Quantitative Electron-Excited X-ray Microanalysis With Low-Energy L-shell X-ray Peaks Measured With Energy-Dispersive Spectrometry.

Quantification of electron-exited X-ray spectra following the standards-based "k-ratio" (unknown/standard intensity) protocol with corrections for "matrix effects" (electron energy loss and backscattering, X-ray absorption, and secondary X-ray fluorescence) is a well-established method with a record of rigorous testing and extensive experience. Two recent studies by Gopon et al. working in the Fe­Si system and Llovet et al. working in the Ni­Si system have renewed interest in studying the accuracy of measurements made using L-shell X-ray peaks. Both have reported unexpectedly large deviations in analytical accuracy when analyzing intermetallic compounds when using the low photon energy Fe or Ni L-shell X-ray peaks with pure element standards and wavelength-dispersive X-ray spectrometry. This study confirms those observations on the Ni-based intermetallic compounds using energy-dispersive X-ray spectrometry and extends the study of analysis with low photon energy L-shell peaks to a wide range of elements, Ti to Se. Within this range of elements, anomalies in analytical accuracy have been found for Fe, Co, and Ge in addition to Ni. For these elements, the use of compound standards instead of pure elements usually resulted in significantly improved analytical accuracy. However, compound standards do not always provide satisfactory accuracy as is demonstrated for L-shell peak analysis in the Fe­S system: FeS and FeS2 unexpectedly do not provide good accuracy when used as mutual standards.

Structural Insights into the Specificity of 8-Oxo-7,8-dihydro-2'-deoxyguanosine Bypass by Family X DNA Polymerases.

8-oxo-guanine (8OG) is a common base lesion, generated by reactive oxygen species, which has been associated with human diseases such as cancer, aging-related neurodegenerative disorders and atherosclerosis. 8OG is highly mutagenic, due to its dual-coding potential it can pair both with adenine or cytidine. Therefore, it creates a challenge for DNA polymerases striving to correctly replicate and/or repair genomic or mitochondrial DNA. Numerous structural studies provide insights into the mechanistic basis of the specificity of 8OG bypass by DNA polymerases from different families. Here, we focus on how repair polymerases from Family X (Pols ß, λ and µ) engage DNA substrates containing the oxidized guanine. We review structures of binary and ternary complexes for the three polymerases, which represent distinct steps in their catalytic cycles-the binding of the DNA substrate and the incoming nucleotide, followed by its insertion and extension. At each of these steps, the polymerase may favor or exclude the correct C or incorrect A, affecting the final outcome, which varies depending on the enzyme.

DNA polymerase mu: An inflexible scaffold for substrate flexibility.

DNA polymerase µ is a Family X member that participates in repair of DNA double strand breaks (DSBs) by non-homologous end joining. Its role is to fill short gaps arising as intermediates in the process of V(D)J recombination and during processing of accidental double strand breaks. Pol µ is the only known template-dependent polymerase that can repair non-complementary DSBs with unpaired 3´primer termini. Here we review the unique properties of Pol µ that allow it to productively engage such a highly unstable substrate to generate a nick that can be sealed by DNA Ligase IV.

Diallyl sulfides: Selective inhibitors of family X DNA polymerases from garlic (Allium sativum L.).

Diallyl sulfides, organosulfur compounds isolated from garlic (Allium sativum L.), selectively inhibit the activities of mammalian family X DNA polymerases (pols), such as pol ß, pol λ and terminal deoxynucleotidyl transferase (TdT), in vitro. The purified fraction (i.e., Sample-A) consisted of diallyl trisulfide, diallyl tetrasulfide and diallyl pentasulfide (molecular ratio: 5.3:3:1). Commercially purchased diallyl sulfides also inhibited the activities of family X pols, and the order of their effect was as follows: Sample-A>diallyl trisulfide>diallyl disulfide>diallyl monosulfide, suggesting that the number of sulfur atoms in the compounds might play an important structural role in enzyme inhibition. The suppression of human cancer cell (promyelocytic leukaemia cell line, HL-60) growth had the same tendency as the inhibition of pol X family among the compounds. Diallyl sulfides were suggested to bind to the pol ß-like region of family X pols.

The anti/syn conformation of 8-oxo-7,8-dihydro-2'-deoxyguanosine is modulated by Bacillus subtilis PolX active site residues His255 and Asn263. Efficient processing of damaged 3'-ends.

8-oxo-7,8-dihydro-2'-deoxyguanosine (8oxodG) is a major lesion resulting from oxidative stress and found in both DNA and dNTP pools. Such a lesion is usually removed from DNA by the Base Excision Repair (BER), a universally conserved DNA repair pathway. 8oxodG usually adopts the favored and promutagenic syn-conformation at the active site of DNA polymerases, allowing the base to hydrogen bonding with adenine during DNA synthesis. Here, we study the structural determinants that affect the glycosidic torsion-angle of 8oxodGTP at the catalytic active site of the family X DNA polymerase from Bacillus subtilis (PolXBs). We show that, unlike most DNA polymerases, PolXBs exhibits a similar efficiency to stabilize the anti and syn conformation of 8oxodGTP at the catalytic site. Kinetic analyses indicate that at least two conserved residues of the nucleotide binding pocket play opposite roles in the anti/syn conformation selectivity, Asn263 and His255 that favor incorporation of 8oxodGMP opposite dA and dC, respectively. In addition, the presence in PolXBs of Mn2+-dependent 3'-phosphatase and 3'-phosphodiesterase activities is also shown. Those activities rely on the catalytic center of the C-terminal Polymerase and Histidinol Phosphatase (PHP) domain of PolXBs and, together with its 3'-5' exonuclease activity allows the enzyme to resume gap-filling after processing of damaged 3' termini.

Structures of the Leishmania infantum polymerase beta.

Protozoans of the genus Leishmania, the pathogenic agent causing leishmaniasis, encode the family X DNA polymerase Li Pol ß. Here, we report the first crystal structures of Li Pol ß. Our pre- and post-catalytic structures show that the polymerase adopts the common family X DNA polymerase fold. However, in contrast to other family X DNA polymerases, the dNTP-induced conformational changes in Li Pol ß are much more subtle. Moreover, pre- and post-catalytic structures reveal that Li Pol ß interacts with the template strand through a nonconserved, variable region known as loop3. Li Pol ß Δloop3 mutants display a higher catalytic rate, catalytic efficiency and overall error rates with respect to WT Li Pol ß. These results further demonstrate the subtle structural variability that exists within this family of enzymes and provides insight into how this variability underlies the substantial functional differences among their members.

The interplay of DNA polymerase λ in diverse DNA damage repair pathways in higher plant genome in response to environmental and genotoxic stress factors.

DNA repair mechanisms are essential for the maintenance of genomic stability, proper cellular function and survival for all organisms. Plants, with their intrinsic immobility, are vastly exposed to a wide range of environmental agents and also endogenous processes which frequently cause damage to DNA and impose genotoxic stress. Therefore, in order to survive under frequent and extreme environmental stress conditions, plants have developed a vast array of efficient and powerful DNA damage repair mechanisms to ensure rapid and precise repair of genetic material for maintaining genome stability and faithful transfer of genetic information over generations. (1) Recently, we have defined the role of DNA polymerase λ in repair of UV-B-induced photoproducts in Arabidopsis thaliana via nucleotide excision repair pathway. (2) Here, we have further discussed potential function of DNA polymerase λ in various DNA repair pathways in higher plant genome in response to environmental and genotoxic stress factors.

Historical review of Lynch syndrome / Revisão histórica da síndrome de Lynch

Lynch syndrome was formerly known as Hereditary Nonpolyposis Colorectal Cancer. Currently, these two nomenclatures each have their unique definitions and are no longer used interchangeably. The history of hereditary nonpolyposis colorectal cancer was first recognized formally in the literature by Henry Lynch in 1967. With advances of molecular genetics, there has been a transformation from clinical phenotype to genotype diagnostics. This has led to the ability to diagnose affected patients before they manifest with cancer, and therefore allow preventative surveillance strategies. Genotype diagnostics has shown a difference in penetrance of different cancer risks dependent on the gene containing the mutation. Surgery is recommended as prevention for some cancers; for others they are reserved for once cancer is noted. Various surveillance strategies are recommended dependent on the relative risk of cancer and the ability to intervene with surgery to impact on survival. Risk reduction through aspirin has shown some recent promise, and continues to be studied. (AU)

A síndrome de Lynch era anteriormente conhecida como "câncer colorretal hereditário não polipose". Atualmente, essas duas nomenclaturas têm, cada uma, sua própria definição original e já não são empregadas de forma intercambiável. O histórico de câncer colorretal hereditário não polipose foi formalmente reconhecido pela primeira vez na literatura por Henry Lynch em 1967. Com os avanços da genética molecular, verificou-se uma mudança do fenótipo clínico para o diagnóstico genotípico. Esse fato levou à capacidade de diagnosticar pacientes afetados antes que o câncer se manifestasse, e, portanto, à utilização de estratégias preventivas de rastreamento. O diagnóstico genotípico mostrou a diferença na penetrância de diferentes riscos de câncer dependendo do gene que contem a mutação. A cirurgia é recomendada para a prevenção de alguns tipos de câncer; para outros, ela é reservada quando há o aparecimento da doença. Várias estratégias de rastreamento são recomendadas, dependendo do risco relativo de câncer, bem como a capacidade para intervir com a cirurgia objetivando um impacto na sobrevivência. A redução do risco através do uso de aspirina recentemente mostrou ser promissor e continua a ser estudada. (AU)