Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction of specific T to C transitions at sites of interaction. However, current analytical tools do not distinguish between non-experimentally and experimentally induced transitions. Furthermore, geometric properties at potential binding sites are not taken into account. To surmount these shortcomings, we developed a two-step algorithm consisting of a non-parametric two-component mixture model and a wavelet-based peak calling procedure. Our algorithm can reduce the number of false positives up to 24% thereby identifying high confidence interaction sites. We successfully employed this approach in conjunction with a modified PAR-CLIP protocol to study the functional role of nuclear Moloney leukemia virus 10, a putative RNA helicase interacting with Argonaute2 and Polycomb. Our method, available as the R package wavClusteR, is generally applicable to any substitution-based inference problem in genomics.     

Glucoraphasatin: Chemistry, occurrence, and biological properties

Glucoraphasatin is an atypical glucosinolate mainly found in Raphanus sativus roots and sprouts. This review focuses on the chemistry, the occurrence, and the biological properties of glucoraphasatin.     

Profiling the changes in signaling pathways in ascorbic acid/β‐glycerophosphate‐induced osteoblastic differentiation

Despite numerous reports on the ability of ascorbic acid and β‐glycerophosphate (AA/β‐GP) to induce osteoblast differentiation, little is known about the molecular mechanisms involved in this phenomenon. In this work, we used a peptide array containing specific consensus sequences (potential substrates) for protein kinases and traditional biochemical techniques to examine the signaling pathways modulated during AA/β‐GP‐induced osteoblast differentiation. The kinomic profile obtained after 7 days of treatment with AA/β‐GP identified 18 kinase substrates with significantly enhanced or reduced phosphorylation. Peptide substrates for Akt, PI3K, PKC, BCR, ABL, PRKG1, PAK1, PAK2, ERK1, ERBB2, and SYK showed a considerable reduction in phosphorylation, whereas enhanced phosphorylation was observed in substrates for CHKB, CHKA, PKA, FAK, ATM, PKA, and VEGFR‐1. These findings confirm the potential usefulness of peptide microarrays for identifying kinases known to be involved in bone development in vivo and in vitro and show that this technique can be used to investigate kinases whose function in osteoblastic differentiation is poorly understood. J. Cell. Biochem. 112: 71–77, 2011. © 2010 Wiley‐Liss, Inc.     

Parasitoids of obscure mealybug,Pseudococcus viburni (Hem.: Pseudococcidae) in California: establishment of Pseudaphycus flavidulus (Hym.: Encyrtidae) and discussion of related parasitoid species

To improve natural suppression of the obscure mealybug, Pseudococcus viburni (Signoret), the parasitoids Pseudaphycus flavidulus (Brèthes) and Leptomastix epona (Walker) (Hymenoptera: Encyrtidae) of Chilean origin were released in California's Central Coast vineyards from 1997 to 1999. A survey for parasitoids of P. viburni was conducted in the Edna Valley appellation wine grape region from 2005 to 2007, 6–8 years after classical biological control releases were discontinued. Two survey methods were used. First, field collections of obscure mealybugs from commercial vineyard blocks (2005–2007) and, second, placement of “sentinel mealybugs” on potted (1 L) grape vines (2006 only). From both survey methods, P. flavidulus was recovered, albeit levels of parasitism were low (less than 0.6%). We also placed longtailed mealybug, Pseudococcus longispinus (Targioni Tozzetti), on potted plants concurrent with placement of sentinel obscure mealybugs in the vineyard in order to measure parasitoid activity on this closely-related mealybug species. No P. flavidulus were recovered from P. longispinus. Other encyrtid parasitoids reared from either P. viburni or P. longispinus were Anagyrus pseudococci (Girault), Leptomastix dactylopii Howard, Leptomastidea abnormis (Girault), Coccidoxenoides perminutus Girault, and Tetracnemoidea peregrina (Compere). A hyperparasitoid, Chaetocerus sp., was also reared. The data are discussed with respect to biological control of vineyard mealybugs and newly developed controls for the Argentine ant, Linepithema humile (Mayr) (Hymenoptera: Formicidae). Because Pseudaphycus species reared from mealybugs are superficially very similar a taxonomic key and discussion of host relationships for selected Pseudaphycus species are provided.     

Liver Accumulation of Plasmodium chabaudi-Infected Red Blood Cells and Modulation of Regulatory T Cell and Dendritic Cell Responses

It is postulated that accumulation of malaria-infected Red Blood Cells (iRBCs) in the liver could be a parasitic escape mechanism against full destruction by the host immune system. Therefore, we evaluated the in vivo mechanism of this accumulation and its potential immunological consequences. A massive liver accumulation of P. c. chabaudi AS-iRBCs (Pc-iRBCs) was observed by intravital microscopy along with an over expression of ICAM-1 on day 7 of the infection, as measured by qRT-PCR. Phenotypic changes were also observed in regulatory T cells (Tregs) and dendritic cells (DCs) that were isolated from infected livers, which indicate a functional role for Tregs in the regulation of the liver inflammatory immune response. In fact, the suppressive function of liver-Tregs was in vitro tested, which demonstrated the capacity of these cells to suppress naive T cell activation to the same extent as that observed for spleen-Tregs. On the other hand, it is already known that CD4+ T cells isolated from spleens of protozoan parasite-infected mice are refractory to proliferate in vivo. In our experiments, we observed a similar lack of in vitro proliferative capacity in liver CD4+ T cells that were isolated on day 7 of infection. It is also known that nitric oxide and IL-10 are partially involved in acute phase immunosuppression; we found high expression levels of IL-10 and iNOS mRNA in day 7-infected livers, which indicates a possible role for these molecules in the observed immune suppression. Taken together, these results indicate that malaria parasite accumulation within the liver could be an escape mechanism to avoid sterile immunity sponsored by a tolerogenic environment.