Next generation sequencing analysis reveals a relationship between rDNA unit diversity and locus number in Nicotiana diploids

© 2012 Matyášek et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited

Strange Quark PDFs and Implications for Drell-Yan Boson Production at the LHC

Global analyses of Parton Distribution Functions (PDFs) have provided incisive constraints on the up and down quark components of the proton, but constraining the other flavor degrees of freedom is more challenging. Higher-order theory predictions and new data sets have contributed to recent improvements. Despite these efforts, the strange quark PDF has a sizable uncertainty, particularly in the small x region. We examine the constraints from experiment and theory, and investigate the impact of this uncertainty on LHC observables. In particular, we study W/Z production to see how the s-quark uncertainty propagates to these observables, and examine the extent to which precise measurements at the LHC can provide additional information on the proton flavor structure.Comment: 14 pages, 11 figures, added reference

Usefulness of Ultrahigh Resolution Microstructural Studies for Understanding Localized Corrosion Behavior of Al Alloys

The corrosion behavior of different tempers of two aluminum alloys, AA7050 and an experimental Al–Mg–Cu–Si alloy, was studied in NaCl solution by anodic polarization and scanning electron microscopy and was correlated with differences in the microstructure. Potentiodynamic polarization experiments were performed on samples from the exact sheets used by others to study the microstructure evolution during the early stages of the precipitation sequence by high-resolution characterization tools [i.e., high-resolution transmission electron microscopy and atom probe tomography (APT)]. The usefulness of information from these state-of-the-art tools to lead to a better understanding about the effects of nanoscale segregation on localized corrosion of aluminum alloys is discussed. APT was able to provide information about the composition of the solid solution matrix region between the fine-scale hardening particles, which is not possible by any other technique. Some of the changes in corrosion behavior, e.g., the breakdown potentials, with temper could be rationalized based on changes in the matrix composition. The formation of corrosion-susceptible surface layers on as-polished AA7050 depended on the predominant type of hardening particle. The lack of detailed knowledge of the grain boundary region limited the applicability of the microstructural information generated by previous studies for understanding intergranular corrosion

Oncogenic viruses associated with vulva cancer in HIV-1 patients in Botswana

BACKGROUND: Oncoviruses such as HPV, KSHV, and EBV have been reported in patients with HIV infection and AIDS. How oncovirus-associated cancers rise in AIDS patients has not been fully established. The purpose of our study was to identify the viral agents in vulvar cancer and to assess their contribution to pathogenesis. METHOD: We retrospectively identified a total of 13 vulva tissue samples from HIV-1 positive and 9 vulvar samples from HIV-1 negative patients from the Botswana National Health Laboratory in Gaborone, Botswana, a Southern African country with a high incidence of HIV. We utilized PCR and IHC to identify HPV, EBV, KSHV, and JC virus in FFPE preserved tissue samples. RESULTS: Using the GP5(+)/GP6(+) primer set we detected several HPV types in tissue samples. EBV was detected in all of the positive cases (100%) and in most of the negative cases (89%). KSHV was detected in 39% of the HIV-1 positive samples and in 11% of the negative samples, and no JC virus was detected in any of the samples. Using IHC we demonstrated that LANA was expressed in 61% of the positive samples and in 44% of the negative samples. The ubiquitous EBV was more consistently expressed in negative cases (100%) than in positive cases (69%). Interestingly, the HPV-16 E6 transcript was detected in 56% of the negative samples compared to 31% of the positive samples. However, the cell cycle protein P21 used as a surrogate marker for HPV was detected in 77% of the positive samples and in 44% of the negative samples, while VEGF signals were similar in both positive (92%) and negative samples (89%). CONCLUSION: Our study, suggests that in Botswana, vulvar squamous cell carcinoma (VSCC) is associated with oncogenic viruses present in the niche but the contribution and progression may be regulated by HPV and other immunosuppressive infections that include HIV-1

Astonishing 35S rDNA diversity in the gymnosperm species Cycas revoluta Thunb

17 p., tablas, gráficos.In all eukaryotes, the highly repeated 35S ribosomal DNA (rDNA) sequences encoding 18S-5.8S-26S ribosomal RNA (rRNA) typically show high levels of intragenomic uniformity due to homogenisation processes, leading to concerted evolution of 35S rDNA repeats. Here, we compared 35S rDNA divergence in several seed plants using next generation sequencing and a range of molecular and cytogenetic approaches. Most species showed similar 35S rDNA homogeneity indicating concerted evolution. However, Cycas revoluta exhibits an extraordinary diversity of rDNA repeats (nucleotide sequence divergence of different copies averaging 12 %), influencing both the coding and non-coding rDNA regions nearly equally. In contrast, its rRNA transcriptome was highly homogeneous suggesting that only a minority of genes ( T substitutions located in symmetrical CG and CHG contexts which were also highly methylated. Both functional genes and pseudogenes appear to cluster on chromosomes. The extraordinary high levels of 35S rDNA diversity in C. revoluta, and probably other species of cycads, indicate that the frequency of repeat homogenisation has been much lower in this lineage, compared with all other land plant lineages studied. This has led to the accumulation of methylation-driven mutations and pseudogenisation. Potentially, the reduced homology between paralogs prevented their elimination by homologous recombination, resulting in long-term retention of rDNA pseudogenes in the genome.The work was supported by the Czech Science Foundation (P501/13/10057S and P501/12/G090) and NERC (UK).Peer reviewe

Longitudinal and transverse electron paramagnetic resonance in a scanning tunneling microscope

Electron paramagnetic resonance (EPR) spectroscopy is widely employed to characterize paramagnetic complexes. Recently, EPR combined with scanning tunneling microscopy (STM) achieved single-spin sensitivity with sub-angstrom spatial resolution. The excitation mechanism of EPR in STM, however, is broadly debated, raising concerns about widespread application of this technique. Here, we present an extensive experimental study and modelling of EPR-STM of Fe and hydrogenated Ti atoms on an MgO surface. Our results support a piezoelectric coupling mechanism, in which the EPR species oscillate adiabatically in the inhomogeneous magnetic field of the STM tip. An analysis based on Bloch equations combined with atomic-multiplet calculations identifies different EPR driving forces. Specifically, transverse magnetic-field gradients drive the spin-1/2 hydrogenated Ti, whereas longitudinal magnetic-field gradients drive the spin-2 Fe. Additionally, our results highlight the potential of piezoelectric coupling to induce electric dipole moments, thereby broadening the scope of EPR-STM to nonpolar species and nonlinear excitation schemes