Search

Nucleoid-associated proteins (NAPs) are crucial in organizing prokaryotic DNA and regulating genes. Vital to these activities are complex nucleoprotein structures, however, how these form remains unclear. Integration host factor (IHF) is an Escherichia coli NAP that creates very sharp bends in DNA at sequences relevant to several functions including transcription and recombination, and is also responsible for general DNA compaction when bound non-specifically. We show that IHF–DNA structural multimodality is more elaborate than previously thought, and provide insights into how this drives mechanical switching towards strongly bent DNA. Using single-molecule atomic force microscopy and atomic molecular dynamics simulations we find three binding modes in roughly equal proportions: “associated” (73° of DNA bend), “half-wrapped” (107°) and “fully-wrapped” (147°), only the latter occurring with sequence specificity. We show IHF bridges two DNA double helices through non-specific recognition that gives IHF a stoichiometry greater than one and enables DNA mesh assembly. We observe that IHF-DNA structural multiplicity is driven through non-specific electrostatic interactions that we anticipate to be a general NAP feature for physical organization of chromosomes.

Atomic-level computer simulations are a very useful tool for describing the structure and dynamics of complex biomolecules such as DNA and for providing detail at a resolution where experimental techniques cannot arrive. Molecular dynamics (MD) simulations of mechanically distorted DNA caused by agents like supercoiling and protein binding are computationally challenging due to the large size of the associated systems and timescales. However, nowadays they are achievable thanks to the efficient usage of GPU and to the improvements of continuum solvation models. This together with the concurrent improvements in the resolution of single-molecule experiments, such as atomic force microscopy (AFM), makes possible the convergence between the two. Here we present detailed protocols for doing so: for performing molecular dynamics (MD) simulations of DNA adopting complex three-dimensional arrangements and for comparing the outcome of the calculations with single-molecule experimental data with a lower resolution than atomic.

CDMX is the capital of the country. This town has historically been at risk of subsidence damage to its civil structures due to its foundation. The area began to be populated with settlements in flooded areas for use in crops, followed by the colonization and subsequent drying out of the lake areas that ended up being urbanized. The areas formerly belonging to Lake Texcoco, previously used for cultivation, were drained to expand the developable coverage. As the water demand grew, it became necessary to extract groundwater from the shallow aquifer to supply the growing city. Although the depletion of this aquifer coincides with subsidence areas, previous studies indicate that there is no linear correlation between them. The objective of this project is to collect the different criteria related to the presence of sinkholes (as an effect of subsidence), such as Population and well density, distance to faults, fractures, roads, drainage, elevation and slope of the terrain, the thickness of subsoil clays, the type of rock and soil, the rate of subsidence and the geotechnical zones in the study area. The criteria maps were compared with previous sinkholes mapping registered between the years 2017 to 2019. The statistics consisted of calculating the percentage of coincidence in coverage, categorized linear regression, and the application of logarithms as a normalization method to evaluate its correlation. The statistics consisted of calculating the percentage of coincidence in coverage, categorized linear regression, and the application of logarithms as a normalization method to evaluate its correlation. The most relevant results include the relationship between the sinkholes and the road zones (60%), the highest correlation registered in clays is 0.437 considering areas of competent rock. Although considering the total study site a 0.36 is reached, obtained from applying the logarithm of the clay values ​​and correlating it with the sinkhole areas. 1Facultad de Ingeniería, Colegio de Geofísica, BUAP, Puebla, Mexico 2Laboratorio de Percepción Remota, Departamento de Recursos Naturales, Instituto de Geofísica, UNAM, CDMX, México 3Departamento de Recursos Naturales, Instituto de Geofísica, UNAM, CDMX, México 4Facultad de Ingeniería Civil, Universidad Nacional Autónoma de México, CDMX, México 5Consejo Nacional de Ciencia y Tecnología, Cátedras CONACYT- Instituto de Geofísica, UNAM, CDMX, México 6Facultad de Ingeniería, UNAM, CDMX, México 7Instituto de Geofísica, UNAM, CDMX, México

A major open topic in cuprates is the interplay between the lattice and electronic dynamics and the importance of their coupling to the mechanism of high-temperature superconductivity (HTSC). As evidenced by Extended X-ray Absorption Fine Structure experiments (EXAFS), anharmonic structural effects are correlated with the charge dynamics and the transition to a superconducting phase in different HTSC compounds. Here we describe how structural anharmonic effects can be coupled to electronic and lattice dynamics in cuprate systems by performing the exact diagonalization of a prototype anharmonic many-body Hamiltonian on a relevant six-atom cluster and show that the EXAFS results can be understood as a Kuramoto synchronization between coupled internal quantum tunneling polarons associated with the two-site distribution of the copper-apical-oxygen ($Cu-O_{ap}$) pair in the dynamic structure. Furthermore, we find that this first order, anti-phase synchronization transition can be fine tuned by temperature and anharmonicity of the lattice vibrations, and promotes the pumping of charge, initially stored at the apical oxygen reservoirs, into the copper-oxide planes. Simultaneously, the internal quantum tunneling polaron extends to the copper-planar-oxygen ($Cu-O_{pl}$) pair. All these findings support an interpretation of the EXAFS data in terms of an effective, quantum mechanical triple-well-potential, which accurately represents the anti-phase synchronization of apical oxygens displacements and lattice-assisted charge transfer to the $CuO_2$ plane., 13 pages, 5 figures. Submitted to Physical Review B

In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species., In cells, DNA is arranged into topologically-constrained (supercoiled) structures, but how this supercoiling affects the detailed double-helical structure of DNA remains unclear. Here authors use atomic force microscopy and atomistic molecular dynamics simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution.

The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments and is important for gene regulation and chromosome packing. However, their sequence-dependence and how bulk elastic constants emerge from local fluctuations is less understood. Here, we present SerraNA, which is an open software that calculates elastic parameters of double-stranded nucleic acids from dinucleotide length up to the whole molecule using ensembles from numerical simulations. The program reveals that global bendability emerge from local periodic bending angles in phase with the DNA helicoidal shape. We apply SerraNA to the whole set of 136 tetra-bp combinations and we observe a high degree of sequence-dependence with differences over 200% for all elastic parameters. Tetramers with TA and CA base-pair steps are especially flexible, while the ones containing AA and AT tend to be the most rigid. Thus, AT-rich motifs can generate extreme mechanical properties, which are critical for creating strong global bends when phased properly. Our results also indicate base mismatches would make DNA more flexible, while protein binding would make it more rigid. SerraNA is a tool to be applied in the next generation of interdisciplinary investigations to further understand what determines the elasticity of DNA.

The resistance of DNA to stretch, twist and bend is broadly well estimated by experiments and is important for gene regulation and chromosome packing. However, their sequence-dependence and how bulk elastic constants emerge from local fluctuations is less understood. Here, we present SerraNA, which is an open software that calculates elastic parameters of double-stranded nucleic acids from dinucleotide length up to the whole molecule using ensembles from numerical simulations. The program reveals that global bendability emerge from local periodic bending angles in phase with the DNA helicoidal shape. We also apply SerraNA to the whole set of 136 tetra-bp combinations and we observe a high degree of sequence-dependence for all elastic parameters with differences over 200%. Tetramers with TA and CA base-pair steps are especially flexible, while tetramers containing AA and AT tend to be the most rigid. Our results thus suggest AT-rich motifs generate extreme mechanical properties depending of the exact sequence ordering, which seems critical for creating strong global bendability on longer sequences when phased properly. SerraNA is a tool to be applied in the next generation of interdisciplinary investigations to further understand what determines the elasticity of DNA.Graphical TOC Entry

In the cell, DNA is arranged into highly-organised and topologically-constrained (supercoiled) structures. It remains unclear how this supercoiling affects the detailed double-helical structure of DNA, largely because of limitations in spatial resolution of the available biophysical tools. Here, we overcome these limitations, by a combination of atomic force microscopy (AFM) and atomistic molecular dynamics (MD) simulations, to resolve structures of negatively-supercoiled DNA minicircles at base-pair resolution. We observe that negative superhelical stress induces local variation in the canonical B-form DNA structure by introducing kinks and defects that affect global minicircle structure and flexibility. We probe how these local and global conformational changes affect DNA interactions through the binding of triplex-forming oligonucleotides to DNA minicircles. We show that the energetics of triplex formation is governed by a delicate balance between electrostatics and bonding interactions. Our results provide mechanistic insight into how DNA supercoiling can affect molecular recognition, that may have broader implications for DNA interactions with other molecular species.

This paper introduces the eigensystem realization (ER)-based identification algorithm and the Z-domain method (ZDM) to improve the impedance estimation of transmission lines under fault conditions, which is achieved by removing the exponential decaying DC offset from current signals in distance relays. Both methods effectively work employing a one-cycle rectangular window; specifically, the Z-domain method works in less than a fifth of one-cycle window, ensuring timely, accurate, and prompt estimates. To confirm the effectiveness and performance of the proposed algorithms, they are evaluated under steady-state and dynamic conditions by using time-domain simulations performed in PSCAD©and DIgSILENT©PowerFactory. They also are compared with the well-known discrete Fourier transform (DFT). The attained results indicate that both the ER-based and Z-domain methods can become a powerful tool to reduce the adverse influence of exponentially decaying DC offsets in distance relays.

We formulate the problem of unconventional d − wave superconductivity, with phase fluctuations, pseudogap phenomenon, and local Cooper pairs, in terms of a synchronization problem in random, quantum dissipative, elasto-nuclear oscillator networks. The nodes of the network correspond to localized, collective quadrupolar vibrations of nuclei-like, elastic inhomogeneities embedded in a dissipative medium. Electrons interacting with such vibrations form local Cooper pairs, with a superfluid d − wave pseudogap Δ PG , due to an effective, short range attractive interaction of d x 2 − y 2 character. Phase coherent, bulk superconductivity, with a d − wave gap Δ, is stabilized when the oscillator network is asymptotically entangled in a nearly decoherence-free environment. Phase coherence will in turn be destroyed, at T c , when the thermal noise becomes comparable to the coupling between oscillators, the superfluid density K. The 2Δ/k B T c ratio is a function of Kuramoto’s order parameter, r = 1 − K c / K , for the loss of synchronization at K c , and is much larger than the nonuniversal 2Δ PG /k B T * ratio, where T * is the temperature at which Δ PG is completely destroyed by thermal fluctuations. We discuss our findings in connection to the available data for various unconventionally high-temperature superconductors.

The 20th century surface air temperature (SAT) records of China from various sources are analyzed using data which include the recently released Twentieth Century Reanalysis Project dataset. Two key features of the Chinese records are confirmed: (1) significant 1920s and 1940s warming in the temperature records, and (2) evidence for a persistent multidecadal modulation of the Chinese surface temperature records in co-variations with both incoming solar radiation at the top of the atmosphere as well as the modulated solar radiation reaching ground surface. New evidence is presented for this Sun–climate link for the instrumental record from 1880 to 2002. Additionally, two non-local physical aspects of solar radiation-induced modulation of the Chinese SAT record are documented and discussed. Teleconnections that provide a persistent and systematic modulation of the temperature response of the Tibetan Plateau and/or the tropospheric air column above the Eurasian continent (e.g., 30°N–70°N; 0°–120°E) are described. These teleconnections may originate from the solar irradiance-Arctic–North Atlantic overturning circulation mechanism proposed by Soon (2009). Also considered is the modulation of large-scale land–sea thermal contrasts both in terms of meridional and zonal gradients between the subtropical western Pacific and mid-latitude North Pacific and the continental landmass of China. The Circum-global teleconnection (CGT) pattern of summer circulation of Ding and Wang (2005) provides a physical framework for study of the Sun–climate connection over East Asia. Our results highlight the importance of solar radiation reaching the ground and the concomitant importance of changes in atmospheric transparency or cloudiness or both in motivating a true physical explanation of any Sun–climate connection. We conclude that ground surface solar radiation is an important modulating factor for Chinese SAT changes on multidecadal to centennial timescales. Therefore, a comprehensive view of local and remote factors of climate change in China must take account of this as well as other natural and anthropogenic forcings.

The direct impact of solar activity on climate has been widely studied through Total Solar Irradiance (TSI). Biological processes also impact climate and are deeply affected by TSI. Marine phytoplankton emissions into the atmosphere have been proposed to change cloud albedo through cloud formation. In this work, we use wavelet analysis to investigate the decadal relation between high-latitude concentrations of methane sulphonic acid, a product of seawater algae, and TSI. We found that some of the methane sulphonic acid main periodicities coincide with periods of solar activity periods.

A novel series of linear, high-molecular-weight polymers was synthesized by one-pot, superacid-catalyzed reaction of pentafluorobenzaldehyde (PFBA) (1) with nonactivated aromatic hydrocarbons: biphenyl, diphenyl ether, p-terphenyl, 4,4′-diphenoxybenzophenone, and 1,3-bis- and 1,4-bis(4′-phenoxybenzoyl)benzenes. The reactions were performed at room temperature in the Bronsted superacid trifluoromethanesulfonic acid (CF3SO3H, TFSA) and in a mixture of TFSA with methylene chloride. The polymer-forming reaction was highly dependent upon the acidity of the reaction medium, as judged from the molecular weights of the polymers obtained. A possible reaction mechanism is suggested. The polymers obtained were soluble in the common organic solvents, and flexible transparent films could be cast from the solutions. 1H and 13C NMR analyses of the polymers synthesized revealed their linear structure. The pendent pentafluorophenyl groups react regioselectively with nucleophiles under basic conditions in polar, aprotic so...

Using unprecedented catalogues of past severe drought data for the Yucatan Peninsula between 1502 and 1900 coming from historical written documentation, we identified five conspicuous time lapses with no droughts between 1577–1647, 1662–1724, 1728–1764, 1774–1799 and 1855–1880, as well as time epochs with most frequent droughts between 1800 and 1850. Moreover, the most prominent periodicity of the historical drought time series was that of ∼40 years. Using the Palmer Drought Severity Index for the Yucatan Peninsula for the period 1921–1987 we found prominent negative phases between ∼1942–1946 and 1949–1952, 1923–1924, 1928–1929, 1935–1936, 1962–1963, 1971–1972 and 1986–1987. Two prominent periodicities clearly appear at ∼5 and 10 years. Most modern and historical severe droughts lasted 1 year, and share a quasi-decadal frequency. Also, in the first 66 years of the twentieth century the frequency of occurrence of severe drought has been lower compared with the nineteenth century. Some of the major effects and impacts of the most severe droughts in the Yucatan region are examined. We also studied the relation between historical and modern droughts and several large scale climate phenomena represented by the Atlantic Multidecadal Oscillation (AMO) and the Southern Oscillation Index (SOI). Our results indicate that historical droughts and the cold phase of the AMO coincide, while the influence of the SOI is less clear. The strongest coherence between historical droughts and AMO occurred at periodicities of ∼40 years. For modern droughts the coherence of a drought indicator (the Palmer Drought Severity Index) is similar with AMO and SOI, although it seems more sustained with the AMO. They are strongest at ∼10 years and very clearly with the AMO cold phase. Concerning the solar activity proxies and historical droughts, the coherence with a record of beryllium isotope Be10, which is a good proxy of cosmic rays, is higher than with Total Solar Irradiance. We notice that the strongest coherence between historical droughts and Be10 occurs at periods ∼60–64 years. When studying modern droughts and solar activity, frequencies of ∼8 years appear, and the coherences are similar for both sunspots and cosmic rays. Comparing natural terrestrial and solar phenomena, we found that the most sustained and strongest modulation of historical drought occurrence is at ∼60–64 years and is between the historical drought series and the solar proxy Be10. For modern droughts we notice that the coherence is similar among AMO, SOI and the solar indices. We can conclude that the sea surface temperatures (AMO) and solar activity leave their signal in terms of severe droughts in the Maya lands, however in the long term, the influence of the SOI on this type of phenomenon is less clear.

A series of novel, linear, soluble, high-molecular-weight, fluorinated aromatic polymers has been obtained for the first time using a superacid-catalyzed polyhydroxyalkylation reaction of fluorinated carbonyl-containing compounds: 1,1,1,-trifluoroacetone (1), 2,2,2-trifluoroacetophenone (2), 2,3,4,5,6,-pentafluorobenzaldehyde (3), and octafluoroacetophenone (4) with aromatic hydrocarbons such as biphenyl (a), phenyl ether (b), terphenyl (c), and 4,4'-diphenoxybenzophenone (d). These Friedel-Crafts-type aromatic electrophilic substitution reactions are performed at room temperature in trifluoromethane sulfonic acid or in its mixtures with dichloromethane. The polymers obtained are soluble in common organic solvents, and colorless transparent films could be cast from the solutions. 1 H and 13 C NMR analyses of the polymers synthesized reveal their linear, highly regular structure. The polymers also possess high thermostability.

A catalog containing an unprecedented amount of historical data in the southeastern part of Mexico covering almost four centuries (1502–1899) is used to construct a drought time series. The catalog records information of agricultural disasters and includes events associated with hydrometeorological phenomena or hazards whose effects were mainly felt in the agricultural sector, such as droughts. An analysis of the historical series of droughts in southeastern Mexico for the period 1502–1899 is performed. The highest drought frequency occurred around the years 1650, 1782, and 1884; no droughts were reported around 1540, between 1630 and 1640, along the largest time lapse of 1672–1714, and between 1740 and 1760. From 1760 until the end of the period of study droughts definitively occur more often than they did from ∼1550 to 1760. In addition, most droughts lasted for 1–2 yr. Analyzing the frequencies of the drought time series it is found that the most conspicuous cycles are ∼3–4 and 7 yr, although cycles of ∼12, 20, 43, and 70 yr are also evident. The relation between droughts and El Niño events indicates that 38% of droughts are associated with El Niño. Sea surface temperature changes, the Southern Oscillation index, and solar activity leave their signals in the southeastern part of Mexico, with the signs in Oaxaca clearer than in the Yucatan Peninsula. However, the dominance of some phenomena over others depends on the time scales considered.

A catalog containing an unprecedented amount of historical data in central Mexico, covering almost six centuries (1450–1900), is used. This is a catalog of agricultural disasters that includes events associated with hydrometeorological phenomena, or hazards, whose effects were mainly felt in the agricultural sector, such as droughts. An analysis of the historical series of droughts in central Mexico for the period of 1450–1900 is performed. Periods of frequent drought centered at the years 1483, 1533, 1571, 1601, 1650, 1691, 1730, 1783, 1818, and 1860 have been identified. In particular, droughts in Mexico City and northwest Mexico that were identified through poor tree-ring growth are included in the frequent drought periods obtained in this work. Moreover, it was found that droughts occurred in El Niño years mainly for events of very strong and strong strengths, at a significant level. Also, most droughts lasted for 1 or 2 yr. Last, by analyzing the periodicities of the drought time series it was found that those that are the most conspicuous are the quasi-bidecadal frequencies of 18.9 and 21 yr.

The measurement of solar B band Ultraviolet radiation (UVB) should be considered a priority in Mexico due to implications on public health throughout the country (total population, 108 million), but this is not carried out at present. Installed sensors cover only 0.12% of the country. However, there are alternative methods for estimating UVB radiation to overcome the lack of surface data. The most successful of these are based on the use of satellites for environmental monitoring. In the present work, UVB maps are constructed for the entire country using a single, daily satellite measurement of UVB at solar noon from 1978-2003. Satellite-derived values are compared with the ground measurements by a surface station located in Mexico City in order to validate the former. Wavelet spectrum analysis is employed to this end. A close correlation is observed between the two sets of data. Moreover, there is qualitative correspondence between the spatial distribution of the satellite-derived data and the surface topography. The difference resulting throughout the period mentioned is

The coating process, of optic-fibers into a polymer matrix is a very difficult and delicate process due to the fragility of the fibers, which can get broken by the stresses and temperature imposed during processing. In this paper we introduce a new control system which is based on measurement of specific power changes in the laser transmitted signal thought the fiber. Those changes are produced by mechanical or thermal stresses on the fiber during processing. Those stresses normally generated by photoelastic effects on the fiber when it is pulled or heated, changing its optical properties. By a meticulous characterization of those effects we are able to establish a real time control system for the coating process, avoiding the deformation or even breaking of the fiber during coating.

There is a limited experience with catheter ablation for treatment of ventricular tachycardia (VT) in Chagasic cardiomyopathy. A 30-year-old woman experienced episodes of palpitations and syncope due to attacks of VT. A diagnosis of Chagas disease was established on a biological basis. Two-dimensional echo and contrast ventriculography showed an apical aneurysm with thrombus. Surgery was indicated to resect the aneurysm and ablate the VT. Ventricular tachycardia recurred 1 month later despite therapy, including amiodarone. Two clinical frequent and well-tolerated tachycardias were identified. The site of origin was located in the right ventricular apex and in the apical-lateral wall of the left ventricle, respectively. Catheter ablation was performed at two sites with DC shocks (total energy 600 J) after unsuccessful radiofrequency ablation. Holter recordings performed during the post-operative period showed only infrequent extrasystoles. After follow-up of 24 months the patient remains asymptomatic. Drug-refractory VT in Chagasic cardiomyopathy can be ablated by medium-energy DC shocks after failure of radiofrequency ablation.

Background: Chagas disease is a chronic parasitic infection whose pathogenesis is related to parasite persistence and a dysfunctional cellular immune response. There is no method to determine the pool of antigen-specific T cells in Trypanosoma cruzi-infected patients. Thus, the goal of this work was to determine the fraction of antigen-specific T cells by measuring the expression of CD154 and membrane TNFα on the bulk of parasite-stimulated PBMCs. Methodology: Twenty-one chagasic patients (CP), 11 healthy controls (HC) and 5 non-chagasic individuals with chronic heart disease (NCC) were analyzed. PBMCs were incubated in the presence of anti-CD28, anti-CD49d, anti-TNFα and TACE inhibitor as follows: non stimulus, T. cruzi-lysate or SEB. Later, the samples were stained for CD3, CD4, CD8 and CD154 and analyzed by flow cytometry. Results: Symptomatic (3.07%, SD ±1.98) and asymptomatic CP (1.24 ±0.59) displayed higher frequencies of CD4+/CD154+ cells after incubation with T. cruzi-lysate in comparison with NCC (0.084 ±0.03) and HC (0.11 ±0.08) donors P

Background: Trypanosoma cruzi persistence has been associated with cardiac and gastrointestinal tissue damage in nearly 30% of the infected individuals; however, the pathogenic mechanisms are yet unknown. This study’s goal was to compare the activation status and proliferative capacity of T lymphocytes among chronic chagasic patients and uninfected controls. Methodology: Twenty-seven chronic chagasic patients, 20 healthy individuals and 28 non-chagasic cardiomyopathy donors were analyzed. Peripheral blood cells were stained with CD3, CD4, CD8, CD28, HLA-DR and CD38. PBMCs were labeled with CFSE and co-cultivated with PHA or T. cruzi lysate; at the fifth day post-stimulation cells were stained for CD3, CD4 and CD8. Results: Chagasic patients displayed higher frequencies of CD4+ (P=0.0001) and CD8+ (P=0.0002) T cells co-expressing HLA-DR and CD38 in comparison with healthy and non-chagasic cardiomyopathy donors. Also, the former group exhibited lower percentages of CD8+/CD28+ T lymphocytes (P=0.0005). After 5 days of stimulation, the proliferation index was lower in both CD4+ (P=0.01) and CD8+ (P=0.04) PHA-stimulated T cells from chagasic donors when compared with both control groups. Conclusions: Despite their increased activation status, the T lymphocytes from chagasic donors displayed reduced proliferative capacity after mitogenic stimulation, corroborating a dysfunctional cellular immune response in the chronic stages of the disease.