Annotated regions of significance of SELDI-TOF-MS spectra for detecting protein biomarkers

Peak detection is a key step in the analysis of SELDI-TOF-MS spectra, but the current default method has low specificity and poor peak annotation. To improve data quality, scientists still have to validate the identified peaks visually, a tedious and time-consuming process, especially for large data sets. Hence, there is a genuine need for methods that minimize manual validation. We have previously reported a multi-spectral signal detection method, called RS for 'region of significance', with improved specificity. Here we extend it to include a peak quantification algorithm based on annotated regions of significance (ARS). For each spectral region flagged as significant by RS, we first identify a dominant spectrum for determining the number of peaks and the m/z region of these peaks. From each m/z region of peaks, a peak template is extracted from all spectra via the principal component analysis. Finally, with the template, we estimate the amplitude and location of the peak in each spectrum with the least-squares method and refine the estimation of the amplitude via the mixture model.We have evaluated the ARS algorithm on patient samples from a clinical study. Comparison with the standard method shows that ARS (i) inherits the superior specificity of RS, and (ii) gives more accurate peak annotations than the standard method. In conclusion, we find that ARS alleviates the main problems in the preprocessing of SELDI-TOF spectra. The R-package ProSpect that implements ARS is freely available for academic use at http://www.meb.ki.se/ yudpaw.     

Body composition and breast cancer in postmenopausal women: a Danish prospective cohort study

Objective: To assess the importance of body fat mass (BFM) and fat free mass (FFM) for the established positive association between BMI and breast cancer among post‐menopausal women. Research Methods and Procedures: A prospective cohort of 23,788 postmenopausal women included in the Danish study Diet, Cancer, and Health during 1993 to 1997 was linked to the Danish Cancer Registry to identify all cases of breast cancer occurring during 1993 to 2002. Breast cancer incidence rate ratios for anthropometric measurements with adjustment for known risk factors for breast cancer were calculated by Cox regression analyses. Results: Among the most commonly used anthropometric measurements, BMI was positively associated with breast cancer among never users of hormone replacement therapy (HRT). By splitting BMI into two indices, BFM index and FFM index, we found that the incidence rate ratio with each 1 kg/m² among never users of HRT was 0.98 (95% confidence interval, 0.93 to 1.03) for BFM index and 1.12 (95% confidence interval, 1.00 to 1.26) for FFM index after mutual adjustment. Discussion: The finding for BMI was in accordance with previous findings. Our results indicate that the FFM component of BMI may play a role for development of breast cancer among never users of HRT.     

Effects of strength training on muscle strength characteristics, functional capabilities, and balance in middle-aged and older women

Progressive strength training can lead to substantial increases in maximal strength and mass of trained muscles, even in older women and men, but little information is available about the effects of strength training on functional capabilities and balance. Thus, the effects of 21 weeks of heavy resistance training--including lower loads performed with high movement velocities--twice a week on isometric maximal force (ISOmax) and force-time curve (force produced in 500 milliseconds, F0-500) and dynamic 1 repetition maximum (1RM) strength of the leg extensors, 10-m walking time (10WALK) and dynamic balance test (DYN.D) were investigated in 26 middle-aged (MI; 52.8 +/- 2.4 years) and 22 older women (O; 63.8 +/- 3.8 years). 1RM, ISOmax, and F0-500 increased significantly in MI by 28 +/- 10%, 20 +/- 19%, 31 +/- 34%, and in O by 27 +/- 8%, 20 +/- 16%, 18 +/- 45%, respectively. 10WALK (MI and O, p < 0.001) shortened and DYN.D improved (MI and O, p < 0.001). The present strength-training protocol led to large increases in maximal and explosive strength characteristics of leg extensors and in walking speed, as well to an improvement in the present dynamic balance test performance in both age groups. Although training-induced increase in explosive strength is an important factor for aging women, there are other factors that contribute to improvements in dynamic balance capacity. This study indicates that total body heavy resistance training, including explosive dynamic training, may be applied in rehabilitation or preventive exercise protocols in aging women to improve dynamic balance capabilities.     

Mimetics of the disulfide bridge between the N- and C-terminal cysteines of the KLK3-stimulating peptide B-2

Human prostate produces kallikrein-related peptidase 3 (KLK3, also known as prostate specific antigen), which is widely used as a prostate cancer marker. Proteolytically active KLK3 has been shown to inhibit angiogenesis and its expression decreases in poorly differentiated tumors. Thus, it may be possible to control prostate cancer growth with agents that stimulate the proteolytic activity of KLK3. We have earlier developed synthetic peptides, which bind specifically to KLK3 and promote its proteolytic activity. These peptides are cyclic, all containing a disulfide bridge between the N- and C-terminal cysteines. To increase the in vivo stability of the KLK3-stimulating peptide B-2, we made differently cyclized analogues by replacing both terminal cysteines and the disulfide bridge between them. A replacement consisting of γ-amino butyric acid and aspartic acid, where the amino group from the former was linked to the main chain carboxyl group of the latter, was found to be, at high concentrations, more active than the B-2 peptide. Furthermore, as compared to the parent peptide, this analog had an improved stability in plasma and against the enzymatic degradation by KLK3. In addition, the series of analogues also provided valuable information of the structure–activity relationships of the B-2 peptide.     

Novel isosteric charge-deficient spermine analogue—1,12-diamino-3,6,9-triazadodecane: synthesis, pK a measurement and biological activity

Ionic interactions are essential for the biological functions of the polyamines spermidine and spermine in mammalian physiology. Here, we describe a simple gram scale method to prepare 1,12-diamino-3,6,9-triazadodecane (SpmTrien), an isosteric charge-deficient spermine analogue. The protonation sites of SpmTrien were determined at pH range of 2.2–11.0 using two-dimensional ¹H-¹⁵N NMR spectroscopy, which proved to be more feasible than conventional methods. The macroscopic pK _a values of SpmTrien (3.3, 6.3, 8.5, 9.5 and 10.3) are significantly lower than those of 1,12-diamino-4,9-diazadodecane (spermine). The effects of SpmTrien and its parent molecule, 1,8-diamino-3,6-diazaoctane (Trien), on cell growth and polyamine metabolism were investigated in DU145 prostate carcinoma cells. SpmTrien downregulated the biosynthetic enzymes ornithine decarboxylase (ODC) and S-adenosyl-l-methionine decarboxylase and decreased intracellular polyamine levels, whereas the effects of Trien alone were minor. Interestingly, both SpmTrien and Trien were able to partially overcome growth arrest induced by an ODC inhibitor, α-difluoromethylornithine, indicating that they are able to mimic some functions of the natural polyamines. Thus, SpmTrien is a novel tool to influence polyamine interaction sites at the molecular level and offers a new means to study the contribution of the protonation of spermine amino group(s) in the regulation of polyamine-dependent biological processes.     

Novel convenient synthesis of biologically active esters of hydroxylamine

Alkylation of ethyl N-hydroxyacetimidate with readily available methanesulfonates of functionally substituted alcohols and subsequent deprotection of aminooxy group is a novel and convenient method to prepare functionally substituted esters of hydroxylamine with high overall yield. This approach is a good alternative to well-known reaction of N-hydroxyphthalimide with alcohols under the Mitsunobu conditions. The properties of ethoxyethylidene protection of aminooxy group on the contrary to that of N-alkoxyphthalimide group allow to perform a wide spectra of the transformations in the radical of N-protected hydroxylamine derivatives. This is essential for synthetic strategies consisting in the introduction of N-protected aminooxy group at one of the first steps of synthesis and subsequent transformations of the radical. The inhibitory effect of one of the newly synthesized compound, 1-guanidinooxy-3-aminopropane (GAPA), was compared with that of well-known inhibitors of ornithine decarboxylase namely, α-difluoromethylornithine (DFMO) and 1-aminooxy-3-aminopropane (APA) on Leishmania donovani, a protozoan parasite that causes visceral leishmaniasis. GAPA, on the contrary with APA and DFMO, in micromolar concentrations, inhibited the growth of both amastigotes and promastigotes of sodium antimony gluconate-resistant forms of L. donovani.     

Biodiversity and ecological forest-cover domains in boreal landscapes

Studies of spatial forest patterns have traditionally focused on habitat remnants within a landscape, but few have explicitly accounted for natural habitat patterns inherent to those landscapes. At broader scales, all cover types are to some degree subdivided. In boreal forest landscapes, forests, peat lands and water bodies form a variety of different spatial structures depending on their proportions and arrangement. To assess the spatial arrangement of forest patches relevant to organisms and ecological processes, we systematically sampled and analysed 57 boreal forest landscapes (10,000 ha in size) in central Finland. Our results show that even though forest is spatially very subdivided into discrete patches in boreal landscapes it becomes generally well-connected if narrow non-forested gaps are ignored. The proportion of forest cover varied from 17.8 to 75.3% and the number of discrete forest patches from 37 to 213. The average percolation threshold for forest cover was 46.8%. If ≤100 m wide non-forested gaps were ignored and forest patches were joined, the percolation threshold dropped to 33.3%. There were on average 13 discrete clusters of forest patches if forest patches within 200 m distance were combined. These results suggest that if a boreal forest species is able to cross even relatively narrow non-forested gaps, it is likely to perceive these boreal forest landscapes as continuous. Even though our present analysis was based on static forest cover patterns, it is important to consider landscape pattern domains when assessing habitat fragmentation and its consequences to populations of organisms.     

Hierarchical ionic self-assembly of rod-comb block copolypeptide-surfactant complexes

Novel hierarchical nanostructures based on ionically self-assembled complexes of diblock copolypeptides and surfactants are presented. Rod-coil diblock copolypeptide poly(gamma-benzyl-L-glutamate)-block-poly(L-lysine), PBLG-b-PLL (Mn = 25,000 and 8000 for PBLG and PLL, respectively, polydispersity index 1.08), was complexed with anionic surfactants dodecanesulfonic acid (DSA) or dodecyl benzenesulfonic acid (DBSA), denoted as PBLG-b-PLL(DSA)1.0 and PBLG-b-PLL(DBSA)1.0, respectively. The complexation leading to supramolecular rod-comb architectures was studied by transmission electron microscopy (TEM), small-angle X-ray scattering (SAXS), Fourier transform infrared spectroscopy (FTIR), and polarized optical microscopy (POM). PBLG-b-PLL, PBLG-b-PLL(DBSA)1.0, and PBLG-b-PLL(DSA)1.0 self-assemble with alternating PBLG lamellae and PLL-containing lamellae with a periodicity of 27-33 nm. Within the PBLG lamellae, the rod-like PBLG helices pack with a periodicity of ca. 1.3 nm. The internal structure of the PLL-containing lamellae depends on the complexation. For pure PBLG-b-PLL, the PLL chains adopt a random coil conformation and the PLL domains are disordered. For PBLG-b-PLL(DSA)1.0, lamellar self-assembly of periodicity of 3.7 nm within the PLL(DSA)1.0 domains is observed due to crystalline packing of the linear n-dodecyl tails. For PBLG-b-PLL(DBSA)1.0 with branched dodecyl tails, a distinct SAXS reflection is observed, suggesting self-assembly within the PLL(DBSA)1.0 domains with a periodicity of 2.9 nm. However, due to the absence of higher order reflections, the internal structure cannot be conclusively assigned. The efficient plasticization which leads to fluid-like liquid crystallinity in PBLG-b-PLL(DBSA)1.0 and an alpha-helical conformation according to FTIR allows us to suggest that the PLL(DBSA)1.0 domains have a hexagonal internal structure. The interplay of self-assembly at different length scales combined with rod-like liquid crystallinity can open new routes to design functional materials.     

Synthesis of novel quaternary chitosan derivatives via N-Chloroacyl-6-O-triphenylmethylchitosans

Various quaternary chitosan derivative structures were synthesized by reacting N-chloroacyl-6-O-triphenylmethylchitosans with tertiary amines. Full substitutions were obtained from the quaternization reactions and the obtained water-soluble quaternary chitosan derivatives were thoroughly characterized with (1)H NMR, (13)C NMR, (1)H-(13)C HSQC NMR, and FT-IR.