Phosphorescent zinc sulfide is a nonradioactive alternative for marking autoradiograms

Phosphorescent zinc sulfide is a nonradioactive alternative for making orientation and identification markings on autoradiograms. Measurements with a luminometer show that light emission is linear with respect to ZnS concentration. A minimum activation time of 5 s has been determined, using an incandescent lamp as a light source. Emission decay kinetics show light emissions reached background levels within minutes, depending on the ZnS concentration. This time period is sufficient for X-ray films to be permanently marked. Because of its efficiency and nontoxicity, this autoradiogram marker could be extremely useful in many protocols, including high-throughput radioactive DNA sequencing. This nonradioactive marker will also be useful in protocols utilizing nonradioactive detection systems, such as those calling for biotinylated and chemiluminescent probes.     

An alternative nonradioactive method for labeling DNA using biotin

An alternative nonradioactive labeling method and a highly sensitive technique for detecting specific DNA sequences are described. The labeling method requires the "Klenow" fragment of DNA polymerase I and random hexanucleotides (synthesized or naturally extracted) as a primer for the production of highly sensitive DNA probes. The system has three main steps: (i) labeling of DNA with biotinylated 11-dUTP; (ii) detection of biotinylated DNA by a one-step procedure with streptavidin-alkaline phosphatase complex; (iii) blocking of background with Tween 20. Twenty attograms (2 X 10(-17) g) of pBR322 plasmid DNA was detected by dot-blot hybridization. Upon Southern blot hybridization, 7.4 fg (7.4 X 10(-15) g) of pBR322 HindIII DNA was detected using the biotinylated pBR322 plasmid DNA probe; 40.8 ag and 7.4 fg of lambda HindIII DNA were detected with the biotinylated whole lambda DNA probe by dot and Southern blot hybridization, respectively. Specific bands were also detected with the biotinylated argininosuccinolyase probe upon Northern blotting of mouse poly(A+) RNA. Further applications for in situ hybridization are also described.     

Biocatalyst-adsorbant systems: a viable alternative to proteolytic processes in solution

Proteolytic biocatalysts were adsorbed and stabilized using alumina as a support medium. Two biocatalyst-adsorbant systems were prepared with different physical characteristics of the adsorbant: alumina powder and alumina pearls. Direct adsorption onto the support medium has the main advantage, over other fixation methods, that preliminary steps are not required for a good interaction between the support and the biocatalyst. Proteases were adsorbed and stabilized without modifying or sterically hindering their active sites. Parameters affecting adsorption (pH, temperature, ionic strength) were varied so as to optimize adsorption conditions. Operational viability of the immobilized biocatalysts was demonstrated, taking into account the rate of desorption, resistance to microbial attack, and stability during storage. Desorption in water was studied in batch and continuous-flow processes, at various flow rates. The systems also proved to be resistant to microorganisms. Tests for stability during storage found the systems' activity remained constant after 60 days, and they performed better than biocatalysts in solution. Proteolysis of a solution of g per litre of azocasein was carried out in continuous-flow and batch modes, using our biocatalyst-adsorbant systems we prepared. In all cases, free amino group concentrations were around 2.5 times greater after treatment with biocatalyst-adsorbants than they were in the starting solution.     

A nonradioactive method for isolating complementary DNAs endocing calmodulin-binding proteins

Calmodulin labeled with¹²⁵I or³⁴S has been used to screen expression libraries to isolate cDNAs encoding calmodulin-binding proteins (CBPs) from several eukaryotic systems. The use of radiolabeled calmodulin has, however, several disadvantages. We have developed a nonradiactive method to isolate cDNAs for CBPs using biotinylated calmodulin. Screening of a cDNA library in an expression vector with biotinylated calmodulin resulted in the isolation of cDNAs encoding CBPs. Avidin and biotin blocking steps, prior to incubation of the filters with biotinylated calmodulin, are found to be essential to eliminate the cDNAs that code for biotin-containing polypeptides. The cDNA clones isolated using this nonradioactive method bound calmodulin in a calcium-dependent manner. The binding of biotinylated calmodulin to these clones was completely abolished by ethylene glycolbis(\-aminoethylether)-N,N′-tetraacetic acid (EGTA), a calcium chelator. Furthermore, the isolated cDNAs were confirmed by probing the clones with³⁵S-labeled calmodulin. All the isolated clones bound to radiolabeled calmodulin in the presence of calcium but not in the presence of EGTA. The method described here is simple, fast, and does not involve preparation and handing of radiolabeled calmodulin. All the materials used in this method are commercially available; hence, this procedure should be widely applicable to isolate cDNAs encoding CBPs from any eukaryotic organism.     

Genetic inference as a method for modelling occurrence: A viable alternative to visual surveys

Management and conservation require a comprehensive understanding of species distributions and habitat requirements. Reliable species occurrence data are critical in the face of climate change and other anthropogenic activity, but are often difficult to obtain, particularly for wide ranging species. This directly affects ecological models of occurrence and habitat suitability and, in turn, conservation and management decisions. We used generalized linear mixed‐effects models to identify ecological determinants of occurrence for four macropod species (across a region of tropical northern Australia) using a non‐invasive genetic scat approach with and without additional observation records from visual surveys. We show that genetically derived occurrence data, alone, can be used to develop informative ecological models that describe the inter‐specific habitat requirements of macropods. Furthermore, we show that genetic scat surveys of macropods are cheaper and less time consuming to conduct, and tend to provide more occurrence records (and less false absences) than visual surveys. We conclude that indirect surveys using molecular approaches have an important role to play in modelling species' occurrence, and developing future management practices and guidelines to aid species conservation.     

Immunodetection of biotinylated lymphocyte-surface proteins by enhanced chemiluminescence: a nonradioactive method for cell-surface protein analysis.

Biotinylation and radioiodination have been compared for labeling lymphocyte-surface proteins and the labeled proteins symmetrically immunoprecipitated with antibodies recognizing major lymphocyte markers such as the murine Thy-1, CD25 (the alpha subunit of the interleukin-2 receptor), CD45, and human CD2 glycoproteins. The detection of biotinylated proteins by enhanced chemiluminescence after transfer to nitrocellulose was found to be fast and as efficient as the detection of iodinated proteins by autoradiography. The vectoriality of cell-surface biotinylation was ascertained by two-dimensional electrophoresis of the cellular extract in which the major cytoplasmic proteins were not found biotinylated. This nonradioactive labeling procedure offers a convenient and efficient alternative to radiolabeling of cell surfaces for the biochemical analysis of extracellular domains of membrane proteins.     

Valproic acid: a viable alternative to sodium butyrate for enhancing protein expression in mammalian cell cultures

Various DNA methyl transferase inhibitors (iDNMTs) and histone deacetylase inhibitors (iHDACs) were screened for their ability to enhance transient gene expression (TGE) in Human Embryonic Kidney 293-EBNA (HEK293E) cells. The effects in HEK293E cells were compared to those in Chinese Hamster Ovary DG44 (CHO-DG44) cells. The iDNMTs and iHDACs were chosen based on their different cellular activities and mechanisms of action. For each inhibitor tested, the optimum concentration was determined for both cell lines, and these conditions were used to evaluate the effect of each compound using a recombinant monoclonal antibody as a reporter protein. All the iHDACs increased transient antibody yield at least 4-fold in HEK293E and at least 1.5-fold in CHO-DG44. By comparison, the iDNMTs increased antibody yields by a maximum of approximately 2-fold. Pairwise combinations of iDNMTs and iHDACs had a linearly additive effect on TGE in CHO-DG44 but not in HEK293E. With valproic acid (VPA), volumetric and specific productivities of 200 mg/L and 20 pg/cell/day, respectively, were achieved in HEK293E cells with a 10-day process. As VPA is both FDA-approved and 5-fold less expensive than sodium butyrate (NaBut), we recommend it as a cost-effective alternative to this widely used enhancer of recombinant protein production from mammalian cells.     

Metabolic oligosaccharide engineering as a tool for glycobiology

Oligosaccharides transact information exchange at the cell surface and modulate the activities and distribution of proteins within cells. Recently, the ability to modify monosaccharide structures within cellular glycans through metabolic processes has offered a new avenue for biological studies. The technique of metabolic oligosaccharide engineering has been used to disrupt glycan biosynthesis, chemically modify cell surfaces, probe metabolic flux inside cells, and to identify specific glycoprotein subtypes from the proteome.     

The human gastric colonizer Helicobacter pylori: a challenge for host-parasite glycobiology

The Gram-negative bacterium Helicobacter pylori was first described in 1983 and currently represents one of the most active single research topics in biomedicine. It is specific for the human stomach and chronically colonizes a majority of the global population, which results in a symptom-free local inflammation. In 10-20% of carriers, gastroduodenal disease develops, including gastric or duodenal ulcer, and atrophic gastritis, which is a precondition to gastric cancer. A probable long coevolution of microbe and homo sapiens in a restricted niche has apparently generated a complex and sophisticated interplay. Access to complete bacterial genome sequences assists in a comparative functional characterization. A dynamic glycosylation of both microbe and host cells is of growing interest to analyze. Several glycoforms of bacterial surface lipopolysaccharides show advanced molecular mimicry of host epitopes and a distinct phase variation. An unusually large family of 32 outer membrane proteins probably reflects the complex interrelationship with the host. The unique diversity found for carbohydrate-binding specificities may be mediated by these surface proteins, of which the Lewis b-binding adhesin is the only known example so far, and these binding activities are subject to phase variation. The host mucosa glycosylation may also vary with different conditions, allowing a modulated crosstalk between microbe and host. The bacterium actively stimulates the host inflammatory response, apparently for nutritional purposes, and there is no evidence for a spontaneous elimination of the microbe. Colonization appears to be preventive for upper stomach and esophageal diseases. Current antibiotic treatment eradicates the microbe and cures ulcer disease. Alternative approaches must, however, be developed for a potential global prevention of disease.     

A nonradioactive screening method for cloning genes encoding sequence-specific DNA binding proteins.

We have developed a novel nonradioactive screening method for cloning genes encoding sequence-specific DNA binding proteins. This method is derived from previously described protocols developed for the same purpose by using radioactively labeled DNA probes containing protein recognition sequences. This nonradioactive strategy relies upon the use of a small hapten, digoxigenin. Fusion proteins expressed from the recombinant bacteriophage lambda gt11/lambda ZAP are immobilized on nitrocellulose filters and probed with digoxigenin-labeled double-stranded DNA as a ligand. The specifically bound DNA probes can be detected through sequential incubations with antibody-enzyme conjugate and enzyme substrates. This technique has been successfully utilized to isolate several cDNA clones encoding DNA binding proteins.     

Structural glycobiology: a game of snakes and ladders

Oligo- and polysaccharides are infamous for being extremely flexible molecules, populating a series of well-defined rotational isomeric states under physiological conditions. Characterization of this heterogeneous conformational ensemble has been a major obstacle impeding high-resolution structure determination of carbohydrates and acting as a bottleneck in the effort to understand the relationship between the carbohydrate structure and function. This challenge has compelled the field to develop and apply theoretical and experimental methods that can explore conformational ensembles by both capturing and deconvoluting the structural and dynamic properties of carbohydrates. This review focuses on computational approaches that have been successfully used in combination with experiment to detail the three-dimensional structure of carbohydrates in a solution and in a complex with proteins. In addition, emerging experimental techniques for three-dimensional structural characterization of carbohydrate-protein complexes and future challenges in the field of structural glycobiology are discussed. The review is divided into five sections: (1) The complexity and plasticity of carbohydrates, (2) Predicting carbohydrate-protein interactions, (3) Calculating relative and absolute binding free energies for carbohydrate-protein complexes, (4) Emerging and evolving techniques for experimental characterization of carbohydrate-protein structures, and (5) Current challenges in structural glycoscience.     

Highlight: Dolce vita - a sample from European glycobiology

No abstract available.     

Distillery and curd whey wastes as viable alternative sources for biosurfactant production

Biosurfactant production from synthetic medium and industrial waste, viz. distillery and whey wastes was investigated by using an oily sludge isolate Pseudomonas aeruginosa strain BS2. In synthetic medium separately supplemented with glucose and hexadecane as water-soluble and -insoluble carbon sources, respectively, strain BS2 reduced the surface tension of the fermentation broth from 57 to 27 mN/m. The culture produced biosurfactant during the stationary growth phase and its yield was 0.97 g/l. The culture utilized distillery and whey wastes for its growth, as maximum cell counts reached to 54 × 10⁸ and 64 × 10⁹ c.f.u./ml from an initial inoculum size of 1 × 0⁵ c.f.u./ml, respectively, within 48 h of incubation and in these wastes the yields of biosurfactant obtained were 0.91 and 0.92 g/l, respectively. In synthetic medium, distillery and whey wastes, strain BS2 produced a crystalline biosurfactant which belonged to the category of secondary metabolites and its maximum production occurred after the onset of nitrogen-limiting conditions. After recovering biosurfactant from the fermented waste, the chemical oxygen demand (COD) of distillery and whey wastes was significantly reduced by 81 and 87%, respectively. Total acids, nitrogen and phosphate levels in distillery waste were reduced by 90, 92 and 92%, respectively, while in case of whey waste the concentration of these nutrients was reduced by 88, 95 and 93%, respectively. The isolated biosurfactant possessed potent surface active properties, as it effectively reduced the surface tension of water from 72 to 27 mN/m and formed 100% stable emulsions of a variety of water-insoluble compounds such as hydrocarbons, viz. hexadecane, crude oil, kerosene and oily sludge and pesticides, viz. dichlorodiphenyltrichloroethane (DDT) and benzene hexachloride (BHC). The effectiveness of biosurfactant was also evident from its low critical micellar concentration (CMC) which was 0.028 mg/ml.     

Flower power: floral reversion as a viable alternative to nodal micropropagation in Cannabis sativa.

In Vitro Cellular & Developmental Biology - Plant - The legalization of recreational and medicinal Cannabis sativa L. has been gaining global momentum, therefore increasing interest in Cannabis...     

Salt-tolerant cation exchanger-containing sulfate groups as a viable alternative for mixed-mode type and heparin-based affinity resins

Ion-exchange chromatography is still one of the most popular protein separation techniques. Before chromatographic separation, the high salt concentration in various samples necessitates additional steps. Therefore, low salt tolerance of ion-exchange resins is a drawback that needs to be addressed. Herein, the differences in salt tolerance and hydrophobicity of strong cation-exchange TOYOPEARL resins of sulfonium and sulfate-types were investigated. Despite only a minor structural difference, differences in selectivity and salt tolerance between the sulfate and sulfonic groups were detected. In silico calculations were also carried out for model substances representing the sulfonium and sulfate groups, wherein significant differences in hydrophobicity was observed. These experiments confirmed the hypothesis that the salt tolerance, higher affinity, and selectivity for certain vitamin K dependent clotting factors are interrelated and dependent on the presence of the sulfate group. Separation of clotting factor IX from the prothrombin complex concentrate further to confirmed the affinity for these proteins. The results show that the use of only a resin with the sulfate ligand and not with the sulfonic acid ligand allows for a facile and rapid separation of clotting factor IX and other vitamin K dependent clotting factors.     

Saliva samples are a viable alternative to blood samples as a source of DNA for high throughput genotyping

ABSTRACT: BACKGROUND: The increasing trend for incorporation of biological sample collection within clinical trials requires sample collection procedures which are convenient and acceptable for both patients and clinicians. This study investigated the feasibility of using saliva-extracted DNA in comparison to blood-derived DNA, across two genotyping platforms: Applied Biosystems Taqman TM and Illumina Beadchip TM genome-wide arrays. METHOD: Patients were recruited from the Pharmacogenetics of Breast Cancer Chemotherapy (PGSNPS) study. Paired blood and saliva samples were collected from 79 study participants. The Oragene DNA Self-Collection kit (DNAgenotek(R)) was used to collect and extract DNA from saliva. DNA from EDTA blood samples (median volume 8 ml) was extracted by GenProbe, Livingstone, UK. DNA yields, standard measures of DNA quality, genotype call rates and genotype concordance between paired, duplicated samples were assessed. RESULTS: Total DNA yields were lower from saliva (mean 24 ug, range 0.2-52 ug) than from blood (mean 210 ug, range 58-577 ug) and a 2-fold difference remained after adjusting for the volume of biological material collected. Protein contamination and DNA fragmentation measures were greater in saliva DNA. 78/79 saliva samples yielded sufficient DNA for use on Illumina Beadchip arrays and using Taqman assays. Four samples were randomly selected for genotyping in duplicate on the Illumina Beadchip arrays. All samples were genotyped using Taqman assays. DNA quality, as assessed by genotype call rates and genotype concordance between matched pairs of DNA was high (>97%) for each measure in both blood and saliva-derived DNA. CONCLUSION: We conclude that DNA from saliva and blood samples is comparable when genotyping using either Taqman assays or genome-wide chip arrays. Saliva sampling has the potential to increase participant recruitment within clinical trials, as well as reducing the resources and organisation required for multicentre sample collection.