Isobornyl and Isocamphyl Photostabilizers in Poly(lactic acid)-Based Electrospun Fibers.

In this work, electrospun polylactide fibers with new photostabilizing additives, 4-methyl-2,6-diisobornylphenol (DIBP) and N-isocamphylaniline (NICA), have been tested under the influence of UV-C radiation (254 nm). The changes in the polymers' chemical structure under UV-C radiation were revealed through the increase in absorption in the 3600-3100 cm-1 region in regard to the FTIR spectra. In the samples that were irradiated for 1 h, the stabilizing effect of the photoprotectors became most noticeable as the difference in the content of the hydroxyl groups in stabilized and the pure PLA reached a maximum. The TG-DSC method revealed that the most sensitive indicator of the irradiation effect was the glass transition temperature (Tg), which persisted after 2 h of irradiation when using photostabilizers and their combinations. The PLA/DIBP(1) and PLA/NICA(1) samples showed the best results in protecting PLA from UV-C radiation based on the Tg values; although, the mixture of DIBP and NICA was not as effective. The chemical structure of the photostabilized PLA samples was studied using NMR, GPC, and Py-GC/MS analysis. The electrospun polylactide fibers were mechanically tested and the effects of the electrospun samples on cell viability were studied.

Macromolecular Hydrodynamics and Fractal Structures of the Lignins of Fir Wood and Oat Husks.

The topological structure of the macromolecules of lignins isolated from oat husk and fir wood was studied by means of macromolecular hydrodynamic methods. The macromolecular properties were analyzed by evaluating the intrinsic viscosity and coefficients of the translational diffusion and the sedimentation velocity of the lignins in dilute dimethylformamide solutions. The average molecular weights (MDη) and polydispersity parameters were calculated based on the results of the fractionation, as follows: Mw = 14.6 × 103, Mn = 9.0, and Mw/Mn = 1.62 for lignins from fir wood and Mw = 14.9 Mn = 13.5 and Mw/Mn = 1.1 for lignins from oat husks. The fractal analysis of the lignin macromolecules allowed us to identify the distinctive characteristics of the fractal and topological structures of these lignins. The measurements indicated that the fractal dimension (df) values of the guaiacyl-syringyl lignins from oat husks were between 1.71 and 1.85, while the df of a typical guaiacyl lignin from fir wood was ~2.3. Thus, we determined that the lignin macromolecules of oat husks belong to the diffusion-limited aggregation-type cluster-cluster class of fractals of the Meakin-Kolb type, with a predominance of characteristics common to a linear configuration. The lignins of softwood fir trees exhibited a branched topological structure, and they belong to the diffusion-limited aggregation-type particle-cluster class of fractals of the Witten-Sander type. Lignins from oat husks have the linear topology of macromolecules while the macromolecules of the lignins from fir wood can be characterized as highly branched polymers.

Tailoring Photoprotection of Polylactide with New Isobornyl Derivatives of Phenol and Aniline.

This article is devoted to the development of new photostabilizers for polylactide (PLA), a polymer that is an environmentally friendly alternative to polymers and is based on fossil raw materials. We have elucidated the role of the reaction center of two potential PLA photoprotectors: N-isobornylaniline and 2-isobornylphenol, in reactions occurring in a polymer matrix under the action of UV-C radiation. PLA samples with the photostabilizers were irradiated under a wavelength of 253.7 nm for 4, 8 and 12 h. The effectiveness of the photostabilizers was evaluated based on FTIR spectrometric data, 1H and 13C NMR, scanning electron microscopy and simultaneous thermal analysis (TG-DSC). Both stabilizers led to the protection of ester bonds between monomer units of PLA. However, 2-isobornylphenol proved to be more effective at a concentration of 0.05 wt.%, while the optimal concentration of N-isobornylaniline was 0.5 wt.% by weight. TG-DSC showed that the addition of N-isobornylaniline led to an increase in PLA resistance to thermal decomposition; the temperature of the onset of weight loss increased by 2.8 °C at 0.05 wt.% and by 8.1 °C at 0.5 wt.% of N-isobornylaniline. The photoprotector 2-isobornylphenol, on the contrary, reduced the thermal stability of PLA.

Various effects of the expression of the xyloglucanase gene from Penicillium canescens in transgenic aspen under semi-natural conditions.

BACKGROUND: Recombinant carbohydrases genes are used to produce transgenic woody plants with improved phenotypic traits. However, cultivation of such plants in open field is challenging due to a number of problems. Therefore, additional research is needed to alleviate them. RESULTS: Results of successful cultivation of the transgenic aspens (Populus tremula) carrying the recombinant xyloglucanase gene (sp-Xeg) from Penicillium canescens in semi-natural conditions are reported in this paper for the first time. Change of carbohydrate composition of wood was observed in transgenic aspens carrying the sp-Xeg gene. The transformed transgenic line Xeg-2-1b demonstrated accelerated growth and increased content of cellulose in wood of trees growing in both greenhouse and outside in comparison with the control untransformed line Pt. The accelerated growth was observed also in the transgenic line Xeg-1-1c. Thicker cell-wall and longer xylem fiber were also observed in both these transgenic lines. Undescribed earlier considerable reduction in the wood decomposition rate of the transgenic aspen stems was also revealed for the transformed transgenic lines. The decomposition rate was approximately twice as lower for the transgenic line Xeg-2-3b in comparison with the control untransformed line Pt. CONCLUSION: A direct dependence of the phenotypic and biochemical traits on the expression of the recombinant gene sp-Xeg was demonstrated. The higher was the level of the sp-Xeg gene expression, the more pronounced were changes in the phenotypic and biochemical traits. All lines showed phenotypic changes in the leave traits. Our results showed that the plants carrying the recombinant sp-Xeg gene do not demonstrate a decrease in growth parameters in semi-natural conditions. In some transgenic lines, a change in the carbohydrate composition of the wood, an increase in the cell wall thickness, and a decrease in the rate of decomposition of wood were observed.

Pectin-glycerol gel beads: Preparation, characterization and swelling behaviour.

Low methyl-esterified pectin (AU701) was found to form gel beads with glycerol. Wet AU701-glycerol gel beads exhibited similar diameter and hardness compared to the AU701-Ca gel beads, prepared by ionotropic gelation with Ca2+ and used for comparison. The morphology of dry pectin gel beads determined by scanning electron microscopy revealed that the beads exhibited rough and grooved surface. The AU701-glycerol gel beads absorbed more grams of water than AU701-Ca gel beads (12.2 g vs 3.9 g per 1 g of the beads). Rheological properties and hardness of the AU701-glycerol gel beads improved with the increase of the pectin/glycerol ratio. Swelling behavior of the AU701-glycerol gel beads was determined after sequential incubation in simulated gastric (SGF) and intestinal (SIF) fluids. The AU701-glycerol gel beads swelled in SGF to a greater extent and revealed higher stability in SIF than the gel beads cross-linked by Ca2+.

In vitro gastrointestinal-resistant pectin hydrogel particles for ß-glucuronidase adsorption.

Pectin hydrogel particles (PHPs) were prepared by ionotropic gelation of low methylesterified pectin of Tanacetum vulgare L. with calcium ions. Wet PHPs prepared from TVF exhibited a smaller diameter and the lower weight as well as exhibited the best textural properties in terms of hardness and elasticity compared to the PHPs prepared from commercial low methylesterified pectin (CU701) used for comparison. Upon air drying, PHPs prepared from CU701 became small and dense microspheres whereas the dry PHPs prepared from TVF exhibited a drop-like shape. The morphology of dry PHPs determined by scanning electron microscopy revealed that the surface of the TVF beads exhibited fibred structures, whereas the PHPs prepared from CU701 exhibited a smooth surface. The characterization of surface roughness using atomic force microscopy indicated less roughness profile of the PHPs prepared from TVF than CU701. PHPs prepared from TVF were found to possess in vitro resistance to successive incubations in simulated gastric (SGF), intestinal (SIF), and colonic fluid (SCF) at 37 °C for 2, 4 and 18 h, respectively. The PHPs prepared from CU701 swelled in SGF and then lost their spherical shape and were fully disintegrated after 4 h of incubation in SIF. The PHPs from TVF, which were subjected to treatment with SGF, SIF and SCF, were found to adsorb microbial ß-glucuronidase (ßG) in vitro. The data obtained offered the prospect for the development of the PHPs from TVF as sorbents of colonic ßG for the inhibition of re-absorption of estrogens.

Clinical Actionability of Comprehensive Genomic Profiling for Management of Rare or Refractory Cancers.

BACKGROUND: The frequency with which targeted tumor sequencing results will lead to implemented change in care is unclear. Prospective assessment of the feasibility and limitations of using genomic sequencing is critically important. METHODS: A prospective clinical study was conducted on 100 patients with diverse-histology, rare, or poor-prognosis cancers to evaluate the clinical actionability of a Clinical Laboratory Improvement Amendments (CLIA)-certified, comprehensive genomic profiling assay (FoundationOne), using formalin-fixed, paraffin-embedded tumors. The primary objectives were to assess utility, feasibility, and limitations of genomic sequencing for genomically guided therapy or other clinical purpose in the setting of a multidisciplinary molecular tumor board. RESULTS: Of the tumors from the 92 patients with sufficient tissue, 88 (96%) had at least one genomic alteration (average 3.6, range 0-10). Commonly altered pathways included p53 (46%), RAS/RAF/MAPK (rat sarcoma; rapidly accelerated fibrosarcoma; mitogen-activated protein kinase) (45%), receptor tyrosine kinases/ligand (44%), PI3K/AKT/mTOR (phosphatidylinositol-4,5-bisphosphate 3-kinase; protein kinase B; mammalian target of rapamycin) (35%), transcription factors/regulators (31%), and cell cycle regulators (30%). Many low frequency but potentially actionable alterations were identified in diverse histologies. Use of comprehensive profiling led to implementable clinical action in 35% of tumors with genomic alterations, including genomically guided therapy, diagnostic modification, and trigger for germline genetic testing. CONCLUSION: Use of targeted next-generation sequencing in the setting of an institutional molecular tumor board led to implementable clinical action in more than one third of patients with rare and poor-prognosis cancers. Major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access. Early and serial sequencing in the clinical course and expanded access to genomically guided early-phase clinical trials and targeted agents may increase actionability. IMPLICATIONS FOR PRACTICE: Identification of key factors that facilitate use of genomic tumor testing results and implementation of genomically guided therapy may lead to enhanced benefit for patients with rare or difficult to treat cancers. Clinical use of a targeted next-generation sequencing assay in the setting of an institutional molecular tumor board led to implementable clinical action in over one third of patients with rare and poor prognosis cancers. The major barriers to implementation of genomically guided therapy were clinical status of the patient and drug access both on trial and off label. Approaches to increase actionability include early and serial sequencing in the clinical course and expanded access to genomically guided early phase clinical trials and targeted agents.

The evolution of MDM2 family genes.

MDM2 and MDM4 are proto-oncoproteins that bind to and inhibit members of the p53 protein family, p53, p73 and possibly p63. p53 is a mammalian tumor suppressor and p63 and p73 are critical for development. With the sequencing of genomes from multiple organisms there is mounting evidence for a consensus scenario of p53 gene family evolution. A single p53/p63/p73 gene is in invertebrates and required for maintenance of germline DNA. Gene duplication occurred in an ancestor in common with cartilaginous fishes, giving rise to a separate p53 gene and at least one ancestral p63/p73 gene. In bony vertebrates, all three p53 gene family paralogs, p53, p63, and p73 are distinct genes. This raises the question of how MDM2 and MDM4 genes evolved. We show evidence that MDM2 and MDM4 arose from a gene duplication event prior to the emergence of bony vertebrates more than 440 millionyears ago. Comparative genome studies indicate that invertebrate organisms have only one MDM homolog. In jawed vertebrates, the p53-binding domains of MDM2 and MDM4 proteins evolved at a high rate, approaching the evolution rate of the MDM2-binding domain of p53. However, the MDM2-binding domain of p73 exhibits markedly stronger conservation suggesting novel p53-independent functions. The most conserved domain within all MDM2 family members is the RING domain of the MDM2 ortholog which is responsible for ubiquitination of p53 and heterodimerization with MDM4. We suggest a model where oligomerization is an ancient function of MDM and ubiquitination activity was acquired later near the MDM gene duplication event coinciding with the time of the emergence of p53 as a distinct gene.

Sequences from ancestral single-stranded DNA viruses in vertebrate genomes: the parvoviridae and circoviridae are more than 40 to 50 million years old.

Vertebrate genomic assemblies were analyzed for endogenous sequences related to any known viruses with single-stranded DNA genomes. Numerous high-confidence examples related to the Circoviridae and two genera in the family Parvoviridae, the parvoviruses and dependoviruses, were found and were broadly distributed among 31 of the 49 vertebrate species tested. Our analyses indicate that the ages of both virus families may exceed 40 to 50 million years. Shared features of the replication strategies of these viruses may explain the high incidence of the integrations.

Unexpected inheritance: multiple integrations of ancient bornavirus and ebolavirus/marburgvirus sequences in vertebrate genomes.

Vertebrate genomes contain numerous copies of retroviral sequences, acquired over the course of evolution. Until recently they were thought to be the only type of RNA viruses to be so represented, because integration of a DNA copy of their genome is required for their replication. In this study, an extensive sequence comparison was conducted in which 5,666 viral genes from all known non-retroviral families with single-stranded RNA genomes were matched against the germline genomes of 48 vertebrate species, to determine if such viruses could also contribute to the vertebrate genetic heritage. In 19 of the tested vertebrate species, we discovered as many as 80 high-confidence examples of genomic DNA sequences that appear to be derived, as long ago as 40 million years, from ancestral members of 4 currently circulating virus families with single strand RNA genomes. Surprisingly, almost all of the sequences are related to only two families in the Order Mononegavirales: the Bornaviruses and the Filoviruses, which cause lethal neurological disease and hemorrhagic fevers, respectively. Based on signature landmarks some, and perhaps all, of the endogenous virus-like DNA sequences appear to be LINE element-facilitated integrations derived from viral mRNAs. The integrations represent genes that encode viral nucleocapsid, RNA-dependent-RNA-polymerase, matrix and, possibly, glycoproteins. Integrations are generally limited to one or very few copies of a related viral gene per species, suggesting that once the initial germline integration was obtained (or selected), later integrations failed or provided little advantage to the host. The conservation of relatively long open reading frames for several of the endogenous sequences, the virus-like protein regions represented, and a potential correlation between their presence and a species' resistance to the diseases caused by these pathogens, are consistent with the notion that their products provide some important biological advantage to the species. In addition, the viruses could also benefit, as some resistant species (e.g. bats) may serve as natural reservoirs for their persistence and transmission. Given the stringent limitations imposed in this informatics search, the examples described here should be considered a low estimate of the number of such integration events that have persisted over evolutionary time scales. Clearly, the sources of genetic information in vertebrate genomes are much more diverse than previously suspected.

The origins and evolution of the p53 family of genes.

A common ancestor to the three p53 family members of human genes p53, p63, and p73 is first detected in the evolution of modern-day sea anemones, in which both structurally and functionally it acts to protect the germ line from genomic instabilities in response to stresses. This p63/p73 common ancestor gene is found in almost all invertebrates and first duplicates to produce a p53 gene and a p63/p73 ancestor in cartilaginous fish. Bony fish contain all three genes, p53, p63, and p73, and the functions of these three transcription factors diversify in the higher vertebrates. Thus, this gene family has preserved its structural features and functional activities for over one billion years of evolution.

Intra-cavity generation of Bessel-like beams with longitudinally dependent cone angles.

We report on two resonator systems for producing Bessel-like beams with longitudinally dependent cone angles (LDBLBs). Such beams have extended propagation distances as compared to conventional Bessel-Gauss beams, with a far field pattern that is also Bessel-like in structure (i.e. not an annular ring). The first resonator system is based on a lens doublet with spherical aberration, while the second resonator system makes use of intra-cavity axicons and lens. In both cases we show that the LDBLB is the lowest loss fundamental mode of the cavity, and show theoretically the extended propagation distance expected from such beams.

Bessel-like beams with z-dependent cone angles.

The conventional means of generating Bessel-Gauss beams by axicons in the laboratory results in the distinct disadvantage of an abrupt change in intensity at the boundary of the non-diffracting region. We outline theoretically and then demonstrate experimentally a concept for the creation of Bessel-like beams that have a z-dependent cone angle, thereby allowing for a far greater quasi non-diffracting propagation region.

Differential levels of transcription of p53-regulated genes by the arginine/proline polymorphism: p53 with arginine at codon 72 favors apoptosis.

Human populations contain a functional coding polymorphism (codon 72) in the p53 gene. To explore whether this polymorphism alters the transcriptional pattern of p53-regulated genes, the human isogenic cell lines harboring p53 with either the proline or arginine at codon 72 were employed to activate p53-mediated transcription. Thirty-four p53-regulated genes were assayed for their increased levels of mRNA using quantitative real-time PCR. The largest difference between p53-arginine and p53-proline was found with the PERP gene involved in cell-cell adhesion and apoptosis. The most common set of genes that are transcribed better by the p53-arginine protein than the p53-proline protein was found in the apoptotic function (DR-4, NOXA, PUMA, and PIG-3). LIF, a cytokine that is required for optimal reproductive function, was produced at 2x higher levels by the p53-arginine than the p53-proline allele. The genes that induced their mRNAs at the highest levels compared to the baseline tended to be synthesized better by the p53-arginine protein than the p53-proline protein. These molecular studies may help to explain the complicated associations observed between this polymorphism and the incidence of some cancers, the longevity of some populations, and the fecundity of different groups.

Electrostatic origin of the genome packing in viruses.

Many ssRNA/ssDNA viruses bind their genome by highly basic semiflexible peptide arms of capsid proteins. Here, we show that nonspecific electrostatic interactions control both the length of the genome and genome conformations. Analysis of available experimental data shows that the genome length is linear in the net charge on the capsid peptide arms, irrespective of the actual amino acid sequence, with a proportionality coefficient of 1.61 +/- 0.03. This ratio is conserved across all ssRNA/ssDNA viruses with highly basic peptide arms, and is different from the one-to-one charge balance expected of specific binding. Genomic nucleotides are predicted to occupy a radially symmetric spherical shell detached from the viral capsid, in agreement with experimental data.

Exclusion zone of convex brushes in the strong-stretching limit.

We investigate asymptotic properties of long polymers grafted to convex cylindrical and spherical surfaces, and, in particular, distribution of chain free ends. The parabolic potential profile, predicted for flat and concave brushes, fails in convex brushes, and chain free ends span only a finite fraction of the brush thickness. In this paper, we extend the self-consistent model developed by Ball, Marko, Milner, and Witten [Macromolecules 24, 693 (1991)] to determine the size of the exclusion zone, i.e., size of the region of the brush free from chain ends. We show that in the limit of strong stretching, the brush can be described by an alternative system of integral equations. This system can be solved exactly in the limit of weakly curved brushes, and numerically for the intermediate to strong curvatures. We find that going from melt state to theta solvent and then to marginal solvent decreases relative size of the exclusion zone. These relative differences grow exponentially as the curvature decreases to zero.

Spreading of block copolymer films and domain alignment at moving terrace steps.

We investigate spreading of phase separated copolymer films, where domain walls and thickness steps influence polymer flow. We show that at early stages of spreading its rate is determined by slow activated flow at terrace steps (i.e., thickness steps). At late stages of spreading, on the other hand, the rate is determined by the flow along terraces, with diffusionlike time dependence t(-1/2). This dependence is similar to de Gennes and Cazabat's prediction for generic layered liquids [P. G. de Gennes and A. M. Cazabat, C.R. Acad. Sci. Paris II 310, 1601 (1990)], as opposed to the classical Tanner's law of drop spreading. We also argue that chain hopping at the spreading terrace steps should lead to the formation of aligned, defect-free domain patterns on the growing terraces.