Design, synthesis and photochemical studies of stilbenoid dendrimers

Stilbenoid dendrimers with stilbene in the periphery and stilbene in periphery as well as core were synthesized by convergent approach except 2nd generation dendrimer with stilbene in the periphery as well as in core (D-5). All dendrimers were characterized by standard techniques such as 1H NMR, 13C NMR, MS and IR spectroscopy. The MALDI-TOF technique proved to be very helpful in the identification of the 2nd generation dendrimer (D-5) with a mass of 3231 a.m.u. The dendrimers were designed in such a way that an intramolecular photochemical CC bond formation was favored. As two stilbene units of the same molecule were close enough so they preferred an intramolecular cyclic process except for zero generation dendrimers. Apart from the cycloaddition, some E/Z isomerization and oligomer formation was also observed on irradiation. These processes were observed by 1H NMR and MALDI-TOF MS. The photochemical behavior was also studied by UV absorption spectroscopy. Irradiating by monochromatic light led to an initial E/Z isomerization and by prolonged irradiation, an irreversible cyclic structure was formed. The choice of the wavelength of incident light is very important as irradiation at 320 nm leads to a reversible E/Z isomerization and a non-reversible cyclobutane formation, but irradiation at 340 nm favors the one-way process E Z. The [2+2] cycloaddition of molecule Tm2De was also studied by irradiating thin films on a quartz surface. An AFM image was taken before irradiation, after 3 sec irradiation and after long irradiation (1 hour). AFM studies show that a short irradiation leads to a cyclic structure as formation of hills of about 20-30 nm on the surface. A prolonged irradiation leads to a CC cross linking which can be monitored on AFM images as disappearance of hills. The roughness goes back to an almost smooth surface. These results prove a very complex material transport, which accompanies the reaction in the surface region.

Preparation of new crystal forms via photochemical, mechanochemical and sol-gel methods

This work of thesis involves various aspects of crystal engineering. Chapter 1 focuses on crystals containing crown ether complexes. Aspects such as the possibility of preparing these materials by non-solution methods, i.e. by direct reaction of the solid components, thermal behavior and also isomorphism and interconversion between hydrates are taken into account. In chapter 2 a study is presented aimed to understanding the relationship between hydrogen bonding capability and shape of the building blocks chosen to construct crystals. The focus is on the control exerted by shape on the organization of sandwich cations such as cobalticinium, decamethylcobalticinium and bisbenzenchromium(I) and on the aggregation of monoanions all containing carboxylic and carboxylate groups, into 0-D, 1-D, 2-D and 3-D networks. Reactions conducted in multi-component molecular assemblies or co-crystals have been recognized as a way to control reactivity in the solid state. The [2+2] photodimerization of olefins is a successful demonstration of how templated solid state synthesis can efficiently synthesize unique materials with remarkable stereoselectivity and under environment-friendly conditions. A demonstration of this synthetic strategy is given in chapter 3. The combination of various types of intermolecular linkages, leading to formation of high order aggregation and crystalline materials or to a random aggregation resulting in an amorphous precipitate, may not go to completeness. In such rare cases an aggregation process intermediate between crystalline and amorphous materials is observed, resulting in the formation of a gel, i.e. a viscoelastic solid-like or liquid-like material. In chapter 4 design of new Low Molecular Weight Gelators is presented. Aspects such as the relationships between molecular structure, crystal packing and gelation properties and the application of this kind of gels as a medium for crystal growth of organic molecules, such as APIs, are also discussed.

Mitochondrial DNA rearrangements during human aging: a study on liver, muscle and adipose tissue

Aging is characterized by a chronic, low-grade inflammatory state called “inflammaging”. Mitochondria are the main source of reactive oxygen species (ROS), which trigger the production of pro-inflammatory molecules. We are interested in studying the age-related modifications of the mitochondrial DNA (mtDNA), which can be affected by the lifelong exposure to ROS and are responsible of mitochondrial dysfunction. Moreover, increasing evidences show that telomere shortening, naturally occurring with aging, is involved in mtDNA damage processes and thus in the pathogenesis of age-related disorders. Thus the primary aim of this thesis was the analysis of mtDNA copy number, deletion level and integrity in different-age human biopsies from liver, vastus lateralis skeletal muscle of healthy subjects and patients with limited mobility of lower limbs (LMLL), as well as adipose tissue. The telomere length and the expression of nuclear genes related to mitobiogenesis, fusion and fission, mitophagy, mitochondrial protein quality control system, hypoxia, production and protection from ROS were also evaluated. In liver the decrease in mtDNA integrity with age is accompanied with an increase in mtDNA copy number, suggesting the existence of a “compensatory mechanism” able to maintain the functionality of this organ. Different is the case of vastus lateralis muscle, where any “compensatory pathway” is activated and mtDNA integrity and copy number decrease with age, both in healthy subjects and in patients. Interestingly, mtDNA rearrangements do not incur in adipose tissue with advancing age. Finally, in all tissues a marked gender difference appears, suggesting that aging and also gender diversely affect mtDNA rearrangements and telomere length in the three human tissues considered, likely depending on their different metabolic needs and inflammatory status.

Porcine circovirus type 2 DNA influences cytoskeleton rearrangements in plasmacytoid and monocyte-derived dendritic cells

Functional disruption of dendritic cells (DC) is an important strategy for viral pathogens to evade host defences. In this context, porcine circovirus type 2 (PCV2), a single-stranded DNA virus, impairs plasmacytoid DC (pDC) and conventional DC activation by certain viruses or Toll-like receptor (TLR) ligands. This inhibitory capacity is associated with the viral DNA, but the impairment does not affect all signalling cascades; TLR7 ligation by small chemical molecules will still induce interleukin-6 (IL-6) and tumour necrosis factor-α secretion, but not interferon-α or IL-12. In this study, the molecular mechanisms by which silencing occurs were investigated. PP2, a potent inhibitor of the Lyn and Hck kinases, produced a similar profile to the PCV2 DNA interference with cytokine secretion by pDC, efficiently inhibiting cell activation induced through TLR9, but not TLR7, ligation. Confocal microscopy and cytometry analysis strongly suggested that PCV2 DNA impairs actin polymerization and endocytosis in pDC and monocyte-derived DC, respectively. Altogether, this study delineates for the first time particular molecular mechanisms involved in PCV2 interference with DC danger recognition, which may be responsible for the virus-induced immunosuppression observed in infected pigs.

Analysis of gene order data supports vertical inheritance of the leukotoxin operon and genome rearrangements in the 5' flanking region in genus Mannheimia

BACKGROUND: The Mannheimia subclades belong to the same bacterial genus, but have taken divergent paths toward their distinct lifestyles. For example, M. haemolytica + M. glucosida are potential pathogens of the respiratory tract in the mammalian suborder Ruminantia, whereas M. ruminalis, the supposed sister group, lives as a commensal in the ovine rumen. We have tested the hypothesis that vertical inheritance of the leukotoxin (lktCABD) operon has occurred from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades by exploring gene order data. RESULTS: We examined the gene order in the 5' flanking region of the leukotoxin operon and found that the 5' flanking gene strings, hslVU-lapB-artJ-lktC and xylAB-lktC, are peculiar to M. haemolytica + M. glucosida and M. granulomatis, respectively, whereas the gene string hslVU-lapB-lktC is present in M. ruminalis, the supposed sister group of M. haemolytica + M. glucosida, and in the most ancient subclade M. varigena. In M. granulomatis, we found remnants of the gene string hslVU-lapB-lktC in the xylB-lktC intergenic region. CONCLUSION: These observations indicate that the gene string hslVU-lapB-lktC is more ancient than the hslVU-lapB-artJ-lktC and xylAB-lktC gene strings. The presence of (remnants of) the ancient gene string hslVU-lapB-lktC among any subclades within genus Mannheimia supports that it has been vertically inherited from the last common ancestor of genus Mannheimia to any ancestor of the diverging subclades, thus reaffirming the hypothesis of vertical inheritance of the leukotoxin operon. The presence of individual 5' flanking regions in M. haemolytica + M. glucosida and M. granulomatis reflects later genome rearrangements within each subclade. The evolution of the novel 5' flanking region in M. haemolytica + M. glucosida resulted in transcriptional coupling between the divergently arranged artJ and lkt promoters. We propose that the chimeric promoter have led to high level expression of the leukotoxin operon which could explain the increased potential of certain M. haemolytica + M. glucosida strains to cause a particular type of infection.

Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes

BACKGROUND: Duplications and deletions in the human genome can cause disease or predispose persons to disease. Advances in technologies to detect these changes allow for the routine identification of submicroscopic imbalances in large numbers of patients. METHODS: We tested for the presence of microdeletions and microduplications at a specific region of chromosome 1q21.1 in two groups of patients with unexplained mental retardation, autism, or congenital anomalies and in unaffected persons. RESULTS: We identified 25 persons with a recurrent 1.35-Mb deletion within 1q21.1 from screening 5218 patients. The microdeletions had arisen de novo in eight patients, were inherited from a mildly affected parent in three patients, were inherited from an apparently unaffected parent in six patients, and were of unknown inheritance in eight patients. The deletion was absent in a series of 4737 control persons (P=1.1x10(-7)). We found considerable variability in the level of phenotypic expression of the microdeletion; phenotypes included mild-to-moderate mental retardation, microcephaly, cardiac abnormalities, and cataracts. The reciprocal duplication was enriched in nine children with mental retardation or autism spectrum disorder and other variable features (P=0.02). We identified three deletions and three duplications of the 1q21.1 region in an independent sample of 788 patients with mental retardation and congenital anomalies. CONCLUSIONS: We have identified recurrent molecular lesions that elude syndromic classification and whose disease manifestations must be considered in a broader context of development as opposed to being assigned to a specific disease. Clinical diagnosis in patients with these lesions may be most readily achieved on the basis of genotype rather than phenotype.

Bothnia dystrophy is caused by domino-like rearrangements in cellular retinaldehyde-binding protein mutant R234W

Cellular retinaldehyde-binding protein (CRALBP) is essential for mammalian vision by routing 11-cis-retinoids for the conversion of photobleached opsin molecules into photosensitive visual pigments. The arginine-to-tryptophan missense mutation in position 234 (R234W) in the human gene RLBP1 encoding CRALBP compromises visual pigment regeneration and is associated with Bothnia dystrophy. Here we report the crystal structures of both wild-type human CRALBP and of its mutant R234W as binary complexes complemented with the endogenous ligand 11-cis-retinal, at 3.0 and 1.7 A resolution, respectively. Our structural model of wild-type CRALBP locates R234 to a positively charged cleft at a distance of 15 A from the hydrophobic core sequestering 11-cis-retinal. The R234W structural model reveals burial of W234 and loss of dianion-binding interactions within the cleft with physiological implications for membrane docking. The burial of W234 is accompanied by a cascade of side-chain flips that effect the intrusion of the side-chain of I238 into the ligand-binding cavity. As consequence of the intrusion, R234W displays 5-fold increased resistance to light-induced photoisomerization relative to wild-type CRALBP, indicating tighter binding to 11-cis-retinal. Overall, our results reveal an unanticipated domino-like structural transition causing Bothnia-type retinal dystrophy by the impaired release of 11-cis-retinal from R234W.

Structural rearrangements of the central region of the morbillivirus attachment protein stalk domain trigger F protein refolding for membrane fusion

It is unknown how receptor binding by the paramyxovirus attachment proteins (HN, H, or G) triggers the fusion (F) protein to fuse with the plasma membrane for cell entry. H-proteins of the morbillivirus genus consist of a stalk ectodomain supporting a cuboidal head; physiological oligomers consist of non-covalent dimer-of-dimers. We report here the successful engineering of intermolecular disulfide bonds within the central region (residues 91-115) of the morbillivirus H-stalk; a sub-domain that also encompasses the putative F-contacting section (residues 111-118). Remarkably, several intersubunit crosslinks abrogated membrane fusion, but bioactivity was restored under reducing conditions. This phenotype extended equally to H proteins derived from virulent and attenuated morbillivirus strains and was independent of the nature of the contacted receptor. Our data reveal that the morbillivirus H-stalk domain is composed of four tightly-packed subunits. Upon receptor binding, these subunits structurally rearrange, possibly inducing conformational changes within the central region of the stalk, which, in turn, promote fusion. Given that the fundamental architecture appears conserved among paramyxovirus attachment protein stalk domains, we predict that these motions may act as a universal paramyxovirus F-triggering mechanism.

Control of chromosomal rearrangements in {\it Escherichia coli\/}

A complete physical map of Escherichia coli K-12 strain MG1655 was constructed by digesting chromosomal DNA with the infrequently cutting restriction enzymes NotI, SfiI and XbaI and separating the fragments by pulsed field gel electrophoresis. The map was used to compare six K-12 strains of E. coli. Although several differences were noted and localized, the map of MG1655 was representative of all the K-12 strains tested. The maps were also used to analyze chromosomal rearrangements in the E. coli strain MG1655. The spontaneous and UV induced frequencies of tandem duplication formation were measured at several loci distributed around the chromosome. The spontaneous duplication frequency varied from 10$\sp{-5}$ to 10$\sp{-3}$ and increased at least ten-fold following mild UV irradiation treatment. Duplications of several regions of the chromosome, including the serA region and the metE region, were mapped using pulsed field gel electrophoresis. Duplications of serA were found to be large, ranging in size from 600 kb to 2100 kb. Several of the duplications isolated at serA were caused by ectopic recombination between IS5 elements and between IS186 elements. Duplications of the metE region, however, were almost exclusively the result of ectopic recombination between ribosomal RNA cistrons. Duplication frequencies were determined at both serA and metE in wild type and mismatch repair mutant strains (mutL, mutS, uvrD and recF). Even though all of the mismatch repair mutations increased duplication frequency of metE, the largest increases were observed in the mutL and mutS strains. Duplication frequency of serA was increased less dramatically by mutations in mismatch repair. Several duplications of metE isolated in a wild type and a mismatch repair mutant were mapped. The results showed that the same repeated sequences were used for duplication formation in the mismatch repair mutant as were used in the wild type strain. Several isolates showed evidence of multiple rearrangements indicating that mismatch repair may play a role in stabilizing the genome by controlling chromosomal rearrangement. ^

(Table 1) Effects of desiccation on photochemical processes and nitrogenase activity in Nostoc commune s.l. colonies

The effects of desiccation on photochemical processes and nitrogenase activity were evaluated in Nostoc commune s.l. colonies in situ from a wet thufur meadow at Petuniabukta, Billefjorden, Central Svalbard, during the 2009 arctic summer. The colonies were collected in the fully hydrated state, and were subjected to slow desiccation at ambient temperatures (5 - 8°C) and low light (30 - 80 µmol/m**2/s). For each colony the weight, area, photochemical performance, and nitrogenase activity were determined at the beginning, as well as on every day during the first four days of the experiment; thereafter, on every second day until desiccation was complete. The photochemical performance was evaluated from variable chlorophyll fluorescence parameters (FV/FM, Phi(PSII) , qP, and NPQ), and the nitrogenase activity was estimated by an acetylene-ethylene reduction assay. A significant decrease in the photochemically active area was recorded from the third day, when the colony had lost approximately 40% of its original weight indicating some changes in the extracellular matrix, and stopped on the 14th to 18th day. No effects of the desiccation on the main photochemical parameters (FV/FM, Phi(PSII), qP) were observed up to the sixth to eighth days of desiccation. Slightly lower values of FV/FM and Phi(PSII) recorded in fully-hydrated colonies could be caused by impaired diffusion of CO2 into cells. The steep reduction of photochemical activity occurred between the eighth and tenth day of the experiment, when the colony had lost approximately 80% of its fully-hydrated weight. The nitrogenase activity was highest on the first day, probably due to improved diffusion of N2 into cells, then declined, but was detectable until the sixth day of the experiment. Since Nostoc commune s.l. colonies were capable of photosynthesis and nitrogen fixation to the level of ca. 60% of its fully-hydrated weight, even partly-hydrated colonies contribute substantially to carbon and nitrogen cycling in the High Arctic wet meadow tundra ecosystem.

Photochemical responses of the diatom Skeletonema costatum grown under elevated CO2 concentrations to short-term changes in pH

Variability in pH is a common occurrence in many aquatic environments, due to physical, chemical and biological processes. In coastal waters, lagoons, estuaries and inland waters, pH can change very rapidly (within seconds or hours) in addition to daily and seasonal changes. At the same time, progressive ocean acidification caused by anthropogenic CO2 emissions is superimposed on these spatial and temporal pH changes. Photosynthetic organisms are therefore unavoidably subject to significant pH variations at the cell surface. Whether this will affect their response to long-term ocean acidification is still unknown, nor is it known whether the short-term sensitivity to pH change is affected by the pCO2 to which the cells are acclimated. We posed the latter open question as our experimental hypothesis: Does acclimation to seawater acidification affect the response of phytoplankton to acute pH variations? The diatom Skeletonema costatum, commonly found in coastal and estuarine waters where short-term acute changes in pH frequently occur, was selected to test the hypothesis. Diatoms were grown at both 390 (pH 8.2, low CO2; LC) and 1000 (pH 7.9, high CO2; HC) µatm CO2 for at least 20 generations, and photosynthetic responses to short-term and acute changes in pH (between 8.2 and 7.6) were investigated. The effective quantum yield of LC-grown cells decreased by ca. 70% only when exposed to pH 7.6; this was not observed when exposed to pH 7.9 or 8.2. HC-grown cells did not show significant responses in any pH treatment. Non-photochemical quenching showed opposite trends. In general, our results indicate that while LC-grown cells are rather sensitive to acidification, HC-grown cells are relatively unresponsive in terms of photochemical performance.

CO2-driven seawater acidification increases photochemical stress in a green alga

Increased CO2 and associated acidification in seawater, known as ocean acidification, decreases calcification of most marine calcifying organisms. However, there is little information available on how marine macroalgae would respond to the chemical changes caused by seawater acidification. We hypothesized that down-regulation of bicarbonate acquisition by algae under increased acidity and CO2 levels would lower the threshold above which photosynthetically active radiation (PAR) becomes excessive. Juveniles of Ulva prolifera derived from zoospores were grown at ambient (390 µatm) and elevated (1000 µatm) CO2 concentrations for 80 days before the hypothesis was tested. Here, the CO2-induced seawater acidification increased the quantum yield under low levels of light, but induced higher nonphotochemical quenching under high light. At the same time, the PAR level at which photosynthesis became saturated was decreased and the photosynthetic affinity for CO2 or inorganic carbon decreased in the high-CO2 grown plants. These findings indicated that ocean acidification, as an environmental stressor, can reduce the threshold above which PAR becomes excessive.