Comparative experimental taphonomy of eight marine arthropods indicates distinct differences in preservation potential

Global biodiversity patterns in deep time can only be understood fully when the relative preservation potential of each clade is known. The relative preservation potential of marine arthropod clades, a diverse and ecologically important component of modern and past ecosystems, is poorly known. We tackled this issue by carrying out a 205‐day long comprehensive, comparative, taphonomic experiment in a laboratory by scoring up to ten taphonomic characters for multiple specimens of seven crustacean and one chelicerate species (two true crabs, one shrimp, one lobster, one hermit crab, one stomatopod, one barnacle and one horseshoe crab). Although the results are preliminary because we used a single experimental setup and algal growth partially hampered observations, some parts of hermit crabs, stomatopods, swimming crabs and barnacles decayed slowly relative to other parts, implying differential preservation potentials within species, largely consistent with the fossil record of these groups. An inferred parasitic isopod, manifested by a bopyriform swelling within a hermit crab carapace, decayed relatively fast. We found limited variation in the decay rate between conspecifics, and we did not observe size‐related trends in decay rate. Conversely, substantial differences in the decay rate between species were seen after c. 50 days, with shrimps and stomatopods decaying fastest, suggesting a relatively low preservation potential, whereas the lobster, calico crabs, horseshoe crabs and barnacles showed relatively slow decay rates, suggesting a higher preservation potential. These results are supported by two modern and fossil record‐based preservation potential metrics that are significantly correlated to decay rate ranks. Furthermore, we speculate that stemward slippage may not be ubiquitous in marine arthropods. Our results imply that diversity studies of true crabs, lobsters, horseshoe crabs and barnacles are more likely to yield patterns that are closer to their true biodiversity patterns than those for stomatopods, shrimps and hermit crabs.     

16S rRNA Phylogeny of Sponge-Associated Cyanobacteria

Phylogenetic analyses of 16S rRNA sequences of sponge-associated cyanobacteria showed them to be polyphyletic, implying that they derived from multiple independent symbiotic events. Most of the symbiont sequences were affiliated to a group of Synechococcus and Prochlorococcus species. However, other symbionts were related to different groups, such as the Oscillatoriales.     

DAP5 promotes cap-independent translation of Bcl-2 and CDK1 to facilitate cell survival during mitosis

DAP5 is an eIF4G protein previously implicated in mediating cap-independent translation in response to cellular stresses. Here we report that DAP5 is crucial for continuous cell survival in nonstressed cells. The knockdown of endogenous DAP5 induced M phase-specific caspase-dependent apoptosis. Bcl-2 and CDK1 were identified by two independent screens as DAP5 translation targets. Notably, the activity of the Bcl-2 IRES was reduced in DAP5 knockdown cells and a selective shift of Bcl-2 mRNA toward light polysomal fractions was detected. Furthermore, a functional IRES was identified in the 5'UTR of CDK1. At the cellular level, attenuated translation of CDK1 by DAP5 knockdown decreased the phosphorylation of its M phase substrates. Ectopic expression of Bcl-2 or CDK1 proteins partially reduced the extent of caspase activation caused by DAP5 knockdown. Thus, DAP5 is necessary for maintaining cell survival during mitosis by promoting cap-independent translation of at least two prosurvival proteins.     

KUTE-BASE: storing, downloading and exporting MIAME-compliant microarray experiments in minutes rather than hours

MOTIVATION: The BioArray Software Environment (BASE) is a very popular MIAME-compliant, web-based microarray data repository. However in BASE, like in most other microarray data repositories, the experiment annotation and raw data uploading can be very timeconsuming, especially for large microarray experiments. RESULTS: We developed KUTE (Karmanos Universal daTabase for microarray Experiments), as a plug-in for BASE 2.0 that addresses these issues. KUTE provides an automatic experiment annotation feature and a completely redesigned data work-flow that dramatically reduce the human-computer interaction time. For instance, in BASE 2.0 a typical Affymetrix experiment involving 100 arrays required 4 h 30 min of user interaction time forexperiment annotation, and 45 min for data upload/download. In contrast, for the same experiment, KUTE required only 28 min of user interaction time for experiment annotation, and 3.3 min for data upload/download. AVAILABILITY: http://vortex.cs.wayne.edu/kute/index.html.     

Assembling an arsenal,the scorpion way

Background  

For survival, scorpions depend on a wide array of short neurotoxic polypeptides. The venoms of scorpions from the most studied group, the Buthida, are a rich source of small, 23–78 amino acid-long peptides, well packed by either three or four disulfide bridges that affect ion channel function in excitable and non-excitable cells.     

EHD2 inhibits ligand-induced endocytosis and signaling of the leucine-rich repeat receptor-like protein LeEix2

Plants are constantly being challenged by aspiring pathogens. In order to protect themselves, plants have developed numerous defense mechanisms that are either specific or non-specific to the pathogen. Pattern recognition receptors can trigger plant defense responses in response to specific ligands or patterns. EIX (ethylene-inducing xylanase) triggers a defense response via the LeEix2 receptor, while bacterial flagellin triggers plant innate immunity via the FLS2 receptor. Endocytosis has been suggested to be crucial for the process in both cases. Here we show that the EIX elicitor triggers internalization of the LeEix2 receptor. Treatment with endocytosis, actin or microtubule inhibitors greatly reduced the internalization of LeEix2. Additionally, we demonstrate that plant EHD2 binds to LeEix2 and is an important factor in its internalization and in regulation of the induction of defense responses such as the hypersensitive response, ethylene biosynthesis and induction of pathogenesis-related protein expression in the case of EIX/LeEix2 (an LRR receptor lacking a kinase domain), but does not appear to be involved in the FLS2 system (an LRR receptor possessing a kinase domain). Our results suggest that various endocytosis pathways are involved in the induction of plant defense responses.     

The paradox of autophagy and its implication in cancer etiology and therapy

Autophagy is a cellular self-catabolic process in which cytoplasmic constituents are sequestered in double membrane vesicles that fuse with lysosomes where they are degraded. As this catabolic activity generates energy, autophagy is often induced under nutrient limiting conditions providing a mechanism to maintain cell viability and may be exploited by cancer cells for survival under metabolic stress. However, progressive autophagy can be cytotoxic and autophagy can under certain settings substitute for apoptosis in induction of cell death. Moreover, loss of autophagy is correlated with tumorigenesis and several inducers of autophagy are tumor-suppressor genes. Thus, the relation of autophagy to cancer development is complex and depends on the genetic composition of the cell as well as on the extra-cellular stresses a cell is exposed to. In this review we describe the intricate nature of autophagy and its regulators, particularly those that have been linked to cancer. We discuss the multifaceted relation of autophagy to tumorigenesis and highlight studies supporting a role for autophagy in both tumor-suppression and tumor-progression. Finally, various autophagy-targeting therapeutic strategies for cancer treatment are presented. This review is dedicated to the memory of Dr. Avner Eisenberg 1953–2004.     

Hsp90 recognizes a common surface on client kinases

Hsp90 is a highly abundant chaperone whose clientele includes hundreds of cellular proteins, many of which are central players in key signal transduction pathways and the majority of which are protein kinases. In light of the variety of Hsp90 clientele, the mechanism of selectivity of the chaperone toward its client proteins is a major open question. Focusing on human kinases, we have demonstrated that the chaperone recognizes a common surface in the amino-terminal lobe of kinases from diverse families, including two newly identified clients, NFkappaB-inducing kinase and death-associated protein kinase, and the oncoprotein HER2/ErbB-2. Surface electrostatics determine the interaction with the Hsp90 chaperone complex such that introduction of a negative charge within this region disrupts recognition. Compiling information on the Hsp90 dependence of 105 protein kinases, including 16 kinases whose relationship to Hsp90 is first examined in this study, reveals that surface features, rather than a contiguous amino acid sequence, define the capacity of the Hsp90 chaperone machine to recognize client kinases. Analyzing Hsp90 regulation of two major signaling cascades, the mitogen-activated protein kinase and phosphatidylinositol 3-kinase, leads us to propose that the selectivity of the chaperone to specific kinases is functional, namely that Hsp90 controls kinases that function as hubs integrating multiple inputs. These lessons bear significance to pharmacological attempts to target the chaperone in human pathologies, such as cancer.