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1.	Mancio-Silva, Liliana, et al. (author) Nutrient sensing modulates malaria parasite virulence 2017 In: Nature. - : Macmillan Publishers Ltd.. - 0028-0836 .- 1476-4687. ; 547:7662, s. 213-216 Journal article (peer-reviewed)abstract The lifestyle of intracellular pathogens, such as malaria parasites, is intimately connected to that of their host, primarily for nutrient supply. Nutrients act not only as primary sources of energy but also as regulators of gene expression, metabolism and growth, through various signalling networks that enable cells to sense and adapt to varying environmental conditions. Canonical nutrient-sensing pathways are presumed to be absent from the causative agent of malaria, Plasmodium, thus raising the question of whether these parasites can sense and cope with fluctuations in host nutrient levels. Here we show that Plasmodium blood-stage parasites actively respond to host dietary calorie alterations through rearrangement of their transcriptome accompanied by substantial adjustment of their multiplication rate. A kinome analysis combined with chemical and genetic approaches identified KIN as a critical regulator that mediates sensing of nutrients and controls a transcriptional response to the host nutritional status. KIN shares homology with SNF1/AMPKα, and yeast complementation studies suggest that it is part of a functionally conserved cellular energy-sensing pathway. Overall, these findings reveal a key parasite nutrient-sensing mechanism that is critical for modulating parasite replication and virulence.
2.	Dias, N., et al. (author) Outcomes of Elective and Non-elective Fenestrated-branched Endovascular Aortic Repair for Treatment of Thoracoabdominal Aortic Aneurysms 2023 In: Annals of Surgery. - : Lippincott Williams & Wilkins. - 0003-4932 .- 1528-1140. ; 278:4, s. 568-577, s. 568-577 Journal article (peer-reviewed)abstract Objective: To describe outcomes after elective and non-elective fenestrated-branched endovascular aortic repair (FB-EVAR) for thoracoabdominal aortic aneurysms (TAAAs).Background: FB-EVAR has been increasingly utilized to treat TAAAs; however, outcomes after non-elective versus elective repair are not well described.Methods: Clinical data of consecutive patients undergoing FB-EVAR for TAAAs at 24 centers (2006-2021) were reviewed. Endpoints including early mortality and major adverse events (MAEs), all-cause mortality, and aortic-related mortality (ARM), were analyzed and compared in patients who had non-elective versus elective repair.Results: A total of 2603 patients (69% males; mean age 72 +/- 10 year old) underwent FB-EVAR for TAAAs. Elective repair was performed in 2187 patients (84%) and non-elective repair in 416 patients [16%; 268 (64%) symptomatic, 148 (36%) ruptured]. Non-elective FB-EVAR was associated with higher early mortality (17% vs 5%, P < 0.001) and rates of MAEs (34% vs 20%, P < 0.001). Median follow-up was 15 months ( interquartile range, 7-37 months). Survival and cumulative incidence of ARM at 3 years were both lower for non-elective versus elective patients (50 +/- 4% vs 70 +/- 1% and 21 +/- 3% vs 7 +/- 1%, P < 0.001). On multivariable analysis, non-elective repair was associated with increased risk of all-cause mortality ( hazard ratio, 1.92; 95% CI] 1.50-2.44; P < 0.001) and ARM (hazard ratio, 2.43; 95% CI, 1.63-3.62; P < 0.001).Conclusions: Non-elective FB-EVAR of symptomatic or ruptured TAAAs is feasible, but carries higher incidence of early MAEs and increased all-cause mortality and ARM than elective repair. Long-term follow-up is warranted to justify the treatment.
3.	Dias-Neto, Marina, et al. (author) Comparison of single- and multistage strategies during fenestrated-branched endovascular aortic repair of thoracoabdominal aortic aneurysms 2023 In: Journal of Vascular Surgery. - : MOSBY-ELSEVIER. - 0741-5214 .- 1097-6809. ; 77:6, s. 1588-1597 Journal article (peer-reviewed)abstract Objective: The aim of this study was to compare outcomes of single or multistage approach during fenestrated-branched endovascular aortic repair (FB-EVAR) of extensive thoracoabdominal aortic aneurysms (TAAAs).Methods: We reviewed the clinical data of consecutive patients treated by FB-EVAR for extent I to III TAAAs in 24 centers (2006-2021). All patients received a single brand manufactured patient-specific or off-the-shelf fenestrated-branched stent grafts. Staging strategies included proximal thoracic aortic repair, minimally invasive segmental artery coil embolization, temporary aneurysm sac perfusion and combinations of these techniques. Endpoints were analyzed for elective repair in patients who had a single-or multistage approach before and after propensity score adjustment for baseline differences, including the composite 30-day/in-hospital mortality and/or permanent paraplegia, major adverse event, patient survival, and freedom from aortic-related mortality.Results: A total of 1947 patients (65% male; mean age, 71 +/- 8 years) underwent FB-EVAR of 155 extent I (10%), 729 extent II (46%), and 713 extent III TAAAs (44%). A single-stage approach was used in 939 patients (48%) and a multistage approach in 1008 patients (52%). A multistage approach was more frequently used in patients undergoing elective compared with non-elective repair (55% vs 35%; P < .001). Staging strategies were proximal thoracic aortic repair in 743 patients (74%), temporary aneurysm sac perfusion in 128 (13%), minimally invasive segmental artery coil embolization in 10 (1%), and combinations in 127 (12%). Among patients undergoing elective repair (n = 1597), the composite endpoint of 30-day/in-hospital mortality and/or permanent paraplegia rate occurred in 14% of single-stage and 6% of multistage approach patients (P < .001). After adjustment with a propensity score, multistage approach was associated with lower rates of 30-day/in-hospital mortality and/or permanent paraplegia (odds ratio, 0.466; 95% confidence interval, 0.271-0.801; P = .006) and higher patient survival at 1 year (86.9 +/- 1.3% vs 79.6 +/- 1.7%) and 3 years (72.7 +/- 2.1% vs 64.2 +/- 2.3%; adjusted hazard ratio, 0.714; 95% confidence interval, 0.528-0.966; P = .029), compared with a single stage approach.Conclusions: Staging elective FB-EVAR of extent I to III TAAAs was associated with decreased risk of mortality and/or permanent paraplegia at 30 days or within hospital stay, and with higher patient survival at 1 and 3 years.
4.	Abolfathi, Bela, et al. (author) The Fourteenth Data Release of the Sloan Digital Sky Survey : First Spectroscopic Data from the Extended Baryon Oscillation Spectroscopic Survey and from the Second Phase of the Apache Point Observatory Galactic Evolution Experiment 2018 In: Astrophysical Journal Supplement Series. - : IOP Publishing Ltd. - 0067-0049 .- 1538-4365. ; 235:2 Journal article (peer-reviewed)abstract The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since 2014 July. This paper describes the second data release from this phase, and the 14th from SDSS overall (making this Data Release Fourteen or DR14). This release makes the data taken by SDSS-IV in its first two years of operation (2014-2016 July) public. Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey; the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data-driven machine-learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from the SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS web site (www.sdss.org) has been updated for this release and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020 and will be followed by SDSS-V.
5.	Aguado, D. S., et al. (author) The Fifteenth Data Release of the Sloan Digital Sky Surveys : First Release of MaNGA-derived Quantities, Data Visualization Tools, and Stellar Library 2019 In: Astrophysical Journal Supplement Series. - : Institute of Physics Publishing (IOPP). - 0067-0049 .- 1538-4365. ; 240:2 Journal article (peer-reviewed)abstract Twenty years have passed since first light for the Sloan Digital Sky Survey (SDSS). Here, we release data taken by the fourth phase of SDSS (SDSS-IV) across its first three years of operation (2014 July-2017 July). This is the third data release for SDSS-IV, and the 15th from SDSS (Data Release Fifteen; DR15). New data come from MaNGA-we release 4824 data cubes, as well as the first stellar spectra in the MaNGA Stellar Library (MaStar), the first set of survey-supported analysis products (e.g., stellar and gas kinematics, emission-line and other maps) from the MaNGA Data Analysis Pipeline, and a new data visualization and access tool we call "Marvin." The next data release, DR16, will include new data from both APOGEE-2 and eBOSS; those surveys release no new data here, but we document updates and corrections to their data processing pipelines. The release is cumulative; it also includes the most recent reductions and calibrations of all data taken by SDSS since first light. In this paper, we describe the location and format of the data and tools and cite technical references describing how it was obtained and processed. The SDSS website (www.sdss.org) has also been updated, providing links to data downloads, tutorials, and examples of data use. Although SDSS-IV will continue to collect astronomical data until 2020, and will be followed by SDSS-V (2020-2025), we end this paper by describing plans to ensure the sustainability of the SDSS data archive for many years beyond the collection of data.
6.	Ainalem, Marie-Louise, et al. (author) DNA compaction induced by a cationic polymer or surfactant impact gene expression and DNA degradation. 2014 In: PLoS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 9:3 Journal article (peer-reviewed)abstract There is an increasing interest in achieving gene regulation in biotechnological and biomedical applications by using synthetic DNA-binding agents. Most studies have so far focused on synthetic sequence-specific DNA-binding agents. Such approaches are relatively complicated and cost intensive and their level of sophistication is not always required, in particular for biotechnological application. Our study is inspired by in vivo data that suggest that DNA compaction might contribute to gene regulation. This study exploits the potential of using synthetic DNA compacting agents that are not sequence-specific to achieve gene regulation for in vitro systems. The semi-synthetic in vitro system we use include common cationic DNA-compacting agents, poly(amido amine) (PAMAM) dendrimers and the surfactant hexadecyltrimethylammonium bromide (CTAB), which we apply to linearized plasmid DNA encoding for the luciferase reporter gene. We show that complexing the DNA with either of the cationic agents leads to gene expression inhibition in a manner that depends on the extent of compaction. This is demonstrated by using a coupled in vitro transcription-translation system. We show that compaction can also protect DNA against degradation in a dose-dependent manner. Furthermore, our study shows that these effects are reversible and DNA can be released from the complexes. Release of DNA leads to restoration of gene expression and makes the DNA susceptible to degradation by Dnase. A highly charged polyelectrolyte, heparin, is needed to release DNA from dendrimers, while DNA complexed with CTAB dissociates with the non-ionic surfactant C12E5. Our results demonstrate the relation between DNA compaction by non-specific DNA-binding agents and gene expression and gene regulation can be achieved in vitro systems in a reliable dose-dependent and reversible manner.
7.	Blanton, Michael R., et al. (author) Sloan Digital Sky Survey IV : Mapping the Milky Way, Nearby Galaxies, and the Distant Universe 2017 In: Astronomical Journal. - : IOP Publishing Ltd. - 0004-6256 .- 1538-3881. ; 154:1 Journal article (peer-reviewed)abstract We describe the Sloan Digital Sky Survey IV (SDSS-IV), a project encompassing three major spectroscopic programs. The Apache Point Observatory Galactic Evolution Experiment 2 (APOGEE-2) is observing hundreds of thousands of Milky Way stars at high resolution and. high signal-to-noise ratios in the near-infrared. The Mapping Nearby Galaxies at Apache Point Observatory (MaNGA) survey is obtaining spatially resolved spectroscopy for thousands of nearby galaxies (median z similar to 0.03). The extended Baryon Oscillation Spectroscopic Survey (eBOSS) is mapping the galaxy, quasar, and neutral gas distributions between z similar to 0.6 and 3.5 to constrain cosmology using baryon acoustic oscillations, redshift space distortions, and the shape of the power spectrum. Within eBOSS, we are conducting two major subprograms: the SPectroscopic IDentification of eROSITA Sources (SPIDERS), investigating X-ray AGNs. and galaxies in X-ray clusters, and the Time Domain Spectroscopic Survey (TDSS), obtaining spectra of variable sources. All programs use the 2.5 m Sloan Foundation Telescope at the. Apache Point Observatory; observations there began in Summer 2014. APOGEE-2 also operates a second near-infrared spectrograph at the 2.5 m du Pont Telescope at Las Campanas Observatory, with observations beginning in early 2017. Observations at both facilities are scheduled to continue through 2020. In keeping with previous SDSS policy, SDSS-IV provides regularly scheduled public data releases; the first one, Data Release 13, was made available in 2016 July.
8.	Carlstedt, Jonas, et al. (author) Condensation and decondensation of DNA by cationic surfactant, spermine, or cationic surfactant–cyclodextrin mixtures : macroscopic phase behavior, aggregate properties, and dissolution mechanisms 2012 In: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 28:21, s. 7976-7989 Journal article (peer-reviewed)abstract The macroscopic phase behavior and other physicochemical properties of dilute aqueous mixtures of DNA and the cationic surfactant hexadecyltrimethylammounium bromide (CTAB), DNA and the polyamine spermine, or DNA, CTAB, and (2-hydroxypropyl)-β-cyclodextrin (2HPβCD) were investigated. When DNA is mixed with CTAB we found, with increasing surfactant concentration, (1) free DNA coexisting with surfactant unimers, (2) free DNA coexisting with aggregates of condensed DNA and CTAB, (3) a miscibility gap where macroscopic phase separation is observed, and (4) positively overcharged aggregates of condensed DNA and CTAB. The presence of a clear solution beyond the miscibility gap cannot be ascribed to self-screening by the charges from the DNA and/or the surfactant; instead, hydrophobic interactions among the surfactants are instrumental for the observed behavior. It is difficult to judge whether the overcharged mixed aggregates represent an equilibrium situation or not. If the excess surfactant was not initially present, but added to a preformed precipitate, redissolution was, in consistency with previous reports, not observed; thus, kinetic effects have major influence on the behavior. Mixtures of DNA and spermine also displayed a miscibility gap; however, positively overcharged aggregates were not identified, and redissolution with excess spermine can be explained by electrostatics. When 2HPβCD was added to a DNA–CTAB precipitate, redissolution was observed, and when it was added to the overcharged aggregates, the behavior was essentially a reversal of that of the DNA–CTAB system. This is attributed to an effectively quantitative formation of 1:1 2HPβCD–surfactant inclusion complexes, which results in a gradual decrease in the concentration of effectively available surfactant with increasing 2HPβCD concentration.
9.	Carlstedt, Jonas, et al. (author) Release of DNA from surfactant complexes induced by 2-hydroxypropyl-beta-cyclodextrin. 2010 In: International Journal of Biological Macromolecules. - : Elsevier BV. - 1879-0003 .- 0141-8130. ; 46:2, s. 153-158 Journal article (peer-reviewed)abstract Decompaction of DNA-CTA self-assembled complexes by 2-hydroxypropyl-beta-cyclodextrin (2-HP-beta-CD) was studied and the results were compared with beta-CD. Different degrees of 2-HP substitution (0.6, 0.8 and 1.0, respectively) were used and the decompaction was successful with all degrees of substitution. Fluorescence microscopy, steady state fluorescence spectroscopy, density and sound velocity measurements, thermal melting and circular dichroism were used. Compared to previous work using alpha- and beta-CD, the fluorescence spectroscopy results showed that the 2-HP-substituted CDs more efficiently released DNA into solution. Furthermore, dissociation of macroscopically phase separated DNA-CTA complexes was achieved upon addition of 2-HP-beta-CD and the results gave strong indications on the non-equilibrium nature of the system. The globule-to-coil transition was not found to proceed through a coexistence region, which seems to be a general phenomenon in DNA decompaction using CDs.
10.	Dasgupta, Antara, et al. (author) Effect of headgroup on DNA - Cationic surfactant interactions 2007 In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 111:29, s. 8502-8508 Journal article (peer-reviewed)abstract The interaction behavior of DNA with different types of hydroxylated cationic surfactants has been studied. Attention was directed to how the introduction of hydroxyl substituents at the headgroup of the cationic surfactants affects the compaction of DNA. The DNA-cationic surfactant interaction was investigated at different charge ratios by several methods like UV melting, ethidium bromide exclusion, and gel electrophoresis. Studies show that there is a discrete transition in the DNA chain from extended coils (free chain) to a compact form and that this transition does not depend substantially on the architecture of the headgroup. However, the accessibility of DNA to ethidium bromide is preserved to a significantly larger extent for the more hydrophilic surfactants. This was discussed in terms of surfactant packing. Observations are interpreted to reflect that the surfactants with more substituents have a larger headgroup and therefore form smaller micellar aggregates; these higher curvature aggregates lead to a less efficient, "patch-like" coverage of DNA. The more hydrophilic surfactants also presented a significantly lower cytotoxicity, which is important for biotechnological applications.
11.	Dias, Rita, et al. (author) Coil-globule transition of DNA molecules induced by cationic surfactants: A dynamic light scattering study 2005 In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 109:20, s. 10458-10463 Journal article (peer-reviewed)abstract The compaction and aggregation of DNA induced by cationic surfactants was studied by dynamic light scattering (DLS). Furthermore, the effect on surfactant-compacted DNA of the addition of nonionic amphiphiles and salt was studied. When using sufficiently low amounts of DNA and cetyltrimethylammonium bromide (CTAB), compacted DNA molecules could be monitored by the appearance of a band characterized by lower hydrodynamic radius and by the decrease in the intensity of the peak corresponding to extended DNA molecules. Notably, we observed a region where compacted molecules coexist with extended ones; these two populations were found to be stable with time. For higher concentrations of CTAB, only compacted molecules were observed and the size of the particles increased with time indicating aggregation. The number of globules present in the coexistence region increased linearly with the surfactant concentrations, as given by the area of the band corresponding to this population, which indicates a double-cooperativity of the binding. The DLS experiments were in good agreement with previous fluorescence microscopy studies, with certain advantages over this technique since there is no need to add fluorescence dyes and antioxidants. Furthermore, it allows the study of molecules which are too small to be visualized by fluorescence microscopy.
12.	Dias, Rita, et al. (author) Colloid Adsorption onto Responsive Membranes. 2008 In: Biophysical Journal. - : Elsevier BV. - 1542-0086 .- 0006-3495. ; 94:10, s. 3760-3768 Journal article (peer-reviewed)abstract The adsorption of colloids with varying sizes and charges onto a surface carrying both negative and positive charges representing a membrane has been investigated by using a simple model employing Monte Carlo simulations. The membrane is made of positive and negative charges (headgroups) that are allowed to move along the membrane, simulating the translational diffusion of the lipids, and are also allow to protrude into the solution, giving rise to a fluid and soft membrane. When an uncharged colloid is placed in the vicinity of the membrane, a short-range repulsion between the colloid and the membrane is observed and the membrane will deflect to avoid the contact with the colloid. When the colloid is charged, the membrane response is two-fold: the headgroups of the membrane move towards the colloid as to partly embrace it, and the positive headgroups of the membrane approach the oppositely charged colloid, inducing the demixing of the lipids (polarization) of the membrane. The presence of protrusions enhances the polarization of the membrane. Potential of mean force calculations show that protrusions give rise to a more long-ranged attractive colloid-membrane potential which however has a smaller magnitude at short separations.
13.	Dias, Rita, et al. (author) Compaction and decompaction of DNA in the presence of catanionic amphiphile mixtures 2002 In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 106:48, s. 12608-12612 Journal article (peer-reviewed)abstract The dissociation of DNA-cationic surfactant complexes with the addition of a negative amphiphile was studied by fluorescence microscopy (FM). The unfolding of DNA molecules previously compacted with cationic surfactant was shown to be dependent on the anionic surfactant chain length; lower amounts of a longer-chain surfactant were needed to release DNA into solution. However, we observed no dependence on the hydrophobicity of the compacting agent. The structures of the aggregates formed by the two surfactants, after the interaction with DNA, were imaged by cryogenic transmission electron microscopy (cryo-TEM). We found that it is possible to predict the structure of the aggregates the surfactants will form, such as vesicle phases, from the behavior of mixed surfactant systems, which brings new insight to this subject and several interesting opportunities for applications.
14.	Dias, Rita, et al. (author) DNA and surfactants in bulk and at interfaces 2004 In: Colloids and Surfaces A: Physicochemical and Engineering Aspects. - : Elsevier BV. - 0927-7757. ; 250:1-3, s. 115-131 Journal article (peer-reviewed)abstract Recent investigations of the DNA interactions with cationic surfactants and catanionic Mixtures are reviewed. Several techniques have been used such as fluorescence microscopy, dynamic light scattering, electron microscopy, and Monte Carlo simulations. The conformational behaviour of large DNA molecules in the presence of cationic surfactant was followed by fluorescence microscopy and also by dynamic light scattering. These techniques were in good agreement and it was possible to observe a discrete transition from extended coils to collapsed globules and their coexistence for intermediate amphiphile concentrations. The dependence on the surfactant alkyl chain was also monitored by fluorescence microscopy and, as expected, lower concentrations of the more hydrophobic surfactant were required to induce DNA compaction, although an excess of positive charges was still required. Monte Carlo simulations on the compaction of a medium size polyanion with shorter polycations were performed. The polyanion chain suffers a sudden collapse as a function of the concentration of condensing agent, and of the number of charges on the polycation molecules. C Further increase in the concentration increases the degree of compaction. The compaction was found to be associated with the polycations promoting bridging between different sites of the polyanion. When the total charge of the polycations was lower than that of the polyanion, a significant translational motion of the compacting agent along the polyanion was observed, producing only a small-degree of intrachain segregation, which can explain the excess of positive charges necessary to compact DNA. Dissociation of the DNA-cationic surfactant complexes and a concomitant release of DNA was achieved by addition of anionic surfactants. The unfolding of DNA molecules, previously compacted with cationic surfactant, was shown to be strongly dependent on the anionic surfactant chain length: lower amounts of a longer chain surfactant were needed to release DNA into solution. On the other hand, no dependence on the hydrophobicity of the compacting agent was observed. The structures of the aggregates formed by the two surfactants, after the interaction with DNA. were imaged by cryogenic transmission electron microscopy. It is possible to predict the structure of the aggregates formed by the surfactants. like vesicles, from the phase behaviour of the mixed surfactant systems. Studies on the interactions between DNA and catanionic mixtures were also performed. It was observed that DNA does not interact with negatively charged vesicles, even though they carry positive amphiphiles; however, in the presence of positively charged vesicles, DNA molecules compact and adsorb on their surface. Finally Monte Carlo simulations were performed on the adsorption of a polyelectrolyte on catanionic surfaces. It was observed that the mobile charges in the surface react to the presence of the polyelectrolyte enabling a strong degree of adsorption even though the membrane was globally neutral. Our observations indicate that the adsorption behaviour of the polyelectrolyte is influenced by the response given by the membrane to its presence and that the number of adsorbed beads increases drastically with the increase of flexibility of the polymer. Calculations involving polymers with three different intrinsic stiffnesses showed that the variation is non-monotonic. It was observed also that a smaller polyanion typically adsorbs more completely than the larger one, which indicates that the polarisation of the membrane becomes less facilitated as the degree of disruption increases. (C) 2004 Elsevier B.V. All rights reserved.
15.	Dias, Rita, et al. (author) DNA compaction and decompaction: bulk and interfaces 2005 In: Coloides e interfases. - 8478005242 ; , s. 403-407 Conference paper (peer-reviewed)
16.	Dias, Rita, et al. (author) DNA interaction with catanionic vesicles 2002 In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 106:48, s. 12600-12607 Journal article (peer-reviewed)abstract DNA-cationic liposome complexes as possible vehicles for gene delivery is currently an important issue. In this work, the interaction between DNA and thermodynamically stable, spontaneously formed, catanionic vesicles with a net positive charge is studied. A phase map was drawn for the aqueous system of DNA and positively charged vesicles, composed of CTAB (cetyltrimethylammonium bromide) and SOS (sodium octyl sulfate), and showed, as expected, a strong associative phase behavior with the formation of a precipitate. A two-phase region was observed over all the studied concentrations. For DNA-surfactant mixing ratios, [DNA]/ [S+] below 1.3 by charge, we found, by optical and electron microscopy, a coexistence between undisturbed vesicles and DNA-surfactant complexes. In samples with a higher excess of DNA, only DNA-vesicle complexes were observed, in solution. The structure of these complexes was studied by both small-angle X-ray diffraction (SAXS) and cryogenic transmission electron microscopy (cryo-TEM), and a short-range lamellar structure composed of amphiphile bilayers with DNA molecules ordered and packed between these stacks was found. This type of structure has already been mentioned in the literature as being the most frequently found structure for DNA-liposome mixtures and shows that the vesicles we used, having major advantages with respect to preparation and stability, have similar behavior and can thus be successfully used as model systems. We observed, however, an interesting difference in comparison with previously studied systems. Thus, the addition of DNA in excess to the samples leads not to the coexistence of DNA-vesicle complexes and DNA, as observed before, but to a probable inclusion of DNA in excess in the complexes and therefore to a coexistence of complexes and anionic surfactant micelles expelled from the bilayers.
17.	Dias, Rita, et al. (author) DNA-Surfactant interactions, compaction, condensation, decompaction and phase separation 2004 In: Journal of the Chinese Chemical Society. - 2192-6549. ; 51:3, s. 447-469 Research review (peer-reviewed)abstract Recent investigations-of the interaction between DNA and alkyltrimethyl ammonium bromides of various chain lengths are reviewed. Several techniques have been used such as phase map determinations, fluorescence microscopy, and electron microscopy. Dissociation of the DNA-surfactant complexes, by the addition of anionic surfactant, has received special attention. Precipitation maps for DNA-cationic surfactant' systems were evaluated by turbidimetry for different salt concentrations, temperatures and surfactant chain lengths. Single-stranded DNA molecules precipitate at lower surfactant concentrations than double-helix ones. It was also observed that these systems precipitate for very low concentrations of both DNA and surfactant, and that the extension of the two-phase region increases for longer chain surfactants; these observations correlate well with fluorescence microscopy results, monitoring the system at a single molecule level. Dissociation of the DNA-cationic surfactant complexes and a concomitant release of DNA was achieved by addition of anionic surfactants. The unfolding of DNA molecules, previously compacted with cationic surfactant, was shown to be strongly dependent on the anionic surfactant chain length; lower amounts of a longer chain surfactant were needed to release DNA into solution. On the other hand, no dependence on the hydrophobicity of the compacting agent was observed. The structures of the aggregates formed by the two surfactants, after the interaction with DNA, were imaged by cryogenic transmission electron microscopy. It is possible to predict the structure of the aggregates formed by the surfactants, like vesicles, from the phase behaviour of the mixed surfactant systems. The compaction of a medium size polyanion with shorter polycations was furthermore studied by means of Monte Carlo simulations. The polyanion chain suffers a sudden collapse as a function of the condensing agent concentration and of the number of charges on the molecules. Further increase of the concentration gives an increase of the degree of compaction. The compaction was found to be associated with the polycations promoting bridging between different sites of the polyanion. When the total charge of the polycations was lower than that of the polyanion, a significant translational motion of the compacting agent along the polyanion was observed, producing only a small-degree of intrachain segregation. However, complete charge neutralization was not a prerequisite to achieve compacted forms.
18.	Dias, Rita, et al. (author) DNA–Surfactant Systems: Particles, Gels, and Nanostructures 2010 In: Nano-Science: Colloidal and Interfacial Aspects. - 9781420065008 ; 147, s. 379-394 Book chapter (other academic/artistic)
19.	Dias, Rita, et al. (author) Electrophoretic properties of complexes between DNA and the cationic surfactant cetyltrimethylammonium bromide 2005 In: Electrophoresis. - : Wiley. - 0173-0835 .- 1522-2683. ; 26:15, s. 2908-2917 Journal article (peer-reviewed)abstract We use agarose gel electrophoresis to characterize how the monovalent catioinic surfactant cetyltrimethylammonium bromide (CTAB) compacts double-stranded DNA, which is detected as a reduction in electrophoretic DNA velocity. The velocity reaches a plateau at a ratio R = 1.8 of CTAB to DNA-phosphate charges, i.e., above the neutralization point, and the complexes retain a net negative charge at least up to R = 200. Condensation experiments on a mixture of two DNA sizes show that the complexes formed contain only one condensed DNA molecule each. These CTAB-DNA globules were further characterized by time-resolved measurements of their velocity inside the gel, which showed that CTAB does not dissociate during the migration but possibly upon entry into the gel. Using the Ogston-model for electrophoresis of spherical particles, the measured in-gel velocity of the globule is quantitatively consistent with CTAB having two opposite effects, reduction of both the electrophoretic charge and DNA coll size. In the case of CTAB the two effects nearly cancel, which can explain why opposite velocity shifts (globule faster than uncomplexed DNA) have been observed with some catioinic condensation agents. Dissociation of the complexes by addition of anionic surfactants was also studied. The DNA release from the globule was complete at a mixing ratio between anionic and cationic surfactants equal to 1, in agreement with equilibrium studies. Circular DNA retained its supercoiling, and this demonstrates a lack of DNA nicking in the compaction-release cycle which is important in DNA transfection and purification applications.
20.	Dias, Rita, et al. (author) Interaction between DNA and Cationic Surfactants: Effect of DNA Conformation and Surfactant Headgroup. 2008 In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 112:46, s. 14446-14452 Journal article (peer-reviewed)abstract The interactions between DNA and a number of different cationic surfactants, differing in headgroup polarity, were investigated by electric conductivity measurements and fluorescence microscopy. It was observed that, the critical association concentration (cac), characterizing the onset of surfactant binding to DNA, does not vary significantly with the architecture of the headgroup. However, comparing with the critical micelle concentration (cmc) in the absence of DNA, it can be inferred that the micelles of a surfactant with a simple quaternary ammonium headgroup are much more stabilized by the presence of DNA than those of surfactants with hydroxylated head-groups. In line with previous studies of polymer-surfactant association, the cac does not vary significantly with either the DNA concentration or its chain length. On the other hand, a novel observation is that the cac is much lower when DNA is denaturated and in the single-stranded conformation, than for the double-helix DNA. This is contrary to expectation for a simple electrostatically driven association. Thus previous studies of polyelectrolyte-surfactant systems have shown that the cac decreases strongly with increasing linear charge density of the polyion. Since double-stranded DNA (dsDNA) has twice as large linear charge density as single-stranded DNA (ssDNA), the stronger binding in the latter case indicates an important role of nonelectrostatic effects. Both a higher flexibility of ssDNA and a higher hydrophobicity due to the exposed bases are found to play a role, with the hydrophobic interaction argued to be more important. The significance of hydrophobic DNA-surfactant interaction is in line with other observations. The significance of nonelectrostatic effects is also indicated in significant differences in cac between different surfactants for ssDNA but not for dsDNA. For lower concentrations of DNA, the conductivity measurements presented an "anomalous" feature, i.e., a second inflection point for surfactant concentrations below the cac; this feature was not displayed at higher concentrations of DNA. The effect is attributed to the presence of a mixture of ss- and dsDNA molecules. Thus the stability of dsDNA is dependent on a certain ion atmosphere; at lower ion concentrations the electrostatic repulsions between the DNA strands become too strong compared to the attractive interactions, and there is a dissociation into the individual strands. Fluorescence microscopy studies, performed at much lower DNA concentrations, demonstrated a transformation of dsDNA from an extended "coil" state to a compact "globule" condition, with a broad concentration region of coexistence of coils and globules. The onset of DNA compaction coincides roughly with the cac values obtained from conductivity measurements. This is in line with the observed independence of cac on the DNA concentration, together with the assumption that the onset of binding corresponds to an initiation of DNA compaction. No major changes in either the onset of compaction or complete compaction were observed as the surfactant headgroup was made more polar.
21.	Dias, Rita, et al. (author) Modeling of DNA compaction by polycations 2003 In: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 119:15, s. 8150-8157 Journal article (peer-reviewed)abstract In this work we study polycations as efficient compacting agents of a medium size polyanion by means of Monte Carlo simulations. The systems are characterized in terms of a conformational analysis in which shape, overall dimensions, structure factors, radial distribution functions, and the degree of accumulation of the compaction agent near the polyanion are taken into consideration. Results show that the degree of compaction depends on the size of the positive chais and their number. The role of electrostatic interactions is paramount in the compaction process, and an increase in the number of molecules of the compacting agent or in the number of charges of each molecule leads to collapse, which may be followed by some unfolding in situations of overcharging. Compaction is associated with polycations promoting bridging between different sites in the polyanion. When the total charge of the polycations is significantly lower than that of the polyanion, interaction produces only a small degree of intrachain segregation in the latter, allowing for significant translational motion of the compacting agent along the longer chain. However, complete charge neutralization is not mandatory to achieve compact forms. (C) 2003 American Institute of Physics.
22.	Dias, Rita, et al. (author) Polyion adsorption onto catanionic surfaces. A Monte Carlo study 2005 In: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 109:23, s. 11781-11788 Journal article (peer-reviewed)abstract The adsorption of a single and negatively charged polyion with varying flexibility onto a surface carrying both negative and positive charges representing a charged membrane surface has been investigated by using a simple model employing Monte Carlo simulations. The polyion was represented by a sequence of negatively charged hard spheres connected with harmonic bonds. The charged surface groups were also represented by charged hard spheres, and they were positioned on a hard surface slightly protruding into the solution. The surface charges were either frozen in a liquidlike structure or laterally mobile. With a large excess of positive surface charges, the classical picture of a strongly adsorbed polyion with an extended and flat configuration emerged. However, adsorption also appeared at a net neutral surface or at a weakly negatively charged surface, and at these conditions the adsorption was stronger with a flexible polyion as compared to a semiflexible one, two features not appearing in simpler models containing homogeneously charged surfaces. The presence of charged surface patches (frozen surface charges) and the ability of polarization of the surface charges (mobile surface charges) are the main reasons for the enhanced adsorption. The stronger adsorption with the flexible chain is caused by its greater ability to spatially correlate with the surface charges.
23.	Gaweda, Sylwia, et al. (author) Cationic agents for DNA compaction 2008 In: Journal of Colloid and Interface Science. - : Elsevier BV. - 1095-7103 .- 0021-9797. ; 323:1, s. 75-83 Journal article (peer-reviewed)abstract Fluorescence microscopy was used to investigate the conformational changes of individual T4 DNA molecules induced by different compacting agents, namely the cationic surfactants, cetyltrimethylammonium bromide (CTAB) and chloride (CTAC), iron(III), lysozyme, and protamine sulfate. A protocol for establishing size estimates is suggested to obtain reproducible results. Observations show that in the presence of lysozyme and protamine sulfate, DNA molecules exhibit a conformational change from an elongated coil structure to compact globules, usually interpreted as a first-order transition. The maximum degree of compaction that is attained when iron(III) or CTAB (CrAC) are used as compacting agents is considerably smaller, and intermediate structures (less elongated coils) are visible even for high concentrations of these agents. Dynamic light scattering experiments were carried out, for some of the systems, to assess the reliability of size estimates from fluorescence microscopy.
24.	Gonzalez Perez, Alfredo, et al. (author) Cyclodextrin-surfactant complex: A new route in DNA decompaction 2008 In: Biomacromolecules. - : American Chemical Society (ACS). - 1526-4602 .- 1525-7797. ; 9:3, s. 772-775 Journal article (peer-reviewed)abstract In the present work, we show a new approach for decompaction of DNA-cationic surfactant complexes, e.g., lipoplexes, by using beta-cyclodextrin (beta-CD). The DNA decompaction was achieved by dissolving the surfactant aggregates in the complex by making use of the high affinity between the beta-CD and the free surfactant in solution. The results from fluorescence microscopy and adiabatic compressibility measurements indicate that coils and globules do not coexist. The reported procedure using beta-CD is an efficient way to decompact DNA surfactant complexes because the association constant of surfactants with beta-CD is large. The surfactant's interaction with beta-CD is specific and the nonspecific interaction between beta-CD and biological interfaces is small.
25.	Gonzalez Perez, Alfredo, et al. (author) Cyclodextrins in DNA decompaction. 2010 In: Colloids and Surfaces B: Biointerfaces. - : Elsevier BV. - 1873-4367 .- 0927-7765. ; 76:1, s. 20-27 Journal article (peer-reviewed)abstract Individual T4DNA molecules, previously compacted by using a cationic surfactant (cetyltrimethylammonium bromide, CTAB), were successfully decompacted by the addition of an appropriate concentration of either alpha-cyclodextrin or beta-cyclodextrin (alpha-CD and beta-CD, respectively) due to the formation of inclusion complexes with the surfactant. The process was shown to be a non first-order transition from globules to coils. Density and sound velocity measurements as well as steady state fluorescence spectroscopy have confirmed the approximate CD concentration at which the globule-to-coil transition occurs. Phase maps of the DNA-CTA-CD systems were produced and the CTAB concentration range at which decompaction can be achieved was determined. Evidences for DNA-CD interaction were found, however, its nature and influence on the decompaction process was not yet determined.

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