p21-activated protein kinase gamma-PAK is activated by ionizing radiation and other DNA-damaging agents. Similarities and differences to alpha-PAK.

The p21-activated protein kinase gamma-PAK is activated 2-5-fold in response to ionizing radiation (IR) in 3T3-L1 fibroblasts and U937 leukemia cells. gamma-PAK is activated in a dose- and time-dependent manner. Doses from 1 to 100 Gy result in significant stimulation of activity at 30 min, whereas maximal stimulation is observed at 120 min after irradiation. UV (80 J/m(2)) and the DNA-damaging drugs cytosine beta-D-arabinofuranoside (AraC) and cis-platinum(II)diammine dichloride (cisplatin) also induce gamma-PAK activation. The activation of gamma-PAK in response to IR or AraC is dependent on tyrosine kinase and phosphoinositide 3-kinase activity, as demonstrated by use of the inhibitors genistein and wortmannin; in contrast activation of gamma-PAK by cisplatin and UV is not affected significantly by these inhibitors, suggesting that gamma-PAK can be activated by more than one pathway in response to different types of DNA damage. In contrast to gamma-PAK, alpha-PAK and JNK are activated only by cisplatin and UV in 3T3-L1 cells, suggesting differential regulation of the protein kinases. This is the first time that members of the Ste20/PAK family of protein kinases have been shown to be involved in the cellular response to IR and other DNA-damaging agents.     

2D-NMR studies of the unnatural duplex alpha-d(TCTAAAC)-beta-d(AGATTTG).

The unnatural oligonucleotide alpha-d(TCTAAAC) was synthesized and was found more resistant towards endonucleases than its beta-analog. 2D-NMR experiments allowed the assignment of all non-exchangeable aromatic and sugar protons except for the overlapping 5' -5" resonances, as well as the exchangeable imino protons of the parallel hybrid duplex alpha-d (TCTAAAC)-beta-d(AGATTTG). NMR studies show that the strength of the association between the alpha-strand and the beta parallel strand is equivalent to that between their anti-parallel complementary beta-analogs beta-d(CAAATCT) and beta-d(AGATTTG). NOE data provide evidence that both duplexes form stable right-helical duplexes with an anti-conformation on the glycosyl linkages and a Watson-Crick pairing. NOESY and COSY spectra allowed us to determine that alpha and beta deoxyriboses adopt a 3' -exo conformation.     

Helix–coil transition in poly(γ-benzyl-L-glutamate) and poly-ε-carbobenzoxy-L-lysine

In this paper two points are considered: the methods of evaluating the helical content θ and the calculation of the parameters of the transition from experimental data and its interpretation. The parameter ΔH obtained is in good agreement with the calorimetric one and v is found to be independent of temperature and solvent and in agreement with the ordinarily accepted value for poly(γ-benzyl-L -glutamate). The different methods of estimating θ are discussed for both polypeptides.     

Examining the relationship between secondary structure and antibody recognition in immunopeptides from foot-and-mouth disease virus

Summary The conformation of a peptide that represents antigenic site A of foot-and-mouth disease virus strain C-S8c1 (residues 136–156 of VP1; YTASARGDLAHLTTTHARHLP) has been studied by circular dichroism and compared with three analogs that reproduce amino acid substitutions at position 146 (HisArg, Gln or Asp) which affect antibody recognition. Four other peptides, incorporating replacements at position 147 predicted to maintain (LeuIle, Nle and Ala) or disrupt (LeuGly) helical structure at this site, have also been studied. In aqueous solution or in 4 M urea, the spectra of all eight peptides were typical of aperiodic conformation and independent of concentration or pH. However, upon addition of solvents such as methanol or hexafluoroisopropanol, spectral patterns evidenced significant levels (ca. 50%) of helical structure. The single residue substitutions at positions 146 and 147 caused minor to significant variations in the calculated amount of -helix of the peptides. An attempt to relate these changes in helical content to the antigenic behaviour of the peptides towards five monoclonal antibodies elicited with virus and mapping at site A could not find any straightforward correspondence between the two sets of results. The parent peptide and its His¹⁴⁶Arg analog were also analyzed by circular dichroism in the presence of the Fab fragment of SD6, a monoclonal antibody mapping at site A and much less reactive with viruses carrying the referred mutation. Although a peptide-antibody interaction was evident from spectral changes, careful inspection of the difference spectra (peptide-Fab minus Fab) of both peptides failed to detect any significant distinction between them that could be attributed to their different immunoreactivity. While these findings do not necessarily conflict with previous reports that the interaction of antigenic site A with antibodies is mediated to some extent by the adoption of a helix structure, they suggest that, at least for C-serotype viruses, other structural features in addition to a helical conformation are critically involved in antigenic recognition.     

Use of olive mill wastewater compost for crop production

Vast amounts of olive mill wastewaters (OMW) are produced in Mediterranean countries, where their treatment and disposal are becoming a serious environmental problem. Increasing attention has been paid to discovering a use for OMW and a wide range of technological treatments are available nowadays for reducing their pollutant effects and for their transformation into valuable products, the most suitable procedures being found to involve recycling rather than the detoxication of these wastes. Direct application of OMW to soil has been considered as an inexpensive method of disposal and recovery of their mineral and organic components but, because of their organic acid and phenol contents, OMW are also a source of pollution. By using composting technologies, it is possible to transform either fresh OMW or sludge from pond-stored OMW mixed with appropriate plant waste waterials (carriers) into organic fertilizers (composts) with no phytotoxicity to improve soil fertility and plant production, the process involving the microbial degradation of the polluting load of the wastes. Results of field and pot experiments using OMW-composts to cultivate horticultural and other crops have shown that yields obtained with organic fertilization are similar, and sometimes higher, to those obtained with a balanced mineral fertilizer. A comparison between the macro and micronutrient contents of plants cultivated with organic or mineral fertilizers did not generally reveal important differences. However, the cases of iron and manganese are worth mentioning as their bio-availability may be linked to the soil humic complexes originated by the OMW organic fertilizers.     

Marker-assisted introgression (MAI) of almond genes into the peach background: a fast method to mine and integrate novel variation from exotic sources in long intergeneration species

This paper proposes a new breeding strategy, marker-assisted introgression (MAI), to obtain lines of perennial species with a single introgressed fragment from a compatible species two generations after the interspecific hybrid. MAI allows enrichment of the genome of a species with genes from a wild or exotic relative in a short timeframe and with an intermediate step that allows a first exploration of genes/QTLs that the donor species can provide to the target crop. This method has three phases: (1) creating a large backcross one (BC1) population to select, with markers, a reduced number of individuals (15–30, called the prIL set) with a low number of introgressions; (2) phenotyping the prIL set for the traits of interest and inferring the inheritance and map position of segregating major genes/QTLs based on the known genotypes of the prILs; and (3) advancing selected lines carrying the traits of interest to a next generation of backcross or selfing to obtain individuals with a single introgression in the background of the elite commercial germplasm. The proof of concept of this strategy was implemented by using peach as the recurrent species and almond as the donor. The whole process can be done in 9–10 years as the identification of the first line with one introgression was after 5 years (2006–2011), and 4–5 additional years are needed for phenotypic evaluation of selected lines. The expansion of this method to other perennial clonally propagated crops and to other species of Prunus compatible with peach is discussed.