DNA ploidy of human breast cancer

Ploidy was determined on 663 resectable primary tumors from untreated patients. Nuclei obtained by mechanical disaggregation of frozen tissue were stained with propidium iodide and analysed in a FACS IV. Aneuploidy was detected in 73% of cases. It was not significantly related to nodal involvement or tumor size, although the highest frequencies were observed in large tumors (88%) or with more than 10 positive nodes (77%). Aneuploidy was more frequently observed in ductal infiltrating (81%) than in lobular histology and in tumors lacking both progesterone and estrogen receptors (85%). Analysis of ploidy in primary and synchronous lymph node metastases from the same patient showed a high agreement rate (90%) of DNA patterns simply defined as diploid or aneuploid. However, differences in DNA stemlines and DNA indices between the two synchronous lesions from the same patient were a rather frequent event.     

A rapid double-staining technique to improve seed viability testing in terrestrial orchids

Abstract

The need to optimize seed banking efforts has stimulated research for rapid methods to estimate quality in seed-lots. For terrestrial orchids, viability testing using tetrazolium (TTC) staining requires chemical scarification, as seeds have an impermeable testa. Different seed-coat permeability may affect TTC staining, thus affecting the results. The aim of this study was to perform a permeability test to assess the effectiveness of the used scarification method and its usefulness to correct TTC viability results. Mature seeds of Anacamptis laxiflora were subjected to eight scarification treatments with sodium hypochlorite solutions with different concentration and duration. Viability tests were performed using the basic TTC methodology, followed by a permeability test performed by means of trypan blue dye. The different scarification methods resulted in estimated TTC viability ranging from 0% and 94% for the same seed lot of A. laxiflora seeds. Our results proved that the used scarification protocol significantly affects both seed coat permeability and subsequent TTC staining (two-way ANOVA, p?< 0.0001). We describe a new rapid protocol that can be used to test terrestrial orchid seed viability. This double-staining method, providing rapid information on seed coat permeability, can be useful to avoid under-estimation of TTC results.     

Abi1 is essential for the formation and activation of a WAVE2 signalling complex

WAVE2 belongs to a family of proteins that mediates actin reorganization by relaying signals from Rac to the Arp2/3 complex, resulting in lamellipodia protrusion. WAVE2 displays Arp2/3-dependent actin nucleation activity in vitro, and does not bind directly to Rac. Instead, it forms macromolecular complexes that have been reported to exert both positive and negative modes of regulation. How these complexes are assembled, localized and activated in vivo remains to be established. Here we use tandem mass spectrometry to identify an Abi1-based complex containing WAVE2, Nap1 (Nck-associated protein) and PIR121. Abi1 interacts directly with the WHD domain of WAVE2, increases WAVE2 actin polymerization activity and mediates the assembly of a WAVE2-Abi1-Nap1-PIR121 complex. The WAVE2-Abi1-Nap1-PIR121 complex is as active as the WAVE2-Abi1 sub-complex in stimulating Arp2/3, and after Rac activation it is re-localized to the leading edge of ruffles in vivo. Consistently, inhibition of Abi1 by RNA interference (RNAi) abrogates Rac-dependent lamellipodia protrusion. Thus, Abi1 orchestrates the proper assembly of the WAVE2 complex and mediates its activation at the leading edge in vivo.     

Direct binding of specific AUF1 isoforms to tandem zinc finger domains of tristetraprolin (TTP) family proteins

Tristetraprolin (TTP) is the prototype of a family of CCCH tandem zinc finger proteins that can bind to AU-rich elements in mRNAs and promote their decay. TTP binds to mRNA through its central tandem zinc finger domain; it then promotes mRNA deadenylation, considered to be the rate-limiting step in eukaryotic mRNA decay. We found that TTP and its related family members could bind to certain isoforms of another AU-rich element-binding protein, HNRNPD/AUF1, as well as a related protein, laAUF1. The interaction domain within AUF1p45 appeared to be a C-terminal "GY" region, and the interaction domain within TTP was the tandem zinc finger domain. Surprisingly, binding of AUF1p45 to TTP occurred even with TTP mutants that lacked RNA binding activity. In cell extracts, binding of AUF1p45 to TTP potentiated TTP binding to ARE-containing RNA probes, as determined by RNA gel shift assays; AUF1p45 did not bind to the RNA probes under these conditions. Using purified, recombinant proteins and a synthetic RNA target in FRET assays, we demonstrated that AUF1p45, but not AUF1p37, increased TTP binding affinity for RNA ～5-fold. These data suggest that certain isoforms of AUF1 can serve as "co-activators" of TTP family protein binding to RNA. The results raise interesting questions about the ability of AUF1 isoforms to regulate the mRNA binding and decay-promoting activities of TTP and its family members as well as the ability of AUF1 proteins to serve as possible physical links between TTP and other mRNA decay proteins and structures.     

Assembly of Functional Ribonucleoprotein Complexes by AU-rich Element RNA-binding Protein 1 (AUF1) Requires Base-dependent and -independent RNA Contacts

AU-rich element RNA-binding protein 1 (AUF1) regulates the stability and/or translational efficiency of diverse mRNA targets, including many encoding products controlling the cell cycle, apoptosis, and inflammation by associating with AU-rich elements residing in their 3′-untranslated regions. Previous biochemical studies showed that optimal AUF1 binding requires 33–34 nucleotides with a strong preference for U-rich RNA despite observations that few AUF1-associated cellular mRNAs contain such extended U-rich domains. Using the smallest AUF1 isoform (p37^AUF1) as a model, we employed fluorescence anisotropy-based approaches to define thermodynamic parameters describing AUF1 ribonucleoprotein (RNP) complex formation across a panel of RNA substrates. These data demonstrated that 15 nucleotides of AU-rich sequence were sufficient to nucleate high affinity p37^AUF1 RNP complexes within a larger RNA context. In particular, p37^AUF1 binding to short AU-rich RNA targets was significantly stabilized by interactions with a 3′-purine residue and largely base-independent but non-ionic contacts 5′ of the AU-rich site. RNP stabilization by the upstream RNA domain was associated with an enhanced negative change in heat capacity consistent with conformational changes in protein and/or RNA components, and fluorescence resonance energy transfer-based assays demonstrated that these contacts were required for p37^AUF1 to remodel local RNA structure. Finally, reporter mRNAs containing minimal high affinity p37^AUF1 target sequences associated with AUF1 and were destabilized in a p37^AUF1-dependent manner in cells. These findings provide a mechanistic explanation for the diverse population of AUF1 target mRNAs but also suggest how AUF1 binding could regulate protein and/or microRNA binding events at adjacent sites.     

Effect of environmental parameters on biodiversity of the fungal component in lithic Antarctic communities

Extremophiles - A wide sampling of rocks, colonized by microbial epi–endolithic communities, was performed along an altitudinal gradient from sea level to 3600&nbsp;m asl and sea distance...