EST Analysis of Ostreococcus lucimarinus, the Most Compact Eukaryotic Genome, Shows an Excess of Introns in Highly Expressed Genes

Background: The genome of the pico-eukaryotic (bacterial-sized) prasinophyte green alga Ostreococcus lucimarinus has one of the highest gene densities known in eukaryotes, yet it contains many introns. Phylogenetic studies suggest this unusually compact genome (13.2 Mb) is an evolutionarily derived state among prasinophytes. The presence of introns in the highly reduced O. lucimarinus genome appears to be in opposition to simple explanations of genome evolution based on unidirectional tendencies, either neutral or selective. Therefore, patterns of intron retention in this species can potentially provide insights into the forces governing intron evolution. Methodology/Principal Findings: Here we studied intron features and levels of expression in O. lucimarinus using expressed sequence tags (ESTs) to annotate the current genome assembly. ESTs were assembled into unigene clusters that were mapped back to the O. lucimarinus Build 2.0 assembly using BLAST and the level of gene expression was inferred from the number of ESTs in each cluster. We find a positive correlation between expression levels and both intron number (R = +0.0893, p =,0.0005) and intron density (number of introns/kb of CDS; R = +0.0753, p =,0.005). Conclusions/Significance: In a species with a genome that has been recently subjected to a great reduction of non-coding DNA, these results imply the existence of selective/functional roles for introns that are principally detectable in highly expressed genes. In these cases, introns are likely maintained by balancing the selective forces favoring their maintenanc

Role of ER Stress Response in Photodynamic Therapy: ROS Generated in Different Subcellular Compartments Trigger Diverse Cell Death Pathways

We have analyzed the molecular mechanisms of photoinduced cell death using porphyrins with similar structure differing only in the position of the ethylene glycol (EG) chain on the phenyl ring. Meta- and para-positioned EG chains targeted porphyrins to different subcellular compartments. After photoactivation, both types of derivatives induced death of tumor cells via reactive oxygen species (ROS). Para derivatives pTPP(EG)4 and pTPPF(EG)4 primarily accumulated in lysosomes activated the p38 MAP kinase cascade, which in turn induced the mitochondrial apoptotic pathway. In contrast, meta porphyrin derivative mTPP(EG)4 localized in the endoplasmic reticulum (ER) induced dramatic changes in Ca2+ homeostasis manifested by Ca2+ rise in the cytoplasm, activation of calpains and stress caspase-12 or caspase-4. ER stress developed into unfolded protein response. Immediately after irradiation the PERK pathway was activated through phosphorylation of PERK, eIF2α and induction of transcription factors ATF4 and CHOP, which regulate stress response genes. PERK knockdown and PERK deficiency protected cells against mTPP(EG)4-mediated apoptosis, confirming the causative role of the PERK pathway

Models of Traumatic Cerebellar Injury

Traumatic brain injury (TBI) is a major cause of morbidity and mortality worldwide. Studies of human TBI demonstrate that the cerebellum is sometimes affected even when the initial mechanical insult is directed to the cerebral cortex. Some of the components of TBI, including ataxia, postural instability, tremor, impairments in balance and fine motor skills, and even cognitive deficits, may be attributed in part to cerebellar damage. Animal models of TBI have begun to explore the vulnerability of the cerebellum. In this paper, we review the clinical presentation, pathogenesis, and putative mechanisms underlying cerebellar damage with an emphasis on experimental models that have been used to further elucidate this poorly understood but important aspect of TBI. Animal models of indirect (supratentorial) trauma to the cerebellum, including fluid percussion, controlled cortical impact, weight drop impact acceleration, and rotational acceleration injuries, are considered. In addition, we describe models that produce direct trauma to the cerebellum as well as those that reproduce specific components of TBI including axotomy, stab injury, in vitro stretch injury, and excitotoxicity. Overall, these models reveal robust characteristics of cerebellar damage including regionally specific Purkinje cell injury or loss, activation of glia in a distinct spatial pattern, and traumatic axonal injury. Further research is needed to better understand the mechanisms underlying the pathogenesis of cerebellar trauma, and the experimental models discussed here offer an important first step toward achieving that objective

Chemical genetics strategies for identification of molecular targets

Chemical genetics is an emerging field that can be used to study the interactions of chemical compounds, including natural products, with proteins. Usually, the identification of molecular targets is the starting point for studying a drug’s mechanism of action and this has been a crucial step in understanding many biological processes. While a great variety of target identification methods have been developed over the last several years, there are still many bioactive compounds whose target proteins have not yet been revealed because no routine protocols can be adopted. This review contains information concerning the most relevant principles of chemical genetics with special emphasis on the different genomic and proteomic approaches used in forward chemical genetics to identify the molecular targets of the bioactive compounds, the advantages and disadvantages of each and a detailed list of successful examples of molecular targets identified with these approaches

Thermal Parameters Analysis During Directional Solidification Of Al-Cu Eutectic Alloys

Al-Cu eutectic alloy samples (Al-33.2wt.%Cu) were solidified directionally upward under conditions which produce the columnar-to-equiaxed transition (CET) phenomenon. The position of the CET was located in each sample and the distance from the bottom of the ingot was measured. During solidification the distribution of temperatures were measured by means of thermocouples located strategically. From the measured temperatures the following parameters were obtained; local temperature gradient, cooling rate of the liquid and solid and growth rate. Three different velocities of heat extraction were employed and the temperature gradient reaches values of 2.1 ºC/cm, 0.1 °C/cm and -4.3ºC/cm, respectively. The results are presented and discussed comparing with the results obtained in the case of CET in dendritic Al-Cu alloysFil: Kociubczyk, Alex Iván. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnológico Nordeste. Instituto de Materiales de Misiones; ArgentinaFil: Cabello, Federico. Consejo Nacional de Investigaciones Científicas y Técnicas; ArgentinaFil: Schvezov, Carlos Enrique. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnológico Nordeste. Instituto de Materiales de Misiones; ArgentinaFil: Gregorutti, Ricardo Walter. Universidad Nacional de La Plata; ArgentinaFil: Ares, Alicia Esther. Consejo Nacional de Investigaciones Cientificas y Tecnicas. Centro Cientifico Tecnológico Nordeste. Instituto de Materiales de Misiones; Argentin

Impact of health claims in prebiotic-enriched breads on purchase intent, emotional response and product liking

The impact of health claims on purchase intent, emotional response and liking has never been previously reported. In this study, prebiotic-enriched bread was used as a model functional food. Purchase intent, emotional response and liking were investigated in three phases: (1) focus groups were used to gauge consumer perception of health claims and functional foods, (2) the impact of health claims on purchase intent and emotional responses were measured using an online survey (n=122) and (3) hedonic ratings on bread rolls presented with or without any associated claims were obtained (n=100). A cluster analysis of the purchase intent data identified two clusters of consumers who were either receptive or nonreceptive to health claims. Receptive and non-receptive consumers significantly differed in the emotions they reported with respect to the claims. The hedonic ratings did not significantly differ between the breads tasted with or without health claims

Calorimetric investigation of Al–Zn alloys using Oelsen method

The results of calorimetric study of binary Al-Zn system done according to the Oelsen thermodynamic method are presented in this paper. Main thermodynamic properties, including activities, activity coefficients, partial/integral molar Gibbs excess, and mixing energies were determined at 1,000 K. Positive deviation from Raoult law was noticed, with minimal values of Delta G (M) about -3 kJ mol(-1) and maximal values of Delta G (E) about +2 kJ mol(-1). The energetics of mixing in liquid Al-Zn alloys has been analyzed through the study of concentration fluctuation in the long-wavelength limit, and weak affinity between Al and Zn atoms in the system was observed. Differential thermal analysis and light optic microscopy were applied in the frame of characterization of investigated binary alloys and phase diagram examination, and the results obtained were in accordance with available literature data