Efficient termination of transcription by RNA polymerase I requires the 5 ' exonuclease Rat1 in yeast

During transcription termination by RNA polymerase II on protein-coding genes, the nuclear 5′ exonuclease Rat1/Xrn2 degrades the nascent transcript downstream from the polyadenylation site and “torpedoes” the polymerase. We report that the activity of Rat1 is also required for efficient termination by RNA polymerase I (Pol I) on the rDNA. In strains lacking catalytically active Rat1 or its cofactor Rai1, Pol I reads through the major, “Reb1-dependent” terminator (T1) but stops downstream at the “fail-safe” terminator (T2) and replication fork barrier (RFB). The absence of both Rat1 and the RFB-binding protein Fob1 increased Pol I read-through of T2 and the RFB. We propose that cotranscriptional cleavage of the pre-rRNA by the endonuclease Rnt1 generates a loading site for the Rat1/Rai1 complex, which then degrades the nascent transcript. When Rat1 catches Pol I, which is predicted to be paused at T1, transcription is terminated

Open licensing of BioBrick parts

This document provides recommendations for licensing of community-created biological parts, especially in BioBrick standard

Analysis of the treg cell population in the peripheral blood of ovarian cancer patients in relation to the long-term outcomes

Objectives: There is growing evidence that Treg cell infiltration into the cancer nest is associated with poor prognosis. How- ever, the Treg cell population in the peripheral blood may change when a different type of anticancer therapy is applied. Since Treg cells may support tumor growth by enhancing the suppressive profile of the cancer microenvironment, the assessment of Treg cells can bring to light important information regarding prognosis. Thus we decided to analyze the Treg cell population in the peripheral blood in relation to long-term outcomes in the group of patients with ovarian cancer.  Material and methods: The 80 patients included in the study were treated surgically followed by chemiotherapy for ovar- ian cancer between October 2010 through May 2011.The peripheral blood samples from the patients were collected directly prior to chemotherapy. Information on any patients who died was retrieved from the database of the Cuiavia-Pomerania Regional Office of the National Health System of Poland. CD4+CD25+FOXP3+ lymphocytes T were assed by flow cytometry. We have analyzed the long term outcomes of treatment regarding to the level of Treg cells in peripheral blood.  Results: We found that patients with serous adenocarcinomas had significantly higher Treg levels compared to those patients with non-serous types. Patients who had a higher percentage of Treg cells within the CD4+ cell population prior to the beginning of the treatment had worse long-term outcomes from the applied therapy.  Conclusions: The assessment of Treg levels prior to the start of chemotherapy is clinically useful and may predict overall survival in ovarian cancer patients.

Proton binding by linear, branched, and hyperbranched polyelectrolytes

This article reviews our understanding of ionization processes of weak polyelectrolytes. The emphasis is put on a general introduction to site binding models, which are able to account for many experimental features of linear and branched polyelectrolytes, including dendrimers. These models are fully compatible with the classical description of acid–base equilibria. The review further discusses the nature of the site–site interaction and role of conformational equilibria. Experimental charging data of numerous weak polyelectrolytes are discussed in terms of these models in detail

Charging of weak polyelectrolytes

The site binding model is capable to capture the protonation behavior of various poly(ethylene imines) and poly(propylene imines). The main tenet of the model is that interactions between neighboring sites are taken into account, which leads to a binding isotherm that cannot be expressed in a simple algebraic form. For small molecules, on the other hand, the model reduces to the classical chemical equilibrium description of the protonation equilibria, whereby the corresponding binding constants are again influenced by the interactions between the sites. The model can be extended to other types of polyelectrolytes, although in many situations one must deal with their tacticity, which is often not known very precisely

Ion binding to polyelectrolytes

Binding of simple ions to polyelectrolytes is reviewed. Proton binding in excess salt is understood quite well. At intermediate distances between the groups, the binding isotherms broaden due to electrostatic interactions, and are captured by a simple mean-field model. At smaller distances between the groups, short-ranged interactions induce plateaus in the binding isotherms, which correspond to ordered intermediate structures. This scenario is equally applicable to linear and branched polyelectrolytes. Molecular conformations may be coupled to proton binding. For example, protonation may be accompanied by a sudden conformational transition signaled by a jump in the binding isotherm. This behavior results from attractive interactions between the polymer backbone segments. For other types of ions, our understanding is more limited, also due to lack of experimental data. Multivalent ions interact with polyelectrolytes strongly, partly due to strong electrostatic interactions and their tendency towards multidentate binding

The intrinsic view of ionization equilibria of polyprotic molecules

The intrinsic approach describing microscopic ionization equilibria is presented. This description massively reduces the number of parameters needed to characterize microequilibria. Particularly, by exploring molecular symmetries and group transferability, this approach is capable of resolving such equilibria even for rather complex molecules. Intrinsic constants are assigned to each ionizable group and interactions between these sites are introduced. These interactions involve pairs or triplets of sites. The strength of these interactions decreases rapidly with the distance between the sites. Once these parameters are known, one can obtain macroconstants, microconstants, microstate mole fractions, and overall or site-specific titration curves. These quantities provide insight into the protonation of the molecules in question. The knowledge of such properties is relevant for a wide range of phenomena, including receptor–ligand interactions, action of drugs, or geochemical processes