Toward an integrated system of clade names

Although the proposition that higher taxa should correspond to clades is widely accepted, current nomenclature does not distinguish clearly between different clades in nested series. In particular, the same name is often applied to a total clade, its crown clade, and clades originating with various nodes, branches, and apomorphies in between. An integrated system of clade names is described based on categories of clades defined with respect to lineages that have survived to the present time. In this system, the most widely known names are applied to crown clades, the names of total clades are formed by adding a standard prefix to the names of the corresponding crowns, and the names of apomorphy clades describe the specific apomorphies with which they originated. Relative to traditional approaches, this integrated approach to naming clades is both more precise concerning the associations of names with particular clades and more efficient with regard to the cognitive effort required to recognize the names of corresponding crown and total clades. It also seems preferable to five alternatives that could be used to make the same distinctions. The integrated system of clade names has several advantages, including the facilitation of communication among biologists who study distantly related clades, promoting a broader conceptualization of the origins of distinctive clades of extant organisms and emphasizing the continuous nature of evolution.     

Inferring species decline from collection records: roller dung beetles in Italy (Coleoptera, Scarabaeidae)

The decline of roller dung beetles (Coleoptera, Scarabaeidae) in Italy, at national and regional level, was described using a database of both literature and unpublished data, since the late of 19th century. The probability of finding roller species was assessed for each decade of the 20th century in order to detect changes in their distribution and status. An analysis of decline was performed using a complementary approach of different extinction indexes, according to IUCN criteria. During the 20th century, both the absolute number of records and the UTM cells where roller beetles were found increased clearly as a consequence of the escalation of entomological surveys. Nevertheless, comparing R species (rollers) with all the scarab dung beetles from the first to the last quarter of the 20th century, the relative frequency of roller records decreased by 31%, while the relative number of occupied UTM cells dropped by 23%. Six roller species showed a significant decline in Italy from the first to the second part of the 20th century, and nine in the last 30years. Other two species disappeared from the majority of the northern regions. Finally, the values of all the extinction indexes were strongly correlated and detected a high risk of extinction in Italy for six species. A gradual change in land use during the last three decades, consisting of a reduced extension of grasslands in favour of either intensive agriculture or reforestation after abandonment of livestock raising, was likely the main factor inducing decline and local extinction of roller species.     

The ingestion of a Nectandra membranacea extract changes the bioavailability of technetium-99m radiobiocomplex in rat organs

The radiobiocomplexes labeled with technetium-99m (Tc-99m) have been widely used in nuclear medicine in single photon emission computed tomography and in basic research. The aim of this study was to assess the influence of a Nectandra membranacea extract on the bioavailability of the sodium pertechnetate (Na(99m)TcO(4)) radiobiocomplex in rat organs. The animals were treated with a N. membranacea extract (30 mg/ ml), for 6 days. Na(99m)TcO(4) was injected, the organs were isolated and weighed, and the radioactivity was determined in each organ (%ATI/organ). The %ATI/organ was divided by the mass of each organ to calculate the %ATI/g. A significant increase of the %ATI/organ of Na(99m)TcO(4) was observed in muscle and thyroid as well as in the %ATI/g in the heart, kidney and thyroid. These findings could result from the interaction between components of the plant extract and the radiobiocomplex which may influence the uptake Na(99m)TcO(4) in rat organs. Therefore, precaution is suggested in the interpretation of nuclear medicine results in patients using this herb.     

PKC α-mediated CREB activation is oxygen and age-dependent in rat myocardial tissue

Both hypoxia and aging affect the morphology and the function of rat myocardial tissue. Moreover the heart tries to counteract the impaired function by activating specific signalling cascades. Here we report the involvement of CREB protein in “in vivo” response to hypoxic challenge and during aging in rat hearts. CREB is activated in parallel to HIF-1α nuclear translocation in the young after hypoxia exposure followed by reoxygenation, while this kind of response is not so dramatic in the old, neither in terms of CREB activation, neither in terms of HIF-1α expression and translocation, suggesting in the old the existence of an impaired oxygen-sensing mechanism or an adaptation of the cells to hypoxia. Moreover in the young a PKC α/Erk pathway seems to be involved in the activation of HIF-1α along with CREB, suggesting an attempt of the young to counteract the damage evoked by hypoxia, while in the old a PKC α/p38 MAPK/CREB pathway could determine the occurrence of both aging and aged cell hypoxia response.     

Insights into prion strains and neurotoxicity

Transmissible spongiform encephalopathies (TSEs) are neurodegenerative diseases that are caused by prions and affect humans and many animal species. It is now widely accepted that the infectious agent that causes TSEs is PrP(Sc), an aggregated moiety of the host-derived membrane glycolipoprotein PrP(C). Although PrP(C) is encoded by the host genome, prions themselves encipher many phenotypic TSE variants, known as prion strains. Prion strains are TSE isolates that, after inoculation into distinct hosts, cause disease with consistent characteristics, such as incubation period, distinct patterns of PrP(Sc) distribution and spongiosis and relative severity of the spongiform changes in the brain. The existence of such strains poses a fascinating challenge to prion research.     

Distribution and Genetic Diversity of Bacteriocin Gene Clusters in Rumen Microbial Genomes

Some species of ruminal bacteria are known to produce antimicrobial peptides, but the screening procedures have mostly been based on in vitro assays using standardized methods. Recent sequencing efforts have made available the genome sequences of hundreds of ruminal microorganisms. In this work, we performed genome mining of the complete and partial genome sequences of 224 ruminal bacteria and 5 ruminal archaea to determine the distribution and diversity of bacteriocin gene clusters. A total of 46 bacteriocin gene clusters were identified in 33 strains of ruminal bacteria. Twenty gene clusters were related to lanthipeptide biosynthesis, while 11 gene clusters were associated with sactipeptide production, 7 gene clusters were associated with class II bacteriocin production, and 8 gene clusters were associated with class III bacteriocin production. The frequency of strains whose genomes encode putative antimicrobial peptide precursors was 14.4%. Clusters related to the production of sactipeptides were identified for the first time among ruminal bacteria. BLAST analysis indicated that the majority of the gene clusters (88%) encoding putative lanthipeptides contained all the essential genes required for lanthipeptide biosynthesis. Most strains of Streptococcus (66.6%) harbored complete lanthipeptide gene clusters, in addition to an open reading frame encoding a putative class II bacteriocin. Albusin B-like proteins were found in 100% of the Ruminococcus albus strains screened in this study. The in silico analysis provided evidence of novel biosynthetic gene clusters in bacterial species not previously related to bacteriocin production, suggesting that the rumen microbiota represents an underexplored source of antimicrobial peptides.     

The Endosomal Sorting Complex Required for Transport Pathway Mediates Chemokine Receptor CXCR4-promoted Lysosomal Degradation of the Mammalian Target of Rapamycin Antagonist DEPTOR

G protein-coupled receptor (GPCR) signaling mediates many cellular functions, including cell survival, proliferation, and cell motility. Many of these processes are mediated by GPCR-promoted activation of Akt signaling by mammalian target of rapamycin complex 2 (mTORC2) and the phosphatidylinositol 3-kinase (PI3K)/phosphoinositide-dependent kinase 1 (PDK1) pathway. However, the molecular mechanisms by which GPCRs govern Akt activation by these kinases remain poorly understood. Here, we show that the endosomal sorting complex required for transport (ESCRT) pathway mediates Akt signaling promoted by the chemokine receptor CXCR4. Pharmacological inhibition of heterotrimeric G protein Gα_i or PI3K signaling and siRNA targeting ESCRTs blocks CXCR4-promoted degradation of DEPTOR, an endogenous antagonist of mTORC2 activity. Depletion of ESCRTs by siRNA leads to increased levels of DEPTOR and attenuated CXCR4-promoted Akt activation and signaling, consistent with decreased mTORC2 activity. In addition, ESCRTs likely have a broad role in Akt signaling because ESCRT depletion also attenuates receptor tyrosine kinase-promoted Akt activation and signaling. Our data reveal a novel role for the ESCRT pathway in promoting intracellular signaling, which may begin to identify the signal transduction pathways that are important in the physiological roles of ESCRTs and Akt.