Editor's choice: AnABlast: a new in silico strategy for the genome-wide search of novel genes and fossil regions

Genome annotation, assisted by computer programs, is one of the great advances in modern biology. Nevertheless, the in silico identification of small and complex coding sequences is still challenging. We observed that amino acid sequences inferred from coding—but rarely from non-coding—DNA sequences accumulated alignments in low-stringency BLAST searches, suggesting that this alignments accumulation could be used to highlight coding regions in sequenced DNA. To investigate this possibility, we developed a computer program (AnABlast) that generates profiles of accumulated alignments in query amino acid sequences using a low-stringency BLAST strategy. To validate this approach, all six-frame translations of DNA sequences between every two annotated exons of the fission yeast genome were analysed with AnABlast. AnABlast-generated profiles identified three new copies of known genes, and four new genes supported by experimental evidence. New pseudogenes, ancestral carboxyl- and amino-terminal subtractions, complex gene rearrangements, and ancient fragments of mitDNA and of bacterial origin, were also inferred. Thus, this novel in silico approach provides a powerful tool to uncover new genes, as well as fossil-coding sequences, thus providing insight into the evolutionary history of annotated genomes.     

A novel mutation in the mitochondrial tRNAAla gene (m.5636T>C) in a patient with progressive external ophthalmoplegia

We report a heteroplasmic novel mutation m.5636T>C in the mt-tRNA^Ala in a patient with bilateral ptosis and ophthalmoparesis in whom a muscle biopsy showed cytochrome c oxdidase (COX) negative and ragged red fibers. Using laser capture microdissection we have isolated COX negative fibers and COX positive fibers from the muscle of the patient and determined that the mutation load was clearly increased in COX negative muscle fibers. Additionally, the mutated m.5636T nucleotide is conserved in all the mammal and non-mammal species analyzed and might be structurally relevant as it is located in a position involved in the formation of tertiary structure of canonical mitochondrial tRNAs.     

How to choose a biodiversity indicator – Redundancy and complementarity of biodiversity metrics in a freshwater ecosystem

A range of biodiversity metrics are available to assess the ecological integrity of aquatic ecosystems. However, performance varies considerably among different types of metrics and provides different information regarding ecosystem conditions, thus making difficult the selection of appropriate metrics for biomonitoring. The present study evaluated the robustness of six biodiversity metrics to assess environmental change and determine their utility as relevant indicators of ecosystem biodiversity and functionality. Traditional metrics such as species richness and Shannon diversity were considered along with alternative metrics such as functional diversity, size diversity and taxonomic distinctness. To that end, invertebrate assemblages in a river floodplain were used as a case study to evaluate the performance of metrics using Generalized Additive Models (GAM). GAM explained between eight and 49% of the variability in biodiversity. The regression models exhibited differences in the response of biodiversity indicators to environmental factors, suggesting that intermediate levels of turbidity and low salinity are conditions favouring increased biodiversity in the study area. Based on correlations among metrics and responses to primary environmental factors, it is concluded that Shannon and functional diversity, and rarefied species richness generated similar information regarding ecosystem conditions (i.e., the metrics were redundant); while size diversity and distinctness provided useful additional data characterizing ecosystem quality (i.e., the metrics were complementary). Functional diversity indicated not only number and dominance of species, but also each species functional role in the community, and was therefore the most informative biodiversity metric. Nevertheless, the use of a combination of metrics, for example functional and size diversity, and variation in taxonomic distinctness, provides complementary data that will serve to achieve a more thorough understanding of ecosystem structure and function, and response to primary environmental influences.     

Marked mitochondrial DNA depletion associated with a novel SUCLG1 gene mutation resulting in lethal neonatal acidosis,multi-organ failure,and interrupted aortic arch

The aim of this study was to identify the causative genetic lesion in two apparently unrelated newborns having lethal lactic acidosis, multi-organ failure and congenital malformations including interrupted aortic arch, who exhibited mild methylmalonic aciduria, combined mitochondrial respiratory chain deficiency, and marked muscle mitochondrial DNA depletion. A novel mutation in the SUCLG1 gene was identified. Phenotype severity in Succinate-CoA ligase dysfunction appears to be more correlated to the muscle mtDNA content than to the tissue distribution of the heterodimer subunits. Prominent impairment of mitochondrial respiratory chain may result in deep ravages in developmental tissues leading to multiple organ failure and malformations.     

Histological evaluation of scar tissue inflammatory response: the role of hGH in diabetic rats

This paper describes a polymer site-specific delivery system containing human growth hormone in an in vivo model of scarring in the diabetic state. Copolymer discs with the hormone were introduced into incisions made in rats previously injected with streptozotocin in order to induce diabetes. Tissue specimens for evaluation were obtained at 3, 7 or 10 days after the procedure. Study groups were healthy rats and diabetic rats untreated or treated with/without the hormone. Histological sections were prepared for light microscopy examination of wound zones. Three and 7 days after surgery, polymer remains could be observed in the subcutaneous tissue. These remnants induced a moderate foreign body reaction. The number of macrophages detected was directly related to neovessel formation and metalloelastase expression. The CD4+/CD8+ ratio was low during the initial follow up stages (3 and 7 days) in untreated diabetic rats, yet an increased ratio corresponding to areas around the polymer remains was noted in the animals treated with copolymer loaded with the growth hormone. Copolymer is biodegradable in vivo and may be used as a vehicle for the slow release of active substances. The presence of the hormone at the site of skin injury induces cell proliferation and enhances the repair process.     

Discovery and SAR of new benzazepines as potent and selective 5-HT(2C) receptor agonists for the treatment of obesity

We report on the synthesis, biological evaluation and structure-activity relationships for a series of 3-benzazepine derivatives as 5-HT(2C) receptor agonists. The compounds were evaluated in functional assays measuring [3H] phosphoinositol turnover in HEK-293 cells transiently transfected with h5-HT(2C), h5-HT(2A) or h5-HT(2B) receptors. Several compounds are shown to be potent and selective 5-HT(2C) receptor agonists, which decrease food intake in a rat feeding model.     

Persistent expression of the ATP-binding cassette transporter, Abcg2, identifies cardiac SP cells in the developing and adult heart

Stem cells are important in the maintenance and repair of adult tissues. A population of cells, termed side population (SP) cells, has stem cell characteristics as they have been shown to contribute to diverse lineages. In this study, we confirm that Abcg2 is a determinant of the SP cell phenotype. Therefore, we examined Abcg2 expression during murine embryogenesis and observed robust expression in the blood islands of the E8.5 yolk sac and in developing tissues including the heart. During the latter stages of embryogenesis, Abcg2 identifies a rare cell population in the developing organs. We further establish that the adult heart contains an Abcg2 expressing SP cell population and these progenitor cells are capable of proliferation and differentiation. We define the molecular signature of cardiac SP cells and compare it to embryonic stem cells and adult cardiomyocytes using emerging technologies. We propose that the cardiac SP cell population functions as a progenitor cell population for the development, maintenance, and repair of the heart.     

Identification of commercial hake and grenadier species by proteomic analysis of the parvalbumin fraction

Analysis of parvalbumin fractions through proteomic methodologies allowed the differential classification of ten commercial, closely related species of the family Merlucciidae. Muscle extracts from nine hake species of the genus Merluccius including two subspecies of Merluccius australis (australis and polylepsis) and one grenadier species Macruronus novaezelandiae with two populations (novaezelandiae and magellanicus) were evaluated by 2-DE and MALDI-TOF MS. 2-DE demonstrated that the species tested displayed a low intra-specific degree of polymorphism and the isoform patterns were noticeably species-specific. MALDI-TOF mass fingerprints showed clear differences in the pattern of peptides produced by tryptic digestion between the Merluccius and the Macruronus, making the genus differentiation possible. In addition, a selective peptide mass present in the spectra from certain hakes allowed its classification in two groups: Euro-African and American hakes. Besides, some specific masses allowed a clearly individual identification for M. bilinearis, M. australis polylepsis, M. australis australis, M. productus, M. paradoxus and M. polli, while the rest of the hake species can be grouped in two clusters, comprising M. hubbsi and M. gayi in one and M. merluccius and M. capensis in the other.     

Molecular cytogenetics and allotetraploidy in the red vizcacha rat, Tympanoctomys barrerae (Rodentia, Octodontidae)

The theoretical impossibility of polyploidy in mammals was overturned by the discovery of tetraploidy in the red vizcacha rat, Tympanoctomys barrerae (2n = 102). As a consequence of genome duplication, remarkably increased cell dimensions are observed in the spermatozoa and in different somatic cell lines of this species. Locus duplication had been previously demonstrated by in situ PCR and Southern blot analysis of single-copy genes. Here, we corroborate duplication of loci in multiple-copy (major rDNAs) and single-copy (Hoxc8) genes by fluorescence in situ hybridization. We also demonstrate that nucleolar dominance, a large-scale epigenetic silencing phenomenon characteristic of allopolyploids, explains the presence of only one Ag-NOR chromosome pair in T. barrerae. Nucleolar dominance, together with the chromosomal heteromorphism detected in the G-banding pattern and synaptonemal complexes of the species' diploid-like meiosis, consistently indicates allotetraploidy. Allotetraploidization can coherently explain the peculiarities of gene silencing, cell dimensions, and karyotypic features of T. barrerae that remain unexplained by assuming diploidy and a large genome size attained by the dispersion of repetitive sequences.