Synthesis of modified nucleosides for incorporation of formyletheno and carboxyetheno adducts of adenine nucleosides into oligonucleotides

Three protected derivatives of 1,N(6)-ethenoadenine nucleosides, viz. 3-[5-O-(4,4'-dimethoxytrityl) of 7-formyl-(1) and 7-(1,2-diacetyloxypropyl)-2'-deoxyadenosine (2), and 3-[5-O-(4,4'-dimethoxytrityl)-2-O-(tert-butyldimethylsilyl)-7-(ethoxycarbonyl)adenosine (3), expected to allow introduction of formyletheno and carboxyethenoadenine adducts into oligonucleotides by the conventional phosphoramidite chemistry, have been synthesized.     

N-glycomic Profiling as a Tool to Separate Rectal Adenomas from Carcinomas

All human cells are covered by glycans, the carbohydrate units of glycoproteins, glycolipids, and proteoglycans. Most glycans are localized to cell surfaces and participate in events essential for cell viability and function. Glycosylation evolves during carcinogenesis, and therefore carcinoma-related glycan structures are potential cancer biomarkers. Colorectal cancer is one of the world''s three most common cancers, and its incidence is rising. Novel biomarkers are essential to identify patients for targeted and individualized therapy. We compared the N-glycan profiles of five rectal adenomas and 18 rectal carcinomas of different stages by matrix-assisted laser desorption-ionization time-of-flight mass spectrometry. Paraffin-embedded tumor samples were deparaffinized, and glycans were enzymatically released and purified. We found differences in glycosylation between adenomas and carcinomas: monoantennary, sialylated, pauci-mannose, and small high-mannose N-glycan structures were more common in carcinomas than in adenomas. We also found differences between stage I–II and stage III carcinomas. Based on these findings, we selected two glycan structures: pauci-mannose and sialyl Lewis a, for immunohistochemical analysis of their tissue expression in 220 colorectal cancer patients. In colorectal cancer, poor prognosis correlated with elevated expression of sialyl Lewis a, and in advanced colorectal cancer, poor prognosis correlated with elevated expression of pauci-mannose. In conclusion, by mass spectrometry we found several carcinoma related glycans, and we demonstrate a method of transforming these results into immunohistochemistry, a readily applicable method to study biomarker expression in patient samples.Glycans, the carbohydrate units of glycoproteins, glycolipids, and proteoglycans, that cover all human cells. Around 1% of the human genome participates in the biosynthesis of glycans(1). This biosynthesis is the most complex post-translational modification of proteins, and the great variability in glycan structures contains a tremendous ability to fine-tune the chemical and biological properties of glycoproteins. The glycosylation process occurs most abundantly in the Golgi apparatus and the endoplasmic reticulum, but also occurs in the cytoplasm and nucleus (2). Most glycoconjugates are localized to cell surfaces, where glycans participate in events essential for cell viability and function, such as cell adhesion, motility, and intracellular signaling (2). Changes in these functions are key steps seen when normal cells transform to malignant ones, and these are also reflected in changes of a cell''s glycan profile, observed in many cancers (3, 4). Specific structural changes in glycans may serve as cancer biomarkers (5, 6), and changes in glycosylation profiles are related to aggressive behavior in tumor cells (7–9).Cancer-associated asparagine-linked glycan (N-glycan) structures may play specific roles in supporting tumor progression; growth (10, 11), invasion (12, 13), and angiogenesis (14). Changes in the N-glycan profile emerge in numerous cancers, including lung (15, 16), breast (17), and colorectal cancer (CRC)¹ (16, 18). Balog et al. (18) comparing the N-glycomic profile of CRC tissue to adjacent normal mucosa, reported differences in specific glycan structures. Moreover, serum N-glycosylation profile from patients with CRC differ from those of healthy controls (19).Colorectal cancer is the third most common cause of cancer-related death worldwide and its incidence is rising; 40% of CRCs are of rectal origin. Roughly 40% of patients have localized disease (stage I–II; Dukes A–B), another 40% loco regional disease (stage III; Dukes C), and 20% metastasized disease (stage IV; Dukes D) (20). Although stage at diagnosis is the most important factor determining prognosis, clinical outcome, and response to adjuvant treatment can markedly vary within each stage. Adjuvant therapy routinely goes to stage III patients, but the benefit of adjuvant treatment for stage II patients is unclear. Of stage II patients, 80% are cured by radical surgery alone. To identify patients who will benefit from postoperative treatment, we need novel biomarkers. The glycan profile of the tumor tissue could provide new biomarkers for diagnosis and prognosis of cancer.In this study, we characterized the N-glycomic profiles of rectal adenomas and carcinomas by MALDI-TOF mass spectrometric (MS) profiling of asparagine-linked glycans. Our aim was to identify differences between adenomas and carcinomas, and also between cancers of different stages. Based on glycan profiling, we also chose, for immunohistochemical expression studies of a series of 220 CRC patients, two glycan markers: sialyl Lewis a and pauci-mannose.     

Applying a framework for landscape planning under climate change for the conservation of biodiversity in the Finnish boreal forest

Conservation strategies are often established without consideration of the impact of climate change. However, this impact is expected to threaten species and ecosystem persistence and to have dramatic effects towards the end of the 21st century. Landscape suitability for species under climate change is determined by several interacting factors including dispersal and human land use. Designing effective conservation strategies at regional scales to improve landscape suitability requires measuring the vulnerabilities of specific regions to climate change and determining their conservation capacities. Although methods for defining vulnerability categories are available, methods for doing this in a systematic, cost‐effective way have not been identified. Here, we use an ecosystem model to define the potential resilience of the Finnish forest landscape by relating its current conservation capacity to its vulnerability to climate change. In applying this framework, we take into account the responses to climate change of a broad range of red‐listed species with different niche requirements. This framework allowed us to identify four categories in which representation in the landscape varies among three IPCC emission scenarios (B1, low; A1B, intermediate; A2, high emissions): (i) susceptible (B1 = 24.7%, A1B = 26.4%, A2 = 26.2%), the most intact forest landscapes vulnerable to climate change, requiring management for heterogeneity and resilience; (ii) resilient (B1 = 2.2%, A1B = 0.5%, A2 = 0.6%), intact areas with low vulnerability that represent potential climate refugia and require conservation capacity maintenance; (iii) resistant (B1 = 6.7%, A1B = 0.8%, A2 = 1.1%), landscapes with low current conservation capacity and low vulnerability that are suitable for restoration projects; (iv) sensitive (B1 = 66.4%, A1B = 72.3%, A2 = 72.0%), low conservation capacity landscapes that are vulnerable and for which alternative conservation measures are required depending on the intensity of climate change. Our results indicate that the Finnish landscape is likely to be dominated by a very high proportion of sensitive and susceptible forest patches, thereby increasing uncertainty for landscape managers in the choice of conservation strategies.     

Models relating stem growth to crown length dynamics: application to loblolly pine and Norway spruce

We derive and analyze a model that relates the growth rate of cross-sectional area (‘csa’) at any height on the central stem of a tree to crown-length dynamics. The derivation is based, in part, on assumptions that (a) active csa on the central stem relates allometrically to the length of crown above the cross section, and (b) inactive csa is proportional to active csa within the crown. We also assume that the deactivation rate of csa beneath the crown is determined, in part, by the rate of crown rise. Integration of the growth-rate model under an additional assumption—that total crown length is constant after stand closure—provides a simple model of annual or periodic growth of total csa that can be fit to standard growth data. Three implications of the assumptions and integration are notable: (1) total csa within the crown scales allometrically with stem length above the cross section; (2) for a special case, total csa beneath the crown scales with stem length above the cross section; more generally, csa scales with a linear combination of the stem and crown lengths; and (3) the stem beneath the crown forms to approximate a frustum of a quadratic paraboloid. Basal area data from a loblolly pine (Pinus taeda L.) spacing trial show good agreement with (1) and (2), and with an empirical model developed from the special case of (2). Data from the plots of a Norway spruce (Picea abies (L.) Karst.) thinning trial, where crown length remained approximately constant, show good agreement with (2) and the empirical model. Prediction (3) is demonstrated by simulation.     

Moose and vole browsing patterns in experimentally assembled pure and mixed forest stands

Plants growing in diverse communities are believed to exhibit associational resistance to herbivores, but this hypothesis has seldom been tested experimentally for vertebrate herbivores in forest ecosystems. We examined browsing patterns of the two principal mammalian herbivores of Finnish boreal forests, moose and voles, in young stands where tree species diversity and composition were experimentally manipulated. The stands were composed either of monocultures or different 2–5 species mixtures of Norway spruce, Scots pine, Siberian larch, silver birch, and black alder. Voles and moose showed contrasting responses to stand diversity and species composition. In accordance with the predictions of the associational resistance hypothesis, vole damage was higher in tree monocultures than in mixed stands, although stand diversity effects were statistically significant only at one of the three study areas. Voles also damaged more trees in coniferous than in deciduous stands. In contrast, moose browsing tended to increase with the number of tree species in a stand and with the presence of the preferred tree species, birch, in a mixture. The observed differences in vole and moose responses to stand diversity and species composition are likely to be due to different feeding specialisation, foraging patterns, and movement ability of these herbivores. Voles switched to trees only when the supply of a more preferred food (grasses and forbs) was depleted and restricted their feeding choice only to the most palatable tree species regardless of the number of tree species present per stand. In contrast, tree branches and foliage represented an important part of moose diet throughout the year; moose may be able to tolerate secondary plant metabolites of different tree species better than voles and may thus benefit from diet broadening when more tree species are available. Furthermore, the home range size and foraging ability of these two very differently sized herbivores may partly explain the observed differences in utilisation of different tree species. Finally, both moose and voles showed high spatial and temporal variation in their feeding; in particular, vole damage was more influenced by tree species diversity in areas and years with high vole densities. Thus, diversification of forest stands may have very different effects on mammalian browsing depending on the herbivores present, their densities, and the tree species used in reforestation.     

Solution structures of the first and fourth TSR domains of F-spondin

F-spondin is a protein mainly associated with neuronal development. It attaches to the extracellular matrix and acts in the axon guidance of the developing nervous system. F-spondin consists of eight domains, six of which are TSR domains. The TSR domain family binds a wide range of targets. Here we present the NMR solution structures of TSR1 and TSR4. TSR domains have an unusual fold that is characterized by a long, nonglobular shape, consisting of two beta-strands and one irregular extended strand. Three disulfide bridges and stack of alternating tryptophan and arginine side-chains stabilize the structure. TSR1 and TSR4 structures are similar to each other and to the previously determined TSR domain X-ray structures from another protein, TSP, although TSR4 exhibits a mobile loop not seen in other structures.     

Solution structure of the first immunoglobulin domain of human myotilin

Myotilin is a 57 kDa actin-binding and -bundling protein that consists of a unique serine-rich amino-terminus, two Ig-domains and a short carboxy-terminus with a PDZ-binding motif. Myotilin localizes in sarcomeric Z-discs, where it interacts with several sarcomeric proteins. Point mutations in myotilin cause muscle disorders morphologically highlighted by sarcomeric disarray and aggregation. The actin-binding and dimerization propensity of myotilin has been mapped to the Ig-domains. Here we present high-resolution structure of the first Ig-domain of myotilin (MyoIg1) determined with solution state NMR spectroscopy. Nearly complete chemical shift assignments of MyoIg1 were achieved despite several missing backbone ¹H-¹⁵N-HSQC signals. The structure derived from distance and dihedral angle restraints using torsion angle dynamics was further refined using molecular dynamics. The structure of MyoIg1 exhibits I-type Ig-fold. The absence of several backbone ¹H-¹⁵N-HSQC signals can be explained by conformational exchange taking place at the hydrophobic core of the protein. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Liposome-based homogeneous luminescence resonance energy transfer

There is an increasing need for developing simple assay formats for biomedical screening purposes. Assays on cell membranes have become important in studies of receptor-ligand interactions and signal pathways. Here luminescence energy transfer was studied on liposomes containing europium ion chelated to 4,4,4-trifluoro-1-(2-naphthalenyl)-1,3-butanedione and trioctylphosphine oxide. Energy transfer efficiency was characterized with biotin-streptavidin interaction, and a model assay concept for a homogeneous time-resolved luminescence resonance energy transfer (LRET) assay was developed. Acceptor-labeled streptavidin was bound to biotinylated lipids on the liposomes, leading to close proximity of the LRET pair. The liposome-based LRET assay was optimized for dye incorporation and concentration, biotinylation degree, liposome size, and kinetics. Sensitivity for a competitive biotin assay was at a picomolar range with a coefficient of variation from 7 to 20%. The developed lipid membrane-based system was feasible in separation free LRET assay concept with high sensitivity, indicating that the assay principle can potentially be used for biologically more relevant target molecules.     

Sleep Restriction Increases the Risk of Developing Cardiovascular Diseases by Augmenting Proinflammatory Responses through IL-17 and CRP

Background

Sleep restriction, leading to deprivation of sleep, is common in modern 24-h societies and is associated with the development of health problems including cardiovascular diseases. Our objective was to investigate the immunological effects of prolonged sleep restriction and subsequent recovery sleep, by simulating a working week and following recovery weekend in a laboratory environment.

Methods and Findings

After 2 baseline nights of 8 hours time in bed (TIB), 13 healthy young men had only 4 hours TIB per night for 5 nights, followed by 2 recovery nights with 8 hours TIB. 6 control subjects had 8 hours TIB per night throughout the experiment. Heart rate, blood pressure, salivary cortisol and serum C-reactive protein (CRP) were measured after the baseline (BL), sleep restriction (SR) and recovery (REC) period. Peripheral blood mononuclear cells (PBMC) were collected at these time points, counted and stimulated with PHA. Cell proliferation was analyzed by thymidine incorporation and cytokine production by ELISA and RT-PCR. CRP was increased after SR (145% of BL; p<0.05), and continued to increase after REC (231% of BL; p<0.05). Heart rate was increased after REC (108% of BL; p<0.05). The amount of circulating NK-cells decreased (65% of BL; p<0.005) and the amount of B-cells increased (121% of BL; p<0.005) after SR, but these cell numbers recovered almost completely during REC. Proliferation of stimulated PBMC increased after SR (233% of BL; p<0.05), accompanied by increased production of IL-1β (137% of BL; p<0.05), IL-6 (163% of BL; p<0.05) and IL-17 (138% of BL; p<0.05) at mRNA level. After REC, IL-17 was still increased at the protein level (119% of BL; p<0.05).

Conclusions

5 nights of sleep restriction increased lymphocyte activation and the production of proinflammatory cytokines including IL-1β IL-6 and IL-17; they remained elevated after 2 nights of recovery sleep, accompanied by increased heart rate and serum CRP, 2 important risk factors for cardiovascular diseases. Therefore, long-term sleep restriction may lead to persistent changes in the immune system and the increased production of IL-17 together with CRP may increase the risk of developing cardiovascular diseases.