Hydrogen Bonding in DNA Base Pairs: Reconciliation of Theory and Experiment

Up till now, there has been a significant disagreement between theory and experiment regarding hydrogen bond lengths in Watson - Crick base pairs. To investigate the possible sources of this discrepancy, we have studied numerous model systems for adenine - thymine (AT) and guanine - cytosine (GC) base pairs at various levels (i.e., BP86, PW91, and BLYP) of nonlocal density functional theory (DFT) in combination with different Slater-type orbital (STO) basis sets. Best agreement with available gas-phase experimental A - T and G - C bond enthalpies (-12.1 and -21.0 kcal/mol) is obtained at the BP86/TZ2P level, which (for 298 K) yields -11.8 and -23.8 kcal/mol. However, the computed hydrogen bond lengths show again the notorious discrepancy with experimental values. The origin of this discrepancy is not the use of the plain nucleic bases as models for nucleotides: the disagreement with experiment remains no matter if we use hydrogen, methyl, deoxyribose, or 5'- deoxyribose monophosphate as the substituents at N9 and N1 of the purine and pyrimidine bases, respectively. Even the BP86/DZP geometry of the Watson- Crick-type dimer of deoxyadenylyl-3',5'-deoxyuridine including one N

Mutations in SRY and WT1 genes required for gonadal development are not responsible for XY partial gonadal dysgenesis

The WT1 transcription factor regulates SRY expression during the initial steps of the sex determination process in humans, activating a gene cascade leading to testis differentiation. In addition to causing Wilms' tumor, mutations in WT1 are often responsible for urogenital defects in men, while SRY mutations are mainly related to 46,XY pure gonadal dysgenesis. In order to evaluate their role in abnormal testicular organogenesis, we screened for SRY and WT1 gene mutations in 10 children with XY partial gonadal dysgenesis, 2 of whom with a history of Wilms' tumor. The open reading frame and 360 bp of the 5' flanking sequence of the SRY gene, and the ten exons and intron boundaries of the WT1 gene were amplified by PCR of genomic DNA. Single-strand conformation polymorphism was initially used for WT1 mutation screening. Since shifts in fragment migration were only observed for intron/exon 4, the ten WT1 exons from all patients were sequenced manually. No mutations were detected in the SRY 5' untranslated region or within SRY open-reading frame sequences. WT1 sequencing revealed one missense mutation (D396N) in the ninth exon of a patient who also had Wilms' tumor. In addition, two silent point mutations were found in the first exon including one described here for the first time. Some non-coding sequence variations were detected, representing one new (IVS4+85A>G) and two already described (-7ATG T>G, IVS9-49 T>C) single nucleotide polymorphisms. Therefore, mutations in two major genes required for gonadal development, SRY and WT1, are not responsible for XY partial gonadal dysgenesis.172

226Ra, 228Ra and 40K as tracers of erosion and accumulation processes: A 3-year study on a beach with different sediment dynamics

The aim of this study is to analyse the role of natural radionuclides 226Ra, 228Ra, 40K and unsupported 210Pb (210Pbex), as erosion and accumulation process tracers. For this purpose, a complex system, including both the characteristic dynamics of a closed beach and those associated with a beach open to wave action, was studied. A 3-year study of monthly variation of 226Ra, 228Ra, 40K and 210Pbex was carried out at Las Canteras beach, on the Island of Gran Canaria (Spain), covering several erosion and accumulation periods. A correlation analysis, ANOVA test and Tukey’s Honestly Significant Difference (HSD) Test proved that the marine erosion and accumulation agents influenced the activity concentration values found for the different radionuclides. Moreover, the geochemical analysis of samples from maximum and minimum activity concentration values showed that the natural radionuclides studied could be suitable tracers for studying beach sediment dynamics in erosion and accumulation periods

An accurate record of volcanic ash fall deposition as characterized by dispersed organic matter in a Lower Permian tonstein bed (Faxinal Coalfield, Paraná Basin, Brazil)

For the first time, the dispersed organic matter in the tonstein layer interbedded with a coal seam in the Faxinal Coalfield (Sakmarian, Southern Paraná Basin, Brazil) is characterized. The deposition of clusters of pollen grains was highly influenced by the intense ash fall process that probably occurred during seasonal dehiscence of reproductive structures. The well-preserved phytoclasts with their upper and lower leaf cuticles stuck together indicate that the rapid fall of ash on this material hindered organic biodegradation. The preservation of seemingly autochthonous Botryococcus colonies at the top of the tonstein layer is evidence of the subaqueous deposition of this layer. The darkening in cuticles and xylem phytoclasts can be attributed to different causes: the thermal influence of ash fall during deposition, chemical effects of the ash, prolonged oxidation of organic matter in low water level conditions or the burning of plant organs by wildfires. Analyses of dispersed organic matter along the tonstein layer showed that the organic matter succession reflects the composition of different plant strata (herbaceous pteridophytes and arboreal glossopterids-cordaitaleans) around the deposition site

An accurate record of volcanic ash fall deposition as characterized by dispersed organic matter in a lower Permian tonstein layer (Faxinal Coalfield, Paraná Basin, Brazil)

For the first time, the dispersed organic matter in the tonstein layer interbedded with a coal seam in the Faxinal Coalfield (Sakmarian, Southern Paraná Basin, Brazil) is characterized. The deposition of clusters of pollen grains was highly influenced by the intense ash fall process that probably occurred during seasonal dehiscence of reproductive structures. The well-preserved phytoclasts with their upper and lower leaf cuticles stuck together indicate that the rapid fall of ash on this material hindered organic biodegradation. The preservation of seemingly autochthonous Botryococcus colonies at the top of the tonstein layer is evidence of the subaqueous deposition of this layer. The darkening in cuticles and xylem phytoclasts can be attributed to different causes: the thermal influence of ash fall during deposition, chemical effects of the ash, prolonged oxidation of organic matter in low water level conditions or the burning of plant organs by wildfires. Analyses of dispersed organic matter along the tonstein layer showed that the organic matter succession reflects the composition of different plant strata (herbaceous pteridophytes and arboreal glossopterids-cordaitaleans) around the deposition site

Prostatic cyst: An unusual cause of hemospermia

AbstractA 31-year-old man was referred to our service because of recurrent hemospermia over the last 4 years, there were no other symptoms like perineal pain, fever, dysuria, nocturia or urgency; this patient only presented hemospermia with clots. Genital examination was normal. Semen analysis showed no change in volume and pH; however, hemospermia and asthenozoospermia were observed. The semen culture was normal. Ultrasonography only revealed the presence of a cystic lesion adjoining the prostate gland, next to the bladder neck. The retrograde urethrogram was normal. The CT scan revealed only a small calcification in the right seminal vesicle. Endoscopic cistourethroscopy demonstrated 2 cystic dilatations arising on both sides of the prostate gland adjacent to the bladder neck, behind the verumontanum with vessels running over the surface prostatic cyst dilatation. The diagnosis of prostatic gland cystic dilatation was reached and confirmed by pathology that reported fibroconnective tissue with fibrosis and hyalinization. Transurethral unroofing of the cyst was performed separately with a successful outcome

Estimating the uncertainties of strain and damage analysis by X-ray diffraction in ion implanted MoO3

N/

Metastable liquid lamellar structures in binary and ternary mixtures of Lennard-Jones fluids

We have carried out extensive equilibrium molecular dynamics (MD) simulations to investigate the Liquid-Vapor coexistence in partially miscible binary and ternary mixtures of Lennard-Jones (LJ) fluids. We have studied in detail the time evolution of the density profiles and the interfacial properties in a temperature region of the phase diagram where the condensed phase is demixed. The composition of the mixtures are fixed, 50% for the binary mixture and 33.33% for the ternary mixture. The results of the simulations clearly indicate that in the range of temperatures $78 < T < 102 ^{\rm o}$K, --in the scale of argon-- the system evolves towards a metastable alternated liquid-liquid lamellar state in coexistence with its vapor phase. These states can be achieved if the initial configuration is fully disordered, that is, when the particles of the fluids are randomly placed on the sites of an FCC crystal or the system is completely mixed. As temperature decreases these states become very well defined and more stables in time. We find that below $90 ^{\rm o}$K, the alternated liquid-liquid lamellar state remains alive for 80 ns, in the scale of argon, the longest simulation we have carried out. Nonetheless, we believe that in this temperature region these states will be alive for even much longer times.Comment: 18 Latex-RevTex pages including 12 encapsulated postscript figures. Figures with better resolution available upon request. Accepted for publication in Phys. Rev. E Dec. 1st issu

Modeling DNA Structure, Elasticity and Deformations at the Base-pair Level

We present a generic model for DNA at the base-pair level. We use a variant of the Gay-Berne potential to represent the stacking energy between neighboring base-pairs. The sugar-phosphate backbones are taken into account by semi-rigid harmonic springs with a non-zero spring length. The competition of these two interactions and the introduction of a simple geometrical constraint leads to a stacked right-handed B-DNA-like conformation. The mapping of the presented model to the Marko-Siggia and the Stack-of-Plates model enables us to optimize the free model parameters so as to reproduce the experimentally known observables such as persistence lengths, mean and mean squared base-pair step parameters. For the optimized model parameters we measured the critical force where the transition from B- to S-DNA occurs to be approximately $140{pN}$. We observe an overstretched S-DNA conformation with highly inclined bases that partially preserves the stacking of successive base-pairs.Comment: 15 pages, 25 figures. submitted to PR