Characteristics of arylsulfatase in Russian sturgeon (Acipenser gueldenstaedti) semen

Spermatozoa of sturgeons (Acipenseriformes), unlike teleosts, possess an acrosome. This paper provides data concerning biochemical characteristics of arylsulfatase (AS), an acrosomal enzyme, found in Russian sturgeon spermatozoa and seminal plasma. The enzymes were purified by a four-step procedure, using n-butanol extraction, ion-exchange chromatography repeated twice and gel filtration. High purity of our enzymes was confirmed by silver staining electrophoresis and an immunological experiment. Kinetic parameters indicated that the purified enzymes belong to arylsulfatase type A. Similarity of the seminal plasma arylsulfatase to the spermatozoan enzyme showed us that arylsulfatase from seminal plasma might originate from damaged spermatozoa. The possible physiological consequences of the presence of arylsulfatase in Russian sturgeon semen are discussed.     

Chemically-induced affinity star restriction specificity: a novel TspGWI/sinefungin endonuclease with theoretical 3-bp cleavage frequency

The type IIS/IIC restriction endonuclease TspGWI recognizes the sequence 5'-ACGGA-3', cleaving DNA 11/9 nucleotides downstream. Here we show that sinefungin, a cofactor analog of S-adenosyl methionine, induces a unique type of relaxation in DNA recognition specificity. In the presence of sinefungin, TspGWI recognizes and cleaves at least 12 degenerate variants of the original recognition sequence that vary by single base pair changes from the original 5-bp restriction site with only a single degeneracy per variant appearing to be allowed. In addition, sinefungin was found to have a stimulatory effect on cleavage at these nondegenerate TspGWI recognition sites, irrespective of their number or the DNA topology. Interestingly, no fixed "core" could be identified among the new recognition sequences. Theoretically, TspGWI cleaves DNA every 1024 bp, while sinefungin-induced activity cleaves every 78.8 bp, corresponding to a putative 3-bp long recognition site. Thus, the combination of sinefungin and TspGWI represents a novel frequent cutter, next only to CviJI/CviJI*, that should prove useful in DNA cloning methodologies.     

Cloning of the thermostable alpha-amylase gene from Pyrococcus woesei in Escherichia coli: isolation and some properties of the enzyme

Pyrococcus woesei (DSM 3773) alpha-amylase gene was cloned into pET21d(+) and pYTB2 plasmids, and the pET21d(+)alpha-amyl and pYTB2alpha-amyl vectors obtained were used for expression of thermostable alpha-amylase or fusion of alpha-amylase and intein in Escherichia coli BL21(DE3) or BL21(DE3)pLysS cells, respectively. As compared with other expression systems, the synthesis of alpha-amylase in fusion with intein in E. coli BL21(DE3)pLysS strain led to a lower level of inclusion bodies formation-they exhibit only 35% of total cell activity-and high productivity of the soluble enzyme form (195,000 U/L of the growth medium). The thermostable alpha-amylase can be purified free of most of the bacterial protein and released from fusion with intein by heat treatment at about 75 degrees C in the presence of thiol compounds. The recombinant enzyme has maximal activity at pH 5.6 and 95 degrees C. The half-life of this preparation in 0.05 M acetate buffer (pH 5.6) at 90 degrees C and 110 degrees C was 11 h and 3.5 h, respectively, and retained 24% of residual activity following incubation for 2 h at 120 degrees C. Maltose was the main end product of starch hydrolysis catalyzed by this alpha-amylase. However, small amounts of glucose and some residual unconverted oligosaccharides were also detected. Furthermore, this enzyme shows remarkable activity toward glycogen (49.9% of the value determined for starch hydrolysis) but not toward pullulan.     

The optimality of the standard genetic code assessed by an eight-objective evolutionary algorithm

Background

The standard genetic code (SGC) is a unique set of rules which assign amino acids to codons. Similar amino acids tend to have similar codons indicating that the code evolved to minimize the costs of amino acid replacements in proteins, caused by mutations or translational errors. However, if such optimization in fact occurred, many different properties of amino acids must have been taken into account during the code evolution. Therefore, this problem can be reformulated as a multi-objective optimization task, in which the selection constraints are represented by measures based on various amino acid properties.

Results

To study the optimality of the SGC we applied a multi-objective evolutionary algorithm and we used the representatives of eight clusters, which grouped over 500 indices describing various physicochemical properties of amino acids. Thanks to that we avoided an arbitrary choice of amino acid features as optimization criteria. As a consequence, we were able to conduct a more general study on the properties of the SGC than the ones presented so far in other papers on this topic. We considered two models of the genetic code, one preserving the characteristic codon blocks structure of the SGC and the other without this restriction. The results revealed that the SGC could be significantly improved in terms of error minimization, hereby it is not fully optimized. Its structure differs significantly from the structure of the codes optimized to minimize the costs of amino acid replacements. On the other hand, using newly defined quality measures that placed the SGC in the global space of theoretical genetic codes, we showed that the SGC is definitely closer to the codes that minimize the costs of amino acids replacements than those maximizing them.

Conclusions

The standard genetic code represents most likely only partially optimized systems, which emerged under the influence of many different factors. Our findings can be useful to researchers involved in modifying the genetic code of the living organisms and designing artificial ones.

     

Correction to: Detection of Borrelia burgdorferi s.l., Anaplasma phagocytophilum and Babesia spp. in Dermacentor reticulatus ticks found within the city of Białystok,Poland—first data

Experimental and Applied Acarology -     

Factors that Affect the Content of Cadmium,Nickel, Copper and Zinc in Tissues of the Knee Joint

Osteoarthritis causes the degradation of the articular cartilage and periarticular bones. Trace elements influence the growth, development and condition of the bone tissue. Changes to the mineral composition of the bone tissue can cause degenerative changes and fractures. The aim of the research was to determine the content of cadmium (Cd), nickel (Ni), copper (Cu) and zinc (Zn) in the tibia, the femur and the meniscus in men and women who underwent a knee replacement surgery. Samples were collected from 50 patients, including 36 women and 14 men. The determination of trace elements content were performed by ICP-AES method, using Varian 710-ES. Average concentration in the tissues of the knee joint teeth amounted for cadmium 0.015, nickel 0.60, copper 0.89 and zinc 80.81 mg/kg wet weight. There were statistically significant differences in the content of cadmium, copper and zinc in different parts of the knee joint. There were no statistically significant differences in the content of cadmium, nickel, copper and zinc in women and men in the examined parts of the knee joint. Among the elements tested, copper and nickel showed a high content in the connective tissue (the meniscus) compared to the bone tissue (the tibia and the femur).