Methylation-specific PCR: four steps in primer design

Methylation-specific PCR (MSP) is still the method of choice for a single gene methylation study. The proper design of the primer pairs is a prerequisite for obtaining reliable PCR results. Despite numerous protocols describing the rules for MSP primer design, none of them provide a comprehensive approach to the problem. Our aim was to depict a workflow for the primer design that is concise and easy to follow. In order to achieve this goal, adequate tools for promoter sequence retrieval, MSP primer design and subsequent in silico analysis are presented and discussed. Furthermore, a few instructive examples regarding a good versus a poor primer design are provided. Finally, primer design is demonstrated according to the proposed workflow. This article aims to provide researchers, interested in a single gene methylation studies, with useful information regarding successful primer design.     

Cloning,Heterologous Expression,Purification and Characterization of M12 Mutant of Aspergillus niger Glucose Oxidase in Yeast Pichia pastoris KM71H

Aspergillus niger glucose oxidase (GOx) genes for wild-type (GenBank accession no. X16061, swiss-Prot; P13006) and M12 mutant (N2Y, K13E, T30 V, I94 V, K152R) were cloned into pPICZαA vector for expression in Pichia pastoris KM71H strain. The highest expression level of 17.5 U/mL of fermentation media was obtained in 0.5 % (v/v) methanol after 9 days of fermentation. The recombinant GOx was purified by cross-flow ultrafiltration using membranes of 30 kDa molecular cutoff and DEAE ion-exchange chromatography at pH 6.0. Purified wt GOx had k _cat of 189.4 s^?1 and K _m of 28.26 mM while M12 GOx had k _cat of 352.0 s^?1 and K _m of 13.33 mM for glucose at pH 5.5. Specificity constants k _cat/K _m of wt (6.70 mM^?1 s^?1) and M12 GOx (26.7 mM^?1 s^?1) expressed in P. pastoris KM71H were around three times higher than for the same enzymes previously expressed in Saccharomyces cerevisiae InvSc1 strain. The pH optimum and sugar specificity of M12 mutant of GOx remained similar to the wild-type form of the enzyme, while thermostability was slightly decreased. M12 GOx expressed in P. pastoris showed three times higher activity compared to the wt GOx toward redox mediators like N,N-dimethyl-nitroso-aniline used for glucose strips manufacturing. M12 mutant of GOx produced in P. pastoris KM71H could be useful for manufacturing of glucose biosensors and biofuel cells.     

A Scoping Review of Published Research on the Relinquishment of Companion Animals

Globally, large populations of companion animals are relinquished each year. The purpose of this scoping review was to identify all published research investigating companion-animal relinquishment to map out and evaluate research gaps, needs, and opportunities. A comprehensive search strategy was implemented in 4 online databases, identified citations were screened, and relevant articles were procured and characterized. From 6,848 unique citations identified, 192 were confirmed relevant, including 115 primary-research articles and 77 reviews and commentaries. The majority of these articles originated from the United States (131; 68.2%); 74 (38.5%) of them have been published since 2006. Among the primary-research articles, 84 (73.0%) investigated reasons for companion-animal relinquishment. The most commonly studied reasons were aggressive companion-animal behaviors (49; 58.3%); moving, rental, or housing issues (45; 53.6%); and caretaker personal issues (42; 50.0%). Only 17 primary-research articles investigated interventions to prevent companion-animal relinquishment. The quantity of research into reasons for relinquishment highlights an opportunity for future knowledge-synthesis activities in this area, including systematic review and meta-analysis. In comparison, the limited research into interventions identifies a priority for new research.     

Systematic Detection of Internal Symmetry in Proteins Using CE-Symm

Symmetry is an important feature of protein tertiary and quaternary structures that has been associated with protein folding, function, evolution, and stability. Its emergence and ensuing prevalence has been attributed to gene duplications, fusion events, and subsequent evolutionary drift in sequence. This process maintains structural similarity and is further supported by this study. To further investigate the question of how internal symmetry evolved, how symmetry and function are related, and the overall frequency of internal symmetry, we developed an algorithm, CE-Symm, to detect pseudo-symmetry within the tertiary structure of protein chains. Using a large manually curated benchmark of 1007 protein domains, we show that CE-Symm performs significantly better than previous approaches. We use CE-Symm to build a census of symmetry among domain superfamilies in SCOP and note that 18% of all superfamilies are pseudo-symmetric. Our results indicate that more domains are pseudo-symmetric than previously estimated. We establish a number of recurring types of symmetry–function relationships and describe several characteristic cases in detail. With the use of the Enzyme Commission classification, symmetry was found to be enriched in some enzyme classes but depleted in others. CE-Symm thus provides a methodology for a more complete and detailed study of the role of symmetry in tertiary protein structure [availability: CE-Symm can be run from the Web at http://source.rcsb.org/jfatcatserver/symmetry.jsp. Source code and software binaries are also available under the GNU Lesser General Public License (version 2.1) at https://github.com/rcsb/symmetry. An interactive census of domains identified as symmetric by CE-Symm is available from http://source.rcsb.org/jfatcatserver/scopResults.jsp].     

Disease intensity of some tomato viroses in Serbia

In this paper we present the data on the disease intensity of the tomato plants grown in glass and plastic-houses, and in the open field. The infection was caused by the following viruses: Tomato mosaic virus (ToMV), Tobacco mosaic virus (TMV), Tomato spotted wilt virus (TSWV), Alfalfa mosaic virus (AMV), Potato virus X (PVX), Potato virus Y (PVY), Tomato black ring virus (TBRV), Tomato ringspot virus (ToRSV), Tomato aspermy virus (TAV), and Cucumber mosaic virus (CMV). These viruses represented most frequent tomato pathogens in Serbia. According to the obtained results, it could be concluded that 92.94% of the tested tomato plants grown in glass and plastic-houses, and 89.82% grown in the open field were infected by one of the above viruses. Most of the plant samples were infected by two or more viruses. The most frequent viruses — tomato pathogens in Serbia were ToMV, PVY and TMV.     

Carbonic anhydrase activity and biomineralization process in embryos, larvae and adult blue mussels Mytilus edulis L.

To decide whether a physiological role can be attributed to enzymatic activity with respect to crystal formation and biomineralization of the first larval shell, carbonic anhydrase (CA) activity was measured in embryos and larvae of the blue mussels Mytilus edulis L. Also, CA activity was determined in the mantle edge and gonads of adult mussels with different shell length and condition index. The intention was to find a possible correlation between CA activity and adult shell calcification, i.e. gonadal maturation. The comparison of CA activity in different developmental stages of mussels and the results of an X-ray diffraction study of biomineralization processes in embryonic and larval shells indicate that CA activity is maximal at the end of several developmental stages. Consequently, the increase in CA activity precedes some physiological changes, i.e. the somatoblast 2d formation and the occurrence of the first calcite and quartz crystals in embryos, shell field formation in the gastrula stage, shell gland and periostracum production in trochophores, and rapid aragonite deposition in larval prodissoconch I and prodissoconch II shells. Furthermore, it was found that in adult mussels CA activity was quite variable and that in the mantle edge it was frequently inversely related to the activity in the gonad. Received: 28 November 1998 / Received in revised form: 30 August 1999 / Accepted: 31 August 1999     

Time-course of changes in amounts of specific proteins upon exposure to hyper-g, 2-D clinorotation, and 3-D random positioning of Arabidopsis cell cultures

In previous studies it has been shown that callus cell cultures of Arabidopsis thaliana respond to changes in gravitational field strengths by altered gene expression. In this study an investigation was carried out into how different g conditions affect the proteome of such cells. For this purpose, callus cells were exposed to 8 g (centrifugation) and simulated microgravity (2-D clinorotation: fast rotating clinostat, yielding 0.0016 g at maximum; and 3-D random positioning) for up to 16 h. Extracts containing total soluble protein were subjected to 2-D SDS-PAGE. Image analysis of Sypro Ruby-stained gels showed that approximately 28 spots reproducibly and significantly (P <0.05) changed in amount after 2 h of hypergravity (18 up- and 10 down-regulated). These spots were analysed by electrospray ionization tandem mass spectrometry (ESI-MS/MS). In the case of 2-D clinorotation, 19 proteins changed in a manner similar to hypergravity, while random positioning affected only eight spots. Identified proteins were mainly stress related, and are involved in detoxification of reactive oxygen species, signalling, and calcium binding. Surprisingly, centrifugation and clinorotation showed homologies which were not detected for random positioning. The data indicate that simulation of weightlessness is different between clinorotation and random positioning.     

Sucrose effects on in vitro fruiting and seed production of Centaurium pulchellum

The effect of sucrose on fruiting, seed production, and seed germination of lesser centaury [Centaurium pulchellum (Sw.) Druce] was examined using explants of flowers and flower buds. Sucrose concentrations in the culture medium ranged from 0.003 to 0.3 M. It has been shown that the number of auxiliary buds, capsules dimension, number of viable seeds per capsule and seed dimensions increased with the increase of sucrose concentrations. The highest values were recorded at sucrose concentrations higher than 0.03 M, except for seeds size, which were larger at sucrose concentration ranging from 0.003 to 0.1 M. The germination of in vitro produced seeds was affected by previous culture history: a higher germination percentage was obtained in seeds that were raised from explants originally grown on medium with sucrose concentrations higher than 0.003 M.     

Specific sensing of poly G by the aluminum-salophen complex

The Al(III)-salophen complex 1 exhibited strong spectroscopic changes specifically upon addition of polyG and GpG, while double stranded DNA and RNA, and single stranded polyA, polyU and polyC induced negligible spectral changes of 1. Titrations with mono-nucleotides yielded no spectroscopic changes, revealing that there must be at least two consecutive guanines in single stranded oligonucleotide structure for a measurable spectroscopic change of 1. Preliminary results show that 1 has moderate antiproliferative effect on a number of human tumour cell lines.