Effective Binding Force Calculation in Dimeric Proteins

We apply the Blue Moon constrained Molecular Dynamics technique to study a particular case of molecular recognition, one of the main issues of modern molecular biology. We investigate the effects of mutation of interface residues on the binding strength of the dimeric protein superoxide dismutase from Photobacterium leiognathi. With our technique we produce a specific path describing the separation of the dimers and we calculate the effective mean force involved in the process. We apply the method to two mutants and compare the results with those obtained in an earlier calculation on the native enzyme. The method is sensitive to the mutations and allows us to establish a semi-quantitative hierarchy for the association strengths of the three enzymes.     

Blue Moon Approach to Rare Events

The "Blue Moon" ensemble is a computationally efficient molecular dynamics method to estimate the rate constants of rare activated events when the process can be described by a reaction coordinate ξ(r), a well-defined function in configuration space. By means of holonomic constraints a number of values of ξ(r) can be prescribed along the relevant path to identify the "bottleneck" region first and to sample an ensemble of starting conditions to generate activated trajectories. These MD trajectories sample phase space according to a biased configurational distribution. With a suitable re-weighting of averages from such ensemble of trajectories one can characterize completely rare events.     

Flow cytometry and live confocal analysis for the evaluation of the uptake and intracellular distribution of FITC-ODN into HaCaT cells

In this study, the mechanism of the internalization and the cellular distribution of 59 fluorescein conjugated PS-ODN (FITC-ODN) after transfection with different mixed lipidic vesicles/oligo complexes (lipoplexes) have been investigated. Mixed lipidic vesicles were prepared with one of the most used cationic lipid (DOTAP) and different amounts of a cholic acid (UDCA) to release the oligo into HaCaT cells. Using flow cytometry, the cellular uptake of the oligo was studied with and without different inhibitors able to block selectively the different pathways involved in the internalization mechanism. The intracellular distribution of the oligo was analyzed by confocal laser scanning microscopy (CLSM), treating the cells with the lipoplexes and directly observing without any fixing procedure. To better carry out the colocalization studies, fluorescent-labeled markers, specific for the different cellular compartments, were coincubated with 59 fluorescein-conjugated 29-mer phosphorotioate oligonucleotide (FITC-ODN). The different lipidic vesicles affect the internalization mechanism of FITC-ODN. After using the inhibitors, the uptake of complexes involved a different internalization mechanism. The live CLSM analysis demonstrated that, after 1 hour from the complex incubation, the oligo was transferred into cells and localized into the endosomes; after 24 hours, the oligo was intracellularly localized close to the nuclear structure in a punctuate pattern. However, the results from fusion experiments showed also a binding of a quite low amount of oligo with the cell membranes.     

Interactions of Quinoxaline Antibiotic and DNA.: The Molecular Structure of a Triostin A—d(GCGTACGC) Complex

Abstract

The crystal structure of a DNA. octamer d(GCGTA.CGC) complexed to an antitumor antibiotic, triostin A, has been solved and refined to 2.2 Å resolution by x-ray diffraction analysis. The antibiotic molecule acts as a true bis intercalator surrouding the d(CpG) sequence at either end of the unwound right-handed DNA. double helix. A.s previously observed in the structure of triostin A.—d(CGTA.CG) complex (A.H.-J. Wang, et. al., Science, 225,1115–1121 (1984)), the alanine amino acid residues of the drug molecule form sequence-specific hydrogen bonds to guanines in the minor groove. The two central A · T base pairs are in Hoogsteen configuration with adenine in the syn conformation. In addition, the two terminal G · C base pairs flanking the quinoxaline rings are also held together by Hoogsteen base pairing. This is the first observation in an oligonucleotide of. Hoogsteen G · C base pairs where the cytosine is protonated. The principal functional components of a bis-intercalative compound are discussed.     

Biological rhythms,chronodisruption and chrono-enhancement: The role of physical activity as synchronizer in correcting steroids circadian rhythm in metabolic dysfunctions and cancer

ABSTRACT

Rhythms can be observed at all levels of the biologic integration in humans. The observation that a biological or physiological variable shows a circadian rhythm can be explained by several multifactorial systems including external (exogenous), internal (endogenous) and psychobiological (lifestyle) mechanisms. Our body clock can be synchronized with the environment by external factors, called “synchronizers”, i.e. the light–dark cycle, but it is also negatively influenced by some pathological conditions or factors, called “chronodisruptors,” i.e. aging or low physical activity (PA). The desynchronization of a 24-h rhythm in a chronic manner has been recently defined “chronodisruption” or “circadian disruption.” A very large number of hormonal variables, such as adrenal and gonadal stress steroids, are governed by circadian rhythmicity. Such hormones, in normal conditions, show a peak in the first part of the day, while their typical diurnal fluctuations are totally out of sync in subjects affected by cancer or metabolic diseases, such as obesity, diabetes and metabolic syndrome. In general, a flatter slope with altered peaks in cortisol and testosterone circadian rhythms has been observed in pathological individuals. PA, specifically chronic exercise, seems to play a key role as synchronizer for the whole circadian system in such pathologies even if specific data on steroids circadian pattern are still sparse and contradictory. Recently, it has been proposed that low-intensity chronic PA could be an effective intervention to decrease morning cortisol levels in pathological subjects. The standardization of all confounding factors is needed to reach more clear evidence-based results.     

Tree-ring wood anatomy and stable isotopes show structural and functional adjustments in olive trees under different water availability

Background and Aims

Olive tree (Olea europaea L.) is a drought-tolerant tree species cultivated in Mediterranean-type environments. Although it is tolerant to drought, dry conditions decrease its productivity. A thorough analysis of the hydraulic architecture and wood anatomical plasticity, as well as of their physiological significance, is needed to understand how olive trees will adapt to the predicted increase in frequency and severity of drought in the Mediterranean region.

Methods

Dendrochronological, stable isotopic (δ¹³C, δ¹⁸O) and wood anatomical analyses were applied to understand how different water availability can affect wood stem structure and function, in rainfed and irrigated at 100 % of crop evapotranspiration (ETc) olive trees in an experimental orchard close to Benevento (Italy) from 1992 to 2009.

Results

Dendrochronological data indicate that cross-dating and synchronization of ring-width time series in olive tree is possible. After the start of irrigation, significantly more negative δ¹³C and lower δ¹⁸O values were recorded in irrigated trees indicating higher stomatal conductance and transpiration rates. Increased water balance induced the formation of a higher number of vessels with higher diameter.

Conclusions

Water balance variations affected wood anatomy and isotopic composition. Anatomical analyses detected structural and functional adjustments in rainfed trees that produced more vessels with lower diameter to prevent cavitation. Isotopic analyses confirmed that irrigated trees continuously showed enhanced transpiration rates.     

Morpho-physiological responses of sugar beet (Beta vulgaris L.) genotypes to drought stress

The identification of morpho-physiological traits related to drought tolerance and high yield potential is a challenge when selecting sugar beet genotypes with greater tolerance to water stress. In this paper, root morphological parameters, antioxidant systems, leaf relative water content (RWC) and H⁺-ATPase activity as key morpho-physiological traits involved in drought tolerance/susceptibility of sugar beet were studied. Genotypes showing a different drought tolerance index (DTI) but a similar yield potential, under moderate (?0.6 Mpa) and severe (?1.2 MPa) water stress, were selected and their morpho-physiological traits were investigated. The results showed a wide genetic variation in morpho-physiological parameters which demonstrated the different adaptive strategies under moderate and severe drought conditions in sugar beet. In particular, an efficient antioxidant system and redox signalling made some sugar beet genotypes more tolerant to drought stress. The alternative strategy of other genotypes was the reduction of root tissue density, which produced a less dense root system improving the axial hydraulic conductivity. These results could be considered as interesting challenge for a better understanding of the drought tolerance mechanisms in sugar beet.     

Two new Andean species of Neocorynura (Hymenoptera: Halictidae: Augochlorini) with notes on their biology

We describe and illustrate the male, female, and pupa of two new species of Neocorynura from the Colombian Andes, and provide information on their nesting behavior, host plants and social organization. Nests of Neocorynura iguaquensis sp. nov. Smith‐Pardo & Gonzalez and N. muiscae sp. nov. Smith‐Pardo & Gonzalez were found in flat or vertical banks, and contained one to three adult females. The percentage of multi‐female nests varied considerably from 8.3% to 40% of the total of dissected nests at different times in 2000 and 2003. The ovarian development, wing and mandibular wear of females in the nests with two or more females indicated that they were the offspring that remained in the nest before dispersal or a mother and a newly emerged daughter. Pollen taken from the nest cells and scopae of museum specimens showed that both species rely heavily on pollen of asteraceans and may be active year‐round. Details on the nest architecture and comments on the phylogenetic placement of both species are also provided. Direct observations on the multi‐female nests are required to determine whether or not such nests contain temporary assemblages or truly semisocial colonies.

Resumen

Describimos e ilustramos el macho, hembra y pupa de dos especies nuevas de Neocorynura de los Andes colombianos, y proporcionamos información sobre su biología de nidificación, plantas hospederas y organización social. Los nidos de Neocorynura iguaquensis sp. nov. Smith‐Pardo & Gonzalez y N. muiscae sp. nov. Smith‐Pardo & Gonzalez fueron encontrados en el suelo, en áreas planas o barrancos verticales, y tenían de una a tres hembras adultas. El porcentaje de nidos con más de una hembra varió considerablemente desde 8.3% al 40% del total de nidos disectados a diferentes meses en el año 2000 y 2003. El desarrollo ovárico, desgaste de las alas y mandíbulas de las hembras en los nidos con dos o más hembras indicaron que ellas fueron las crías que permanecieron en el nido antes de dispersarse o una madre con la hija recién nacida. El polen tomado de las celdas de cría y escopas de especimenes de museo mostró que ambas especies dependen principalmente de asteraceas y que podrían estar activas todo el año. También oferecemos detalles de la arquitectura del nidos y comentarios sobre la posición filogenética de ambas especies. Observaciones directas de los nido con más de una hembra son necesarias para determinar si tales nidos son agrupaciones temporales o verdaderas colonias semisociales.