase binds to fat via two hydrogen bonds at Gln146 (A) and Glu203 (A). Under different conditions (temperature, metal ions, organic solvents, and surfactants), lipase can maintain enzymatic activity. Under different types of kitchen oils, lipase has low activity only for ‘chicken oil’, in treating other substrates, the enzyme activity can exceed 50%.ConclusionsThis study reveals the potential of lipase for waste oil removal, and future research will be devoted to the application of lipase.

Pentapeptide-Zinc Chelate from Sweet Almond Expeller Amandin Hydrolysates: Structural and Physicochemical Characteristics, Stability and Zinc Transport Ability In Vitro.

To promote the application of almond expellers, sweet almond expeller globulin (amandin) was extracted for the preparation of bioactive peptides. After dual enzymatic hydrolysis, Sephadex G-15 gel isolation, reverse-phase high-performance liquid chromatography purification and ESI-MS/MS analysis, two novel peptides Val-Asp-Leu-Val-Ala-Glu-Val-Pro-Arg-Gly-Leu (1164.45 Da) and Leu-Asp-Arg-Leu-Glu (644.77 Da) were identified in sweet almond expeller amandin hydrolysates. Leu-Asp-Arg-Leu-Glu (LDRLE) of excellent zinc-chelating capacity (24.73 mg/g) was selected for preparation of peptide-zinc chelate. Structural analysis revealed that zinc ions were mainly bonded to amino group and carboxyl group of LDRLE. Potential toxicity and some physicochemical properties of LDRLE and Val-Asp-Leu-Val-Ala-Glu-Val-Pro-Arg-Gly-Leu (VDLVAEVPRGL) were predicted in silico. The results demonstrated that both LDRLE and VDLVAEVPRGL were not toxic. Additionally, zinc solubility of LDRLE-zinc chelate was much higher than that of zinc sulphate and zinc gluconate at pH 6.0-10.0 and against gastrointestinal digestion at 37 °C (p < 0.05). However, incubation at 100 °C for 20-60 min significantly reduced zinc-solubility of LDRLE-zinc chelate. Moreover, the chelate showed higher zinc transport ability in vitro than zinc sulphate and zinc gluconate (p < 0.05). Therefore, peptides isolated from sweet almond expeller amandin have potential applications as ingredient of zinc supplements.

Isolation of single-stranded DNA.

Single-stranded DNA (ssDNA) is often used for DNA sequencing as well as microarray and hybridization technologies. Asymmetric PCR or exonuclease digestion followed by urea gel separation and isolation on streptavidin-coated magnetic beads are commonly used for this purpose. These two methods may not yield large amounts of highly purified ssDNA. This protocol for ssDNA isolation from PCR-amplified DNA involves biotin labeling of one strand and subsequent strand separation utilizing streptavidin-coated magnetic beads.

Fluid Shear Stress Regulates the Invasive Potential of Glioma Cells via Modulation of Migratory Activity and Matrix Metalloproteinase Expression

BackgroundGlioma cells are exposed to elevated interstitial fluid flow during the onset of angiogenesis, at the tumor periphery while invading normal parenchyma, within white matter tracts, and during vascular normalization therapy. Glioma cell lines that have been exposed to fluid flow forces in vivo have much lower invasive potentials than in vitro cell motility assays without flow would indicate.Methodology/Principal FindingsA 3D Modified Boyden chamber (Darcy flow through collagen/cell suspension) model was designed to mimic the fluid dynamic microenvironment to study the effects of fluid shear stress on the migratory activity of glioma cells. Novel methods for gel compaction and isolation of chemotactic migration from flow stimulation were utilized for three glioma cell lines: U87, CNS-1, and U251. All physiologic levels of fluid shear stress suppressed the migratory activity of U87 and CNS-1 cell lines. U251 motility remained unaltered within the 3D interstitial flow model. Matrix Metalloproteinase (MMP) inhibition experiments and assays demonstrated that the glioma cells depended on MMP activity to invade, and suppression in motility correlated with downregulation of MMP-1 and MMP-2 levels. This was confirmed by RT-PCR and with the aid of MMP-1 and MMP-2 shRNA constructs.Conclusions/SignificanceFluid shear stress in the tumor microenvironment may explain reduced glioma invasion through modulation of cell motility and MMP levels. The flow-induced migration trends were consistent with reported invasive potentials of implanted gliomas. The models developed for this study imply that flow-modulated motility involves mechanotransduction of fluid shear stress affecting MMP activation and expression. These models should be useful for the continued study of interstitial flow effects on processes that affect tumor progression.

PCR cloning of partial nbs sequences from grape (Vitis aestivalis Michx)

Plants defend themselves against pathogens via the expressions of disease resistance (R) genes. Many plant R gene products contain the characteristic nucleotide-binding site (NBS) and leucine-rich repeat (LRR) domains. There are highly conserved motifs within the NBS domain which could be targeted for polymerase chain reaction (PCR) cloning of R genes. Here, we report a 4-week undergraduate laboratory exercise that mimics the research environment to PCR-clone partial nbs sequences using degenerate primers corresponding to the phosphate-binding loop (P-loop) and GLPL motifs within the NBS domain of potential R gene products from the North American grape, Vitis aestivalis Michx. Students were able to complete the laboratory procedures successfully and obtained four different clones, among which three are new. Through the laboratory exercise, students learned a variety of important molecular techniques including genomic DNA isolation, DNA quantification, PCR, agarose gel electrophoresis, DNA extraction from agarose gel, ligation, bacterial transformation, and plasmid DNA isolation and purification. They also used currently available web-based bioinformatic programs for sequence analysis. The laboratory exercise provides students the hands-on experience on PCR cloning and shows them how it is done in a research environment. The clones obtained may be further tested for their potential use as markers to differentiate resistant cultivars from the susceptible ones, a useful tool in breeding programs.

Homogeneous and one-step fluorescent allele-specific PCR for SNP genotyping assays using conjugated polyelectrolytes

A new label-free, homogenous, sensitive and economical one-step method to detect SNP genotyping of genomic DNA has been developed by combining allele-specific PCR technique with water-soluble cationic conjugated polyelectrolytes (CCP). The amplification of target DNA and fluorescence detection steps are combined into one-step. The target DNA fragment containing a G allele site acts as PCR template. For the G allele-specific forward primer whose 3′-terminal base is complementary to the G allele template, after the first step of reverse primer extension, G allele-specific primer perfectly anneals with newly formed strand and the extension reaction of forward primer starts. During the extension, dGTP-Fl and dUTP-Fl are incorporated into extension chain in the presence of Taq DNA polymerase and more fluorescein-labeled PCR amplicons are yielded. Upon adding the CCP, strong electrostatic interactions between DNA and CCP bring them close and efficient FRET from CCP to fluorescein occurs. For the C allele-specific forward primer, less fluorescein-labeled PCR amplicons are yielded and inefficient FRET occurs. By triggering the change of emission intensity of CCP and fluorescein, it is possible to assay the SNP genotypes. In contrast to previous reports, this method does not require designing dye-labeled primers, and gel electrophoresis and isolation step after PCR were avoided in this homogenous method. The genotyping of 50ng genomic DNA from human lung cancer cell is easily detected using our new method. These qualities will make the new detection system ideal for SNP genotyping.

Photoaffinity Labeling of the Plasmodium falciparum Chloroquine Resistance Transporter with a Novel Perfluorophenylazido Chloroquine

Several models describing how amino acid substitutions in the Plasmodium falciparum chloroquine resistance transporter (PfCRT) confer resistance to chloroquine (CQ) and other antimalarial drugs have been proposed. Further progress requires molecular analysis of interactions between purified reconstituted PfCRT protein and these drugs. We have thus designed and synthesized several perfluorophenyl azido (pfpa) CQ analogues for PfCRT photolabeling studies. One particularly useful probe (AzBCQ) places the pfpa group at the terminal aliphatic N of CQ via a flexible four-carbon ester linker and includes a convenient biotin tag. This probe photolabels PfCRT in situ with high specificity. Using reconstituted proteoliposomes harboring partially purified recombinant PfCRT, we analyze AzBCQ photolabeling versus competition with CQ and other drugs to probe the nature of the CQ binding site. We also inspect how pH, the chemoreversal agent verapamil (VPL), and various amino acid mutations in PfCRT that cause CQ resistance (CQR) affect the efficiency of AzBCQ photolabeling. Upon gel isolation of AzBCQ-labeled PfCRT followed by trypsin digestion and mass spectrometry analysis, we are able to define a single AzBCQ covalent attachment site lying within the digestive vacuolar-disposed loop between putative helices 9 and 10 of PfCRT. Taken together, the data provide important new insight into PfCRT function and, along with previous results, allow us to propose a model for a single CQ binding site in the PfCRT protein.

Vectors for co-expression of an unrestricted number of proteins

A vector system is presented that allows generation of E. coli co-expression clones by a standardized, robust cloning procedure. The number of co-expressed proteins is not limited. Five ‘pQLink’ vectors for expression of His-tag and GST-tag fusion proteins as well as untagged proteins and for cloning by restriction enzymes or Gateway cloning were generated. The vectors allow proteins to be expressed individually; to achieve co-expression, two pQLink plasmids are combined by ligation-independent cloning. pQLink co-expression plasmids can accept an unrestricted number of genes. As an example, the co-expression of a heterotetrameric human transport protein particle (TRAPP) complex from a single plasmid, its isolation and analysis of its stoichiometry are shown. pQLink clones can be used directly for pull-down experiments if the proteins are expressed with different tags. We demonstrate pull-down experiments of human valosin-containing protein (VCP) with fragments of the autocrine motility factor receptor (AMFR). The cloning method avoids PCR or gel isolation of restriction fragments, and a single resistance marker and origin of replication are used, allowing over-expression of rare tRNAs from a second plasmid. It is expected that applications are not restricted to bacteria, but could include co-expression in other hosts such as Bacluovirus/insect cells.

Polymorphisms in 16S rRNA genes of Flavobacterium psychrophilum correlate with elastin hydrolysis and tetracycline resistance

Flavobacterium psychrophilum is the etiological agent of bacterial coldwater disease, which causes significant problems to aquaculture worldwide. A recent study (Soule M, Cain K, LaFrentz S, Call DR [2005] Infect Immun 73:3799-3802) identified two 16S rRNA gene sequence variants (6 base differences) within the variable stem-loop region 3 for F. psychrophilum strains ATCC 49418 and CSF 259-93. That study also hypothesized that F. psychrophilum is composed of at least 2 distinct genetic lineages (I and II) described by a microarray-based comparative genomics study. In the present study, we augmented an existing 16S rDNA microarray to detect both 16S rRNA sequence variants from F. psychrophilum. Subsequent microarray experiments showed that CSF 259-93 hybridized as expected, but ATCC 49418 was positive for both sequence variants. We then developed a PCR-restriction fragment length polymorphism (RFLP) assay (MnlI and MaeIII) to distinguish between the 2 sequences. Gel isolation of PCR-RFLP products, cloning, and sequencing confirmed that ATCC 49418 harbors both 16S rRNA sequences. Microarray experiments showed that 11 of 14 strains from genetic Lineage I harbor both the CSF 259-93 and ATCC 49418 16S rRNA sequence variants, whereas all 15 Lineage II strains were only positive for the CSF 259-93 sequence (p < 0.0001). Elastin hydrolysis and tetracycline resistance were most closely associated with the latter strains (p < 0.0001 and p = 0.024, respectively). These data support the hypothesis that F. psychrophilum is composed of at least 2 distinct genetic lineages that are closely associated with host origin.

DNA Microarray Probe Preparation by Gel Isolation Nested PCR

To develop a simplified method that can rapidly prepare DNA microarray probes in a massive scale, a lambda phage genomic DNA-fragments library was constructed for the microarray-probes collection. Four methods of DNA band recovery from the first PCR products were tested and compared. The DNA microarray probes were collected by a novel method of nested PCR that was mediated by gel isolation of the first PCR products. This method was named GIN-PCR. The probes that were prepared by this GIN-PCR technique were used as subjects to fabricate a DNA microarray. The results showed that a wooden toothpick was superior to the other 3 methods, since this technique can steadily transfer the DNA bands as the template of the second PCR after the first PCR. A group of probes were successfully collected and DNA microarrays were constructed using these probes. Hybridization results demonstrated that this technique of DNA recovery and probe preparation was rapid, efficient, and effective. We developed a cost-effective and less labor-intensive method for DNA microarray probe preparation by nested PCR that is mediated by wooden toothpick transfer of the DNA bands in the gel after electrophoresis.

Inhibition of DNA methyltransferase inhibits DNA replication.

Ectopic expression of DNA methyltransferase transforms vertebrate cells, and inhibition of DNA methyltransferase reverses the transformed phenotype by an unknown mechanism. We tested the hypothesis that the presence of an active DNA methyltransferase is required for DNA replication in human non-small cell lung carcinoma A549 cells. We show that the inhibition of DNA methyltransferase by two novel mechanisms negatively affects DNA synthesis and progression through the cell cycle. Competitive polymerase chain reaction of newly synthesized DNA shows decreased origin activity at three previously characterized origins of replication following DNA methyltransferase inhibition. We suggest that the requirement of an active DNA methyltransferase for the functioning of the replication machinery has evolved to coordinate DNA replication and inheritance of the DNA methylation pattern.

Preliminary Characterization of a Potyvirus, the Causal Agent of Green-Sterile Disease of Guar

A potyvirus named guar green-sterile virus (GGSV) has been reported to be associated with a disease of guar (Cyamopsis tetragonoloba (L.)) in southern Africa. Symptoms of leaf chlorosis/ localized necrosis and sterility in guar were obtained using a sucrose-gradient purified GGSV preparation for mechanical inoculation. Potyviruses were also isolated from sterile guar plants grown from seed and from mechanically inoculated guar and bean cultivar hosts, which indicates that GGSV is the causal agent of disease symptoms in guar. Polyacrylamide gel electrophoresis, Western blot (immunoblot), serological analyses, and isolation of an RNA species of approximately 9,4 Kb indicate that GGSV is a potyvirus. Results of mechanical transmissions to bean cultivars used to differentiate bean common mosaic virus (BCMV) and bean common mosaic necrosis virus (BCMNV) strains, comparisons with a local strain of BCMV (BCMV-SA), and serological tests with antisera to BCMV and BCMNV indicate that GGSV may serologically react with several BCMV strains but it is not a known strain or serotype of BCMV. Thus, GGSV may be a new guar legume potyvirus

RAPD analysis in flax: Optimization of yield and reproducibility using klenTaq 1 DNA polymerase, chelex 100, and gel purification of genomic DNA

We have developed an optimized RAPD analysis approach using the unusually heat-stable KlenTaq1 DNA polymerase. This enzyme is used in conjunction with a genomic DNA isolation method that includes a modified CTAB DNA isolation protocol, ethanol re-precipitation of resuspended nucleic acids from 2M NaCl, and Chelex 100 treatment. When needed, additional gel purification and isolation of high molecular weight DNA for use as a template in RAPD analysis is shown to remove amplification product ambiguity from within isolates of the same line as well as from between lines. This optimized RAPD analysis was used to define polymorphisms in lines of flax nearly isogenic for rust resistance at theL locus. It should also be useful for any plant species.

Reduced hepatic iron uptake from rat aglycotransferrin

Rat aglycotransferrin (rAgTf) was produced from the disialosyl diantennary fraction of rat transferrin (rTf) by treatment with peptide: N-glycosidase F. Following removal of the enzyme by gel filtration and isolation of the deglycosylated protein by lectin chromatography, rAgTf was compared to rTf both in vitro and in vivo. No significant differences were found between the two proteins with respect to affinity for iron and kinetics of Fe release from the N-lobe and C-lobe. The fluorescence emission spectrum of apo-rTf was red-shifted by approximately 3 nm relative to diferric rTf; however, no spectral difference was detected between rTf and rAgTf when the analogous forms (apo or diferric) were compared. Plasma clearance of radioactive iron administered to rats as either rTf or rAgTf was comparable. Reticulocytes took up iron from rAgTf slightly faster than from rTf. In contrast, Fe acquisition by the liver from rAgTf was significantly reduced relative to rTf. This finding contrasts sharply with earlier observations with asialotransferrin (rAsTf) and provides a basis for discounting charge loss as the mechanism of enhanced hepatic Fe uptake from rAsTf. It is suggested that the glycan complement of rTf, while unimportant for interaction of the protein with specific receptors, probably plays a role in the interaction with low-affinity hepatic binding sites.

ChemInform Abstract: Mechanistic Studies on the Reaction of Chromium Carbene Complexes with Acetylenes: Furan Formation and the Dependence of the Product Distribution on the Stereochemistry of Reaction Intermediates.

AbstractThe reaction of the chromium complex (I) with acetylenes such as (II) yields mixtures of the phenols (III) and the furans (IV) (silica gel isolation of (IIIa) yields a 1:2.4 mixture of the phenol and its corresponding lactone).

The T cell antigen receptor zeta chain is tyrosine phosphorylated upon activation.

The T cell antigen receptor is composed of at least seven chains derived from six different gene products. Upon stimulation, several chains can be phosphorylated. Two of these, CD3-gamma and CD3-epsilon are phosphorylated on serine residues. In addition, a 21-kDa nonglycosylated receptor component is phosphorylated, upon activation, on tyrosine residues. We have referred to this phosphoprotein as p21 because we have previously not been able to assign the tyrosine phosphorylation to any of the described receptor subunits (Samelson, L. E., Patel, M. D., Weissman, A. M., Harford, J. B., and Klausner, R. D. (1986) Cell 46, 1083-1090). In this paper, we demonstrate that it is the 16-kDa zeta chain which is the tyrosine phosphorylated subunit, and thus the p21 nomenclature can be replaced. This phosphorylation results in a shift of the apparent Mr of zeta to 21 kDa. Proof that p21 is tyrosine phosphorylated zeta was afforded by a number of approaches. Specific anti-zeta antibodies directly precipitated phospho-p21. Metabolically labeled protein corresponding to p21 could only be observed after activation. When this 21-kDa band was isolated after sodium dodecyl sulfate-polyacrylamide gel electrophoresis and reanalyzed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis after treatment with alkaline phosphatase, its migration was identical with that of zeta. Furthermore, peptide mapping of metabolically labeled p21 (after gel isolation and dephosphorylation) showed it to be indistinguishable from p21. Thus, one of the early events of T cell activation is the tyrosine phosphorylation of the zeta chain of the T cell antigen receptor.

A transferrin variant Tf I in crosses of the wild and domestic pigs.

In crosses of the wild pig (Sus scrofa attila Thomas) with the domestic pig a transferrin variant, Tf I, was detected, electrophoretic mobility of which was slightly faster than the mobility of the variant Tf A. From the results of starch gel electrophoresis, isolation, neuraminidase treatment, autoradiography, and genetic analysis of several families, it can be concluded that the Tf I variant is genetically controlled by the allele Tf1. Thus the number of alleles in the transferrin system of the pig has increased to six (Tf1, TfA, TfB, TfC, TfD and TfE).

Base analysis of ribopolynucleotides by tritium incorporation following analytical polycrylamide gel electrophoresis

A procedure is described for tritium base composition analysis of major and modified constituents of 4S RNA following extraction of the RNA from analytical slab gels. Gel electrophoresis and isolation of RNA are shown not to lead to chemical alterations of RNA bases, degradation or preferential losses of RNA species.