On the traces of XPD: cell cycle matters - untangling the genotype-phenotype relationship of XPD mutations

Abstract Mutations in the human gene coding for XPD lead to segmental progeria - the premature appearance of some of the phenotypes normally associated with aging - which may or may not be accompanied by increased cancer incidence. XPD is required for at least three different critical cellular functions: in addition to participating in the process of nucleotide excision repair (NER), which removes bulky DNA lesions, XPD also regulates transcription as part of the general transcription factor IIH (TFIIH) and controls cell cycle progression through its interaction with CAK, a pivotal activator of cyclin dependent kinases (CDKs). The study of inherited XPD disorders offers the opportunity to gain insights into the coordination of important cellular events and may shed light on the mechanisms that regulate the delicate equilibrium between cell proliferation and functional senescence, which is notably altered during physiological aging and in cancer. The phenotypic manifestations in the different XPD disorders are the sum of disturbances in the vital processes carried out by TFIIH and CAK. In addition, further TFIIH- and CAK-independent cellular activities of XPD may also play a role. This, added to the complex feedback networks that are in place to guarantee the coordination between cell cycle, DNA repair and transcription, complicates the interpretation of clinical observations. While results obtained from patient cell isolates as well as from murine models have been elementary in revealing such complexity, the Drosophila embryo has proven useful to analyze the role of XPD as a cell cycle regulator independently from its other cellular functions. Together with data from the biochemical and structural analysis of XPD and of the TFIIH complex these results combine into a new picture of the XPD activities that provides ground for a better understanding of the patophysiology of XPD diseases and for future development of diagnostic and therapeutic tools.

Acompañar a los enfermos en la antesala del final de su ciclo vital

Objetivo. Realizar una etnografía, en una Unidad de Paliativos, para estudiar las interacciones de los actores, en particular la de los médicos con los enfermos, que están viviendo esa determinada situación de tránsito hacia la muerte; y la opinión de aquellos sobre los cuidados paliativos. Metodología. El paradigma al que nos adscribimos es el cualitativo, ontológicamente constructivista y epistemológicamente, desde el punto de vista de las sociologías de la vida, siendo nuestro método la etnografía. Resultados. Procedentes del discurso, sobre todo de las entrevistas con los médicos han sido recogidos textualmente. Conclusiones. Entre otras, sobre el escenario, un microespacio dentro del Hospitalito, llamado Unidad de Cuidados Medios, representaba diacrónicamente la dicotomía tesis / antítesis: la tesis de que era una unidad que formalmente se había inaugurado como una Unidad de Paliativos, suponemos que con un propósito propagandístico; pero la antítesis, era la realidad y esta era sin duda que seguía siendo una Unidad de Cuidados Medios.

The Plasmodium serine-type SERA proteases display distinct expression patterns and non-essential in vivo roles during life cycle progression of the malaria parasite

Parasite proteases play key roles in several fundamental steps of the Plasmodium life cycle, including haemoglobin degradation, host cell invasion and parasite egress. Plasmodium exit from infected host cells appears to be mediated by a class of papain-like cysteine proteases called 'serine repeat antigens' (SERAs). A SERA subfamily, represented by Plasmodium falciparum SERA5, contains an atypical active site serine residue instead of a catalytic cysteine. Members of this SERAser subfamily are abundantly expressed in asexual blood stages, rendering them attractive drug and vaccine targets. In this study, we show by antibody localization and in vivo fluorescent tagging with the red fluorescent protein mCherry that the two P. berghei serine-type family members, PbSERA1 and PbSERA2, display differential expression towards the final stages of merozoite formation. Via targeted gene replacement, we generated single and double gene knockouts of the P. berghei SERAser genes. These loss-of-function lines progressed normally through the parasite life cycle, suggesting a specialized, non-vital role for serine-type SERAs in vivo. Parasites lacking PbSERAser showed increased expression of the cysteine-type PbSERA3. Compensatory mechanisms between distinct SERA subfamilies may thus explain the absence of phenotypical defect in SERAser disruptants, and challenge the suitability to develop potent antimalarial drugs based on specific inhibitors of Plasmodium serine-type SERAs.

The topography of transmembrane segment six is altered during the catalytic cycle of P-glycoprotein

Structural evidence has demonstrated that P-glycoprotein (P-gp) undergoes considerable conformational changes during catalysis, and these alterations are important in drug interaction. Knowledge of which regions in P-gp undergo conformational alterations will provide vital information to elucidate the locations of drug binding sites and the mechanism of coupling. A number of investigations have implicated transmembrane segment six (TM6) in drug-P-gp interactions, and a cysteine-scanning mutagenesis approach was directed to this segment. Introduction of cysteine residues into TM6 did not disturb basal or drug-stimulated ATPase activity per se. Under basal conditions the hydrophobic probe coumarin maleimide readily labeled all introduced cysteine residues, whereas the hydrophilic fluorescein maleimide only labeled residue Cys-343. The amphiphilic BODIPY-maleimide displayed a more complex labeling profile. The extent of labeling with coumarin maleimide did not vary during the catalytic cycle, whereas fluorescein maleimide labeling of F343C was lost after nucleotide binding or hydrolysis. BODIPY-maleimide labeling was markedly altered during the catalytic cycle and indicated that the adenosine 5'-(beta,gamma-imino)triphosphate-bound and ADP/vanadate-trapped intermediates were conformationally distinct. Our data are reconciled with a recent atomic scale model of P-gp and are consistent with a tilting of TM6 in response to nucleotide binding and ATP hydrolysis.

Dimensioning BCH codes for coherent DQPSK systems with laser phase noise and cycle slips

Forward error correction (FEC) plays a vital role in coherent optical systems employing multi-level modulation. However, much of coding theory assumes that additive white Gaussian noise (AWGN) is dominant, whereas coherent optical systems have significant phase noise (PN) in addition to AWGN. This changes the error statistics and impacts FEC performance. In this paper, we propose a novel semianalytical method for dimensioning binary Bose-Chaudhuri-Hocquenghem (BCH) codes for systems with PN. Our method involves extracting statistics from pre-FEC bit error rate (BER) simulations. We use these statistics to parameterize a bivariate binomial model that describes the distribution of bit errors. In this way, we relate pre-FEC statistics to post-FEC BER and BCH codes. Our method is applicable to pre-FEC BER around 10-3 and any post-FEC BER. Using numerical simulations, we evaluate the accuracy of our approach for a target post-FEC BER of 10-5. Codes dimensioned with our bivariate binomial model meet the target within 0.2-dB signal-to-noise ratio.

Integrating health and sustainability in life cycle assessment

Until now health impact assessment and environmental impact assessment are two different issues, often not addressed together. Both issues have to be dealt with for sustainable building. The aim of this paper is to link healthy and sustainable housing in life cycle assessment. Two strategies are studied: clean air as a functional unity and health as a quality indicator. The strategies are illustrated with an example on the basis of Eco-Quantum, which is a Dutch whole-building assessment tool. It turns out that both strategies do not conflict with the LCA methodology. The LCA methodology has to be refined for this purpose.

Particle and gaseous emissions from commercial aircraft at each stage of the landing and takeoff cycle

A novel technique was used to measure emission factors for commonly used commercial aircraft including a range of Boeing and Airbus airframes under real world conditions. Engine exhaust emission factors for particles in terms of particle number and mass (PM2.5), along with those for CO2, and NOx were measured for over 280 individual aircraft during the various modes of landing/takeoff (LTO) cycle. Results from this study show that particle number, and NOx emission factors are dependant on aircraft engine thrust level. Minimum and maximum emissions factors for particle number, PM2.5, and NOx emissions were found to be in the range of 4.16×1015-5.42×1016 kg-1, 0.03-0.72 g.kg-1, and 3.25-37.94 g.kg-1 respectively for all measured airframes and LTO cycle modes. Number size distributions of emitted particles for the naturally diluted aircraft plumes in each mode of LTO cycle showed that particles were predominantly in the range of 4 to 100 nm in diameter in all cases. In general, size distributions exhibit similar modality during all phases of the LTO cycle. A very distinct nucleation mode was observed in all particle size distributions, except for taxiing and landing of A320 aircraft. Accumulation modes were also observed in all particle size distributions. Analysis of aircraft engine emissions during LTO cycle showed that aircraft thrust level is considerably higher during taxiing than idling suggesting that International Civil Aviation Organization (ICAO) standards need to be modified as the thrust levels for taxi and idle are considered to be the same (7% of total thrust) [1].