ATG7(2) Interacts With Metabolic Proteins and Regulates Central Energy Metabolism

Macroautophagy/autophagy is an essential catabolic process that targets a wide variety of cellular components including proteins, organelles, and pathogens. ATG7, a protein involved in the autophagy process, plays a crucial role in maintaining cellular homeostasis and can contribute to the development of diseases such as cancer. ATG7 initiates autophagy by facilitating the lipidation of the ATG8 proteins in the growing autophagosome membrane. The noncanonical isoform ATG7(2) is unable to perform ATG8 lipidation; however, its cellular regulation and function are unknown. Here, we uncovered a distinct regulation and function of ATG7(2) in contrast with ATG7(1), the canonical isoform. First, affinity-purification mass spectrometry analysis revealed that ATG7(2) establishes direct protein–protein interactions (PPIs) with metabolic proteins, whereas ATG7(1) primarily interacts with autophagy machinery proteins. Furthermore, we identified that ATG7(2) mediates a decrease in metabolic activity, highlighting a novel splice-dependent function of this important autophagy protein. Then, we found a divergent expression pattern of ATG7(1) and ATG7(2) across human tissues. Conclusively, our work uncovers the divergent patterns of expression, protein interactions, and function of ATG7(2) in contrast to ATG7(1). These findings suggest a molecular switch between main catabolic processes through isoform-dependent expression of a key autophagy gene.     

Medical treatment of pulmonary hydatid disease: for which child?

There have been many encouraging studies on medical treatment of pulmonary hydatid disease due to Echinococcus granulosus infection. Our aims were to demonstrate the safety and efficacy of medical treatment in pulmonary hydatid disease and to describe a pediatric population who would benefit from medical treatment, especially in respect to the diameter of the hydatid cyst. All patients were treated with mebendazole or albendazole. Treatment outcome was defined as cure, improvement or failure. Among 82 patients, 34.1% were cured, 34.1% improved and 31.8% failed. When 102 cysts were individually evaluated, 36.31% were cured, 32.4% improved and 31.3% failed. The cure and the failure rates were statistically insignificant in cysts treated with mebendazole and albendazole; however statistically significantly more cysts were improved with albendazole. The results were statistically insignificant between continuous and cyclic albendazole treatment. The mean size of successfully treated cysts was 5.3+/-3.4 cm, but "failed" for cyst with a mean size of 7.3+/-4.3 cm. There was a positive, weak and statistically significant correlation between the cyst size and treatment results. The major complication was infection. We suggest that selected pediatric patients with uncomplicated pulmonary hydatid cysts sized less than 5 cm should have a trial of medical treatment with a very close follow up.     

<Emphasis Type="Italic">Roncus travuniensis</Emphasis> sp. n. (Neobisiidae,Pseudoscorpiones), a troglobitic false scorpion from Bosnia-Herzegovina

A new pseudoscorpion species, Roncus travuniensis sp. n. (Neobisiidae, Pseudoscorpiones), was collected in the Arenstorfova Pećina Cave, near Trebinje, Bosnia and Herzegovina. The main morphological traits of the specimen studied clearly demonstrate its affinities with Roncus vulcanius Beier, 1938. Additionally, some taxonomic and biogeographical traits of this new pseudoscorpion are also discussed.     

First evidence of DNA methylation in insect Tribolium castaneum

DNA methylation has been studied in many eukaryotic organisms, in particular vertebrates, and was implicated in developmental and phenotypic variations. Little is known about the role of DNA methylation in invertebrates, although insects are considered as excellent models for studying the evolution of DNA methylation. In the red flour beetle, Tribolium castaneum (Tenebrionidae, Coleoptera), no evidence of DNA methylation has been found till now. In this paper, a cytosine methylation in Tribolium castaneum embryos was detected by methylation sensitive restriction endonucleases and immuno-dot blot assay. DNA methylation in embryos is followed by a global demethylation in larvae, pupae and adults. DNA demethylation seems to proceed actively through 5-hydroxymethylcytosine, most probably by the action of TET enzyme. Bisulfite sequencing of a highly abundant satellite DNA located in pericentromeric heterochromatin revealed similar profile of cytosine methylation in adults and embryos. Cytosine methylation was not only restricted to CpG sites but was found at CpA, CpT and CpC sites. In addition, complete cytosine demethylation of heterochromatic satellite DNA was induced by heat stress. The results reveal existence of DNA methylation cycling in T. castaneum ranging from strong overall cytosine methylation in embryos to a weak DNA methylation in other developmental stages. Nevertheless, DNA methylation is preserved within heterochromatin during development, indicating its role in heterochromatin formation and maintenance. It is, however, strongly affected by heat stress, suggesting a role for DNA methylation in heterochromatin structure modulation during heat stress response.     

Mitochondrial respiration in human viable platelets—Methodology and influence of gender,age and storage

Studying whole cell preparations with intact mitochondria and respiratory complexes has a clear benefit compared to isolated or disrupted mitochondria due to the dynamic interplay between mitochondria and other cellular compartments. Platelet mitochondria have a potential to serve as a source of human viable mitochondria when studying mitochondrial physiology and pathogenic mechanisms, as well as for the diagnostics of mitochondrial diseases. The objective of the present study was to perform a detailed evaluation of platelet mitochondrial respiration using high-resolution respirometry. Further, we aimed to explore the limits of sample size and the impact of storage as well as to establish a wide range of reference data from different pediatric and adult cohorts. Our results indicate that platelet mitochondria are well suited for ex-vivo analysis with the need for minute sample amounts and excellent reproducibility and stability.     

A combined approach for genome wide protein function annotation/prediction

Background

Today large scale genome sequencing technologies are uncovering an increasing amount of new genes and proteins, which remain uncharacterized. Experimental procedures for protein function prediction are low throughput by nature and thus can't be used to keep up with the rate at which new proteins are discovered. On the other hand, proteins are the prominent stakeholders in almost all biological processes, and therefore the need to precisely know their functions for a better understanding of the underlying biological mechanism is inevitable. The challenge of annotating uncharacterized proteins in functional genomics and biology in general motivates the use of computational techniques well orchestrated to accurately predict their functions.

Methods

We propose a computational flow for the functional annotation of a protein able to assign the most probable functions to a protein by aggregating heterogeneous information. Considered information include: protein motifs, protein sequence similarity, and protein homology data gathered from interacting proteins, combined with data from highly similar non-interacting proteins (hereinafter called Similactors). Moreover, to increase the predictive power of our model we also compute and integrate term specific relationships among functional terms based on Gene Ontology (GO).

Results

We tested our method on Saccharomyces Cerevisiae and Homo sapiens species proteins. The aggregation of different structural and functional evidence with GO relationships outperforms, in terms of precision and accuracy of prediction than the other methods reported in literature. The predicted precision and accuracy is 100% for more than half of the input set for both species; overall, we obtained 85.38% precision and 81.95% accuracy for Homo sapiens and 79.73% precision and 80.06% accuracy for Saccharomyces Cerevisiae species proteins.

     

Endometrial gene expression profiling of recurrent implantation failure after in vitro fertilization

Molecular Biology Reports - Recurrent implantation failure (RIF) is diagnosed when good-quality embryos repeatedly fail to implant after transfer in several in vitro fertilization (IVF) treatment...     

Determination of subnanomolar concentrations of vanadium in environmental water samples using flow injection with luminol chemiluminescence detection

A flow injection chemiluminescence method is described for the determination of subnanomolar concentrations of vanadium in environmental water samples. The procedure is based on the oxidation of luminol in the presence of dissolved oxygen catalyzed by vanadium(IV). Vanadium(V) reduction and preconcentration of vanadium(IV) was carried out using in‐line silver reductor and 8‐hydroxyquinoline chelating columns at pH 3.15, respectively. The calibration graph for vanadium(IV) was linear in the concentration range of 0.025–10 µg/L with relative standard deviation in the range of 0.4–5.58%. The detection limit (3s blank) was 3.8 × 10^?3 µg/L without preconcentration; when the vanadium(IV) was preconcentrated with an 8‐HQ column for 1 min (2.0 mL of sample loaded), the detection limit of 5.1 × 10^?4 µg/L was achieved. One analytical cycle can be completed in 2.0 min. The analysis of certified reference materials (CASS‐4, NASS‐5 and SLRS‐4) by the proposed method showed good agreement with the certified values. The method was successfully applied to the determination of total dissolved vanadium in environmental water samples. Copyright © 2010 John Wiley & Sons, Ltd.