Interplay between pleiotropy and secondary selection determines rise and fall of mutators in stress response

Dramatic rise of mutators has been found to accompany adaptation of bacteria in response to many kinds of stress. Two views on the evolutionary origin of this phenomenon emerged: the pleiotropic hypothesis positing that it is a byproduct of environmental stress or other specific stress response mechanisms and the second order selection which states that mutators hitchhike to fixation with unrelated beneficial alleles. Conventional population genetics models could not fully resolve this controversy because they are based on certain assumptions about fitness landscape. Here we address this problem using a microscopic multiscale model, which couples physically realistic molecular descriptions of proteins and their interactions with population genetics of carrier organisms without assuming any a priori fitness landscape. We found that both pleiotropy and second order selection play a crucial role at different stages of adaptation: the supply of mutators is provided through destabilization of error correction complexes or fluctuations of production levels of prototypic mismatch repair proteins (pleiotropic effects), while rise and fixation of mutators occur when there is a sufficient supply of beneficial mutations in replication-controlling genes. This general mechanism assures a robust and reliable adaptation of organisms to unforeseen challenges. This study highlights physical principles underlying physical biological mechanisms of stress response and adaptation

The Caenorhabditis elegans GATA Factor ELT-1 Works through the Cell Proliferation Regulator BRO-1 and the Fusogen EFF-1 to Maintain the Seam Stem-Like Fate

Seam cells in Caenorhabditis elegans provide a paradigm for the stem cell mode of division, with the ability to both self-renew and produce daughters that differentiate. The transcription factor RNT-1 and its DNA binding partner BRO-1 (homologues of the mammalian cancer-associated stem cell regulators RUNX and CBFβ, respectively) are known rate-limiting regulators of seam cell proliferation. Here, we show, using a combination of comparative genomics and DNA binding assays, that bro-1 expression is directly regulated by the GATA factor ELT-1. elt-1(RNAi) animals display similar seam cell lineage defects to bro-1 mutants, but have an additional phenotype in which seam cells lose their stem cell-like properties and differentiate inappropriately by fusing with the hyp7 epidermal syncytium. This phenotype is dependent on the fusogen EFF-1, which we show is repressed by ELT-1 in seam cells. Overall, our data suggest that ELT-1 has dual roles in the stem-like seam cells, acting both to promote proliferation and prevent differentiation

Search for rare quark-annihilation decays, B --> Ds(*) Phi

We report on searches for B- --> Ds- Phi and B- --> Ds*- Phi. In the context of the Standard Model, these decays are expected to be highly suppressed since they proceed through annihilation of the b and u-bar quarks in the B- meson. Our results are based on 234 million Upsilon(4S) --> B Bbar decays collected with the BABAR detector at SLAC. We find no evidence for these decays, and we set Bayesian 90% confidence level upper limits on the branching fractions BF(B- --> Ds- Phi) Ds*- Phi)<1.2x10^(-5). These results are consistent with Standard Model expectations.Comment: 8 pages, 3 postscript figues, submitted to Phys. Rev. D (Rapid Communications

Identifying barriers and improving communication between cancer service providers and Aboriginal patients and their families: the perspective of service providers

BACKGROUND: Aboriginal Australians experience poorer outcomes from cancer compared to the non-Aboriginal population. Some progress has been made in understanding Aboriginal Australians’ perspectives about cancer and their experiences with cancer services. However, little is known of cancer service providers’ (CSPs) thoughts and perceptions regarding Aboriginal patients and their experiences providing optimal cancer care to Aboriginal people. Communication between Aboriginal patients and non-Aboriginal health service providers has been identified as an impediment to good Aboriginal health outcomes. This paper reports on CSPs’ views about the factors impairing communication and offers practical strategies for promoting effective communication with Aboriginal patients in Western Australia (WA).METHODS: A qualitative study involving in-depth interviews with 62 Aboriginal and non-Aboriginal CSPs from across WA was conducted between March 2006 - September 2007 and April-October 2011. CSPs were asked to share their experiences with Aboriginal patients and families experiencing cancer. Thematic analysis was carried out. Our analysis was primarily underpinned by the socio-ecological model, but concepts of Whiteness and privilege, and cultural security also guided our analysis.RESULTS: CSPs’ lack of knowledge about the needs of Aboriginal people with cancer and Aboriginal patients’ limited understanding of the Western medical system were identified as the two major impediments to communication. For effective patient–provider communication, attention is needed to language, communication style, knowledge and use of medical terminology and cross-cultural differences in the concept of time. Aboriginal marginalization within mainstream society and Aboriginal people’s distrust of the health system were also key issues impacting on communication. Potential solutions to effective Aboriginal patient-provider communication included recruiting more Aboriginal staff, providing appropriate cultural training for CSPs, cancer education for Aboriginal stakeholders, continuity of care, avoiding use of medical jargon, accommodating patients’ psychosocial and logistical needs, and in-service coordination.CONCLUSION: Individual CSPs identified challenges in cross-cultural communication and their willingness to accommodate culture-specific needs within the wider health care system including better communication with Aboriginal patients. However, participants’ comments indicated a lack of concerted effort at the system level to address Aboriginal disadvantage in cancer outcomes

Unfinished Decolonisation and Globalisation

This article locates John Darwin’s work on decolonisation within an Oxbridge tradition which portrays a British world system, of which formal empire was but one part, emerging to increasing global dominance from the early nineteenth century. In this mental universe, decolonisation was the mirror image of that expanding global power. According to this point of view, it was not the sloughing off of individual territories, but rather the shrinking away of the system and of the international norms that supported it, until only its ghost remained by the end of the 1960s. The article then asks, echoing the title of Darwin’s Unfinished Empire, whether the decolonisation project is all but complete, or still ongoing. In addition, what is the responsibility of the imperial historian to engage with, inform, or indeed refrain from, contemporary debates that relate to some of these issues? The answer is twofold. On the one hand, the toolkit that the Oxbridge tradition and Darwin provide remains relevant, and also useful in thinking about contemporary issues such as China’s move towards being a global power, the United States’ declining hegemony, and some states and groups desires to rearticulate their relationship with the global. On the other hand, the decline of world systems of power needs to be recognised as just one of several types of, and approaches to, analysing ‘decolonisation’. One which cannot be allowed to ignore or marginalise the study of others, such as experience, first nations issues, the shaping of the postcolonial state, and empire legacies. The article concludes by placing the Oxbridge tradition into a broader typology of types and methodologies of decolonisation, and by asking what a new historiography of decolonisation might look like. It suggests that it would address the Oxbridge concern with the lifecycles of systems of power and their relationship to global changes, but also place them alongside, and in dialogue with, a much broader set of perspectives and analytical approaches

Bioinformatics and Functional Analysis of an Entamoeba histolytica Mannosyltransferase Necessary for Parasite Complement Resistance and Hepatical Infection

The glycosylphosphatidylinositol (GPI) moiety is one of the ways by which many cell surface proteins, such as Gal/GalNAc lectin and proteophosphoglycans (PPGs) attach to the surface of Entamoeba histolytica, the agent of human amoebiasis. It is believed that these GPI-anchored molecules are involved in parasite adhesion to cells, mucus and the extracellular matrix. We identified an E. histolytica homolog of PIG-M, which is a mannosyltransferase required for synthesis of GPI. The sequence and structural analysis led to the conclusion that EhPIG-M1 is composed of one signal peptide and 11 transmembrane domains with two large intra luminal loops, one of which contains the DXD motif, involved in the enzymatic catalysis and conserved in most glycosyltransferases. Expressing a fragment of the EhPIG-M1 encoding gene in antisense orientation generated parasite lines diminished in EhPIG-M1 levels; these lines displayed reduced GPI production, were highly sensitive to complement and were dramatically inhibited for amoebic abscess formation. The data suggest a role for GPI surface anchored molecules in the survival of E. histolytica during pathogenesis

Development of a Tetrameric Streptavidin Mutein with Reversible Biotin Binding Capability: Engineering a Mobile Loop as an Exit Door for Biotin

A novel form of tetrameric streptavidin has been engineered to have reversible biotin binding capability. In wild-type streptavidin, loop3–4 functions as a lid for the entry and exit of biotin. When biotin is bound, interactions between biotin and key residues in loop3–4 keep this lid in the closed state. In the engineered mutein, a second biotin exit door is created by changing the amino acid sequence of loop7–8. This door is mobile even in the presence of the bound biotin and can facilitate the release of biotin from the mutein. Since loop7–8 is involved in subunit interactions, alteration of this loop in the engineered mutein results in an 11° rotation between the two dimers in reference to wild-type streptavidin. The tetrameric state of the engineered mutein is stabilized by a H127C mutation, which leads to the formation of inter-subunit disulfide bonds. The biotin binding kinetic parameters (koff of 4.28×10−4 s−1 and Kd of 1.9×10−8 M) make this engineered mutein a superb affinity agent for the purification of biotinylated biomolecules. Affinity matrices can be regenerated using gentle procedures, and regenerated matrices can be reused at least ten times without any observable reduction in binding capacity. With the combination of both the engineered mutein and wild-type streptavidin, biotinylated biomolecules can easily be affinity purified to high purity and immobilized to desirable platforms without any leakage concerns. Other potential biotechnological applications, such as development of an automated high-throughput protein purification system, are feasible

The bZIP Transcription Factor Rca1p Is a Central Regulator of a Novel CO2 Sensing Pathway in Yeast

Like many organisms the fungal pathogen Candida albicans senses changes in the environmental CO2 concentration. This response involves two major proteins: adenylyl cyclase and carbonic anhydrase (CA). Here, we demonstrate that CA expression is tightly controlled by the availability of CO2 and identify the bZIP transcription factor Rca1p as the first CO2 regulator of CA expression in yeast. We show that Rca1p upregulates CA expression during contact with mammalian phagocytes and demonstrate that serine 124 is critical for Rca1p signaling, which occurs independently of adenylyl cyclase. ChIP-chip analysis and the identification of Rca1p orthologs in the model yeast Saccharomyces cerevisiae (Cst6p) point to the broad significance of this novel pathway in fungi. By using advanced microscopy we visualize for the first time the impact of CO2 build-up on gene expression in entire fungal populations with an exceptional level of detail. Our results present the bZIP protein Rca1p as the first fungal regulator of carbonic anhydrase, and reveal the existence of an adenylyl cyclase independent CO2 sensing pathway in yeast. Rca1p appears to regulate cellular metabolism in response to CO2 availability in environments as diverse as the phagosome, yeast communities or liquid culture