DNA Conformational Changes and Phase Transitions Induced by Tension and Twist

DNA is a double stranded helical molecule with an intrinsic right handed twist. Its structure can be changed by applying forces and torques in single molecule experiments. In these experiments DNA has been seen to form super-helical structures (supercoils), collapse into tightly condensed states (toroids) and undergo structural changes (phase transitions). Our work focuses on studying all these phenomena by accounting for DNA elasticity, entropic effects due to thermal fluctuations and electrostatics. First, we study the DNA compaction problem in super-helices and toroidal structures. To do so we combine a fluctuating elastic rod model of DNA with electrostatic models for DNA-DNA interactions. Our models are able to predict the onset of the transition to supercoils and toroids under a wide range of experimental conditions. Next, we address DNA phase changes in the presence of mechanical loads.A phenomenon well known from experiments is the overstretching transition associated with the sudden change of DNA extension at high tensions. Depending on the ionic concentration, temperature and pulling rate, DNA can either transform into a melted state (inner strand separation) or S-DNA. Motivated by this, we study the equilibrium and kinetics of the DNA overstretching transitions making use of a quartic potential and non-gaussian integrals to evaluate the free energy of the system. We find that the cooperativity of the transition is a key variable that characterizes the overstretched state. In a separate study we make use of a heterogeneous fluctuating rod model to examine the hypothesis that a newly discovered left-handed form called L-DNA is a mixture of two relatively well-characterized DNA phases - S-DNA and Z-DNA. L-DNA is stable at high tensions and negative twist. We show that if the idea of a mixed state is correct, then the content of S-DNA and Z-DNA varies as a function of the ionic concentration. Finally, we also use our fluctuating rod model to study the mechanical properties of drug-DNA complexes. We show that our methods can predict the results of experiments from various labs if we use only one set of experiments to fit the data to our model

A ~ 12 kpc HI extension and other HI asymmetries in the isolated galaxy CIG 340 (IC 2487)

HI kinematic asymmetries are common in late-type galaxies irrespective of environment, although the amplitudes are strikingly low in isolated galaxies. As part of our studies of the HI morphology and kinematics in isolated late-type galaxies we have chosen several very isolated galaxies from the AMIGA sample for HI mapping. Here we present GMRT 21-cm HI line mapping of CIG 340 which was selected because its integrated HI spectrum has a very symmetric profile, Aflux = 1.03. Optical images of the galaxy hinted at a warped disk in contrast to the symmetric integrated HI spectrum profile. Our aim is to determine the extent to which the optical asymmetry is reflected in the resolved HI morphology and kinematics. GMRT observations reveal significant HI morphological asymmetries in CIG 340 despite it's overall symmetric optical form and highly symmetric HI spectrum. The most notable HI features are: 1) a warp in the HI disk (with an optical counterpart), 2) the HI north/south flux ratio = 1.32 is much larger than expected from the integrated HI spectrum profile and 3) a ~ 45" (12 kpc) HI extension, containing ~ 6% of the detected HI mass on the northern side of the disk. We conclude that in isolated galaxies a highly symmetric HI spectrum can mask significant HI morphological asymmetries. The northern HI extension appears to be the result of a recent perturbation (10^8 yr), possibly by a satellite which is now disrupted or projected within the disk. This study provides an important step in our ongoing program to determine the predominant source of HI asymmetries in isolated galaxies. For CIG 340 the isolation from major companions, symmetric HI spectrum, optical morphology and interaction timescales have allowed us to narrow the possible causes the HI asymmetries and identify tests to further constrain the source of the asymmetries.Comment: 10 page

Highly perturbed molecular gas in infalling cluster galaxies : the case of CGCG97-079

Date of Acceptance: 14/07/2015We report on CO (J = 2 → 1) mapping with the IRAM 30-m HEtrodyne Receiver Array (HERA) of CGCG 97-079, an irregular galaxy in the merging galaxy cluster Abell 1367 (z = 0.022). We find that ˜80 per cent of the detected CO (J = 2 → 1) is projected within a 16 arcsec2 (6.5 kpc2) region to the north and west of the optical/NIR centre, with the intensity maximum offset ˜10 arcsec (4 kpc) NW of the optical/NIR centre and ˜7 arcsec (3 kpc) south-east of the H I intensity maximum. Evolutionary synthesis models indicate CGCG 97-079 experienced a burst of star formation ˜108 yr ago, most likely triggered by a tidal interaction with CGCG 97-073. For CGCG 97-079 we deduce an infall velocity to the cluster of ˜1000 km s-1 and moderate ram pressure (Pram ≈ 10-11 dyne cm-2). The observed offset in CGCG 97-079 of the highest density H I and CO (J = 2 → 1) from the stellar components has not previously been observed in galaxies currently undergoing ram pressure stripping, although previous detailed studies of gas morphology and kinematics during ram pressure stripping were restricted to significantly more massive galaxies with deeper gravitational potential wells. We conclude the observed cold gas density maxima offsets are most likely the result of ram pressure and/or the high-speed tidal interaction with CGCG 97-073. However ram pressure stripping is likely to be playing a major role in the perturbation of lower density gas.Peer reviewe

Características morfológicas e histológicas de los ovarios de dos grupos genéticos de cuyes (Cavia porcellus) de América del Sur

This study aimed to describe morphological and histological characteristics of ovaries of two genetic groups of guinea pigs from Latin America. Ovaries from 20 improved and 20 native guinea pigs were collected after slaughtering. One ovary from each animal was weighed, measured, counted for visible follicles on the ovarian surface, and used for subsequent oocyte collection by the slicing method. Contralateral ovaries were used to prepare histological sections and quantify follicles. Body and ovary weight and ovary length were significantly greater in improved than in native guinea pigs (p<0.01). Ovarian weight was greater in diestrus than in proestrus (p=0.0632) only in improved animals. The number of primordial, primary, secondary, and total follicles did not differ between genetic groups. The number of antral follicles was significantly greater in improved than in native guinea pigs. The thickness of zona pellucida and oocyte diameter did not differ between groups. The thickness of the zona pellucida was significantly greater in oocytes of category A than B and C in both groups of guinea pigs. In conclusion, ovaries from improved guinea pigs were heavier and longer than those from native animals. The number of antral follicles was greater in improved than native guinea pigs. Zona pellucida thickness and oocyte diameter were similar in both groups of guinea pigs.El estudio tuvo como objetivo describir las características morfológicas e histológicas de los ovarios de dos grupos genéticos de cuyes de América Latina. Se recolectaron ovarios de 20 cuyes mejorados y 20 nativos después del sacrificio. Se pesó y midió un ovario de cada animal, se contaron los folículos visibles en la superficie ovárica y se colectaron los ovocitos mediante cortes seriados de la corteza ovárica. Los ovarios contralaterales se utilizaron para preparar cortes histológicos y cuantificar los folículos. El peso corporal y la longitud y peso de los ovarios fueron significativamente mayores en los cuyes mejorados que en los nativos (p<0.01). El peso de los ovarios fue mayor en diestro que en proestro (p=0.0632) en los animales mejorados. El número de folículos primordiales, primarios, secundarios y totales no difirió entre los grupos genéticos. El número de folículos antrales fue significativamente mayor en los cuyes mejorados que en los nativos. El grosor de la zona pelúcida y el diámetro de los ovocitos no difirieron entre los grupos. El grosor de la zona pelúcida fue significativamente mayor en los ovocitos de la categoría A que en los de la B y C en ambos grupos de cuyes. En conclusión, los ovarios de los cuyes mejorados fueron más pesados y largos que los de los animales nativos. El número de folículos antrales fue mayor en los cutes mejorados que en los nativos. El grosor de la zona pelúcida y el diámetro de los ovocitos fueron similares en ambos grupos de cuyes

Follicle Wave and Natural Estrus Synchronization Superovulation in Holstein Cows.

The effects of two superovulation protocols were compared (synchronization of the follicle wave SFW and natural estrus  NE) in embryos collected from Holstein cows. Twenty cows were chosen as donors, body condition of 2.75  -3.5; between 40 and 60 months, with normal cycles and no breeding problems. The cows were randomly assigned to SFW treatment (n=10), and the NE treatment (n=10). The SFW group was synchronized with intravaginal progester-one plus estradiol  benzoate, on day 0, and increasing doses  of FSH for 4 days, twice a day, from  the 4th on. The im-plant was removed on the 6thday, and prostaglandin was applied. On the 8th day, insemination was made at 6 am and 6 pm. The NE group received  increasing doses of FSH twice a day, during 4 days, from the 10th day. On the 12th day prostaglandin was administered, and insemination took place on the 14th day, at 6 am and 6 pm.  The em-bryos were recovered from the two groups without surgery, 7 days after the first artificial insemination. The values of embryos for transference were 5.7 + 0.76 and 2.8 + 0.31 (P < 0.05) for SFW and NE, respectively

Assessment of two Superovulation Protocols for Embryo Production in Holstein Cows

The aim of this paper was to compare the effects of two superovulation protocols (synchronization of the follicular wave (SFW), and natural estrus (NE) induction of embryos produced for transference in Holstein cows. Twenty cows were chosen as donors, with a body condition (BC) of 2.75-3.5; 40-60 months old; 1-2 previous gestation services, and without reproductive problems. Two superovulation protocols were applied: SFW and NE. SFW was not observed to produce more embryos than NE in the blastocysts and morula stages

Efecto de la adición de melatonina en el medio de maduración y/o vitrificación de ovocitos sobre la producción in vitro de embriones bovinos

The effect of the addition of melatonin (Mt) on the maturation and / or vitrification of bovine oocytes on cleavage and subsequent embryonic development was evaluated. Oocyte-cumulus cell complexes (COCs) were obtained from creole cows by ovum pick up (OPU) and by follicular aspiration from abattoir ovaries (AO). From the pool of oocytes obtained from both sources, those with homogenous cytoplasm and three or more compact layers of cluster cells were selected. The selected COCs were randomly assigned to five treatments: T1, matured with Mt and vitrified without Mt; T2, matured and vitrified with Mt; T3, matured without Mt and vitrified with Mt; T4 (control) matured and vitrified without Mt; T5, matured without Mt and not vitrified. The concentration of Mt in the maturation and vitrification media was 0.01 μM (10-9 M). The oocytes were matured, vitrified, fertilized and the presumed zygotes cultured until day 7 post-fertilization in vitro. The data were analysed by logistic regression. Regardless of the origin of the oocytes, cleavage rate (C) and embryo production (EP) was similar between treatments. The C in the OPU oocytes was greater in T4, and the EP was similar between treatments. In AO, the results did not vary between treatment in C and EP. In conclusion, Mt reduced the C in oocytes collected by OPU, while it did not affect EP. In the AO oocyte source, the addition of Mt did not affect the C nor the EP.Se evaluó el efecto de la adición de melatonina (Mt) en el medio de maduración y/o de vitrificación de ovocitos bovinos sobre clivaje y posterior desarrollo embrionario. Los complejos ovocito-células del cúmulo (COCs) fueron obtenidos de vacas criollas mediante la técnica de aspiración transvaginal guiada por ultrasonografía (OPU) y de ovarios de matadero (OM). Del pool de ovocitos obtenidos de ambas fuentes se seleccionaron los que tenían citoplasma homogéneo y tres o más capas compactas de células del cúmulo. Los COCs seleccionados fueron asignados aleatoriamente a cinco tratamientos: T1, madurados con Mt y vitrificados sin Mt; T2, madurados y vitrificados con Mt; T3, madurados sin Mt y vitrificados con Mt; T4 (control) madurados y vitrificados sin Mt; T5, madurados sin Mt y no vitrificados. La concentración de Mt en los medios de maduración y vitrificación fue de 0.01 μM (10-9 M). Los ovocitos fueron madurados, vitrificados, fecundados y los presuntos cigotos cultivados hasta el día 7 pos-fecundación in vitro. Los datos fueron analizados por regresión logística. Independientemente del origen de los ovocitos, el porcentaje de clivaje (PC) y de producción de embriones (PIV) fue similar entre tratamientos. El PC en los ovocitos de OPU fue mayor en T4, y la PIV fue similar entre tratamientos. En los de OM, los resultados no variaron entre tratamiento en PC y PIV. En conclusión, la Mt redujo el PC en ovocitos colectados por OPU, mientras que no afectó la PIV. En los colectados de OM la adición de Mt no afectó el PC ni la PI