USP1 deubiquitinase: cellular functions, regulatory mechanisms and emerging potential as target in cancer therapy

12 p.

Climate adaptation and the fifth amendment of the United States Constitution: How do adaptation strategies impact regulatory takings claims?

As the impacts and potential of climate change are realized at the governance level, states are moving towards adaptation strategies that include greater regulatory restrictions on development within coastal zones. The purpose of this paper is to outline the impacts of existing and planned regulatory mechanisms on the Fifth Amendment to the United States Constitution, which prevents the government taking of private property for public use without just compensation. A short history of regulatory takings is explained, and the potential legal issues surrounding mitigation and adaptation measures for coastal communities are discussed. The goal is to gain an understanding of the legal issues that must be resolved by governments to effectively deal with regulatory takings claims as coastal mitigation and adaptation plans are implemented. (PDF contains 3 pages)

Role of feedback and dynamics in a gene regulatory network

Cells exhibit a diverse repertoire of dynamic behaviors. These dynamic functions are implemented by circuits of interacting biomolecules. Although these regulatory networks function deterministically by executing specific programs in response to extracellular signals, molecular interactions are inherently governed by stochastic fluctuations. This molecular noise can manifest as cell-to-cell phenotypic heterogeneity in a well-mixed environment. Single-cell variability may seem like a design flaw but the coexistence of diverse phenotypes in an isogenic population of cells can also serve a biological function by increasing the probability of survival of individual cells upon an abrupt change in environmental conditions. Decades of extensive molecular and biochemical characterization have revealed the connectivity and mechanisms that constitute regulatory networks. We are now confronted with the challenge of integrating this information to link the structure of these circuits to systems-level properties such as cellular decision making. To investigate cellular decision-making, we used the well studied galactose gene-regulatory network in \textit{Saccharomyces cerevisiae}. We analyzed the mechanism and dynamics of the coexistence of two stable on and off states for pathway activity. We demonstrate that this bimodality in the pathway activity originates from two positive feedback loops that trigger bistability in the network. By measuring the dynamics of single-cells in a mixed sugar environment, we observe that the bimodality in gene expression is a transient phenomenon. Our experiments indicate that early pathway activation in a cohort of cells prior to galactose metabolism can accelerate galactose consumption and provide a transient increase in growth rate. Together these results provide important insights into strategies implemented by cells that may have been evolutionary advantageous in competitive environments.

The combinatorics of transcriptional regulation

The ability to regulate gene expression is of central importance for the adaptability of living organisms to changes in their internal and external environment. At the transcriptional level, binding of transcription factors (TFs) in the vicinity of promoters can modulate the rate at which transcripts are produced, and as such play an important role in gene regulation. TFs with regulatory action at multiple promoters is the rule rather than the exception, with examples ranging from TFs like the cAMP receptor protein (CRP) in E. coli that regulates hundreds of different genes, to situations involving multiple copies of the same gene, such as on plasmids, or viral DNA. When the number of TFs heavily exceeds the number of binding sites, TF binding to each promoter can be regarded as independent. However, when the number of TF molecules is comparable to the number of binding sites, TF titration will result in coupling ("entanglement") between transcription of different genes. The last few decades have seen rapid advances in our ability to quantitatively measure such effects, which calls for biophysical models to explain these data. Here we develop a statistical mechanical model which takes the TF titration effect into account and use it to predict both the level of gene expression and the resulting correlation in transcription rates for a general set of promoters. To test these predictions experimentally, we create genetic constructs with known TF copy number, binding site affinities, and gene copy number; hence avoiding the need to use free fit parameters. Our results clearly prove the TF titration effect and that the statistical mechanical model can accurately predict the fold change in gene expression for the studied cases. We also generalize these experimental efforts to cover systems with multiple different genes, using the method of mRNA fluorescence in situ hybridization (FISH). Interestingly, we can use the TF titration affect as a tool to measure the plasmid copy number at different points in the cell cycle, as well as the plasmid copy number variance. Finally, we investigate the strategies of transcriptional regulation used in a real organism by analyzing the thousands of known regulatory interactions in E. coli. We introduce a "random promoter architecture model" to identify overrepresented regulatory strategies, such as TF pairs which coregulate the same genes more frequently than would be expected by chance, indicating a related biological function. Furthermore, we investigate whether promoter architecture has a systematic effect on gene expression by linking the regulatory data of E. coli to genome-wide expression censuses.

Isolation of the murine interleukin 2 gene and characterization of its regulatory architecture

Interleukin 2 (IL2) is the primary growth hormone used by mature T cells and this lymphokine plays an important role in the magnification of cell-mediated immune responses. Under normal circumstances its expression is limited to antigen-activated type 1 helper T cells (T_H1) and the ability to transcribe this gene is often regarded as evidence for commitment to this developmental lineage. There is, however, abundant evidence than many non-T_H1 T cells, under appropriate conditions, possess the ability to express this gene. Of paramount interest in the study of T-cell development is the mechanisms by which differentiating thymocytes are endowed with particular combinations of cell surface proteins and response repertoires. For example, why do most helper T cells express the CD4 differentiation antigen?

As a first step in understanding these developmental processes the gene encoding IL2 was isolated from a mouse genomic library by probing with a conspecific IL2 cDNA. The sequence of the 5' flanking region from + 1 to -2800 was determined and compared to the previously reported human sequence. Extensive identity exists between +1 and -580 (86%) and sites previously shown to be crucial for the proper expression of the human gene are well conserved in both sequence location in the mouse counterpart.

Transient expression assays were used to evaluate the contribution of various genomic sequences to high-level gene expression mediated by a cloned IL2 promoter fragment. Differing lengths of 5' flanking DNA, all terminating in the 5' untranslated region, were linked to a reporter gene, bacterial chloramphenicol acetyltransferase (CAT) and enzyme activity was measured after introduction into IL2-producing cell lines. No CAT was ever detected without stimulation of the recipient cells. A cloned promoter fragment containing only 321 bp of upstream DNA was expressed well in both Jurkat and EL4.El cells. Addition of intragenic or downstream DNA to these 5' IL2-CAT constructs showed that no obvious regulatory regions resided there. However, increasing the extent of 5' DNA from -321 to -2800 revealed several positive and negative regulatory elements. One negative region that was well characterized resided between -750 and -1000 and consisted almost exclusively of alternating purine and pyrimidines. There is no sequence resembling this in the human gene now, but there is evidence that there may have once been.

No region, when deleted, could relax either the stringent induction-dependence on cell-type specificity displayed by this promoter. Reagents that modulated endogenous IL2 expression, such as cAMP, cyclosporin A, and IL1, affected expression of the 5' IL2-CAT constructs also. For a given reagent, expression from all expressible constructs was suppressed or enhanced to the same extent. This suggests that these modulators affect IL2 expression through perturbation of a central inductive signal rather than by summation of the effects of discrete, independently regulated, negative and positive transcription factors.

A Previdência Social no estado contemporâneo Fundamentos, financiamento e regulação

A previdência social brasileira, apesar de constituir um dos modelos mais antigos e tradicionais de proteção social da América Latina, não muito distante dos modelos europeus quanto a sua gênese, passa por momentos difíceis. Em um contexto de rápido envelhecimento populacional, acelerada redução de natalidade e novas realidades de trabalho, nas quais a mão-de-obra assalariada perde seu espaço, o modelo tradicional de cobertura, nos moldes bismarckianos, carece de revisão, de forma a não somente adequar-se às novas premissas demográficas, mas permitir uma universalidade de cobertura efetiva. Para tanto, adota-se, como fundamento de um novo modelo, a justiça social em três dimensões necessidade, igualdade e mérito. A necessidade visa atender e assegurar a qualquer pessoa, dentro das necessidades sociais cobertas, um pagamento mínimo de forma a assegurar o mínimo existencial. A dimensão da igualdade, no viés material, visa preservar nível de bem-estar compatível, em alguma medida, com o usufruído durante a vida ativa. Já o mérito individual implica fornecer prestações mais elevadas aos que, conscientemente, reduziram o consumo presente, preservando parte de suas receitas para o futuro. As duas primeiras dimensões são, na proposta apresentada, organizadas pelo Estado, em pilares compulsórios e financiados, preponderantemente, por repartição simples. O modelo de financiamento adotado, no longo prazo, tem se mostrado mais seguro e isonômico frente a modelos capitalizados. As variantes demográficas podem ser adequadas mediante novos limites de idade para aposentadorias e, em especial, estímulo a natalidade, como novos serviços da previdência social, incluindo creches e pré-escolas. O terceiro pilar, fundado no mérito individual, é a previdência complementar, organizado de forma privada, autônoma e voluntária. Aqui, o financiamento sugerido é a capitalização, de forma a priorizar o rendimento e a eficiência, com as externalidades positivas para a economia e a sociedade, com risco assumido e aceitável em razão do papel subsidiário deste pilar protetivo. Os pilares estatais, no modelo proposto, serão financiados, exclusivamente, por impostos, pondo-se fim às contribuições sociais, que perdem a importância em um modelo universal de proteção. Troca-se a solidariedade do grupo pela solidariedade social e, como conseqüência, saem as contribuições e ingressam os impostos. Mesmo o segundo pilar, que visa prestações correlacionadas com os rendimentos em atividade, será financiado por adicional de imposto de renda. Sistema mais simples, eficaz, e com estímulo à formalização da receita por parte das pessoas. A gestão do modelo previdenciário, em todos os segmentos, contará com forte regulação estatal, mas com efetiva participação dos interessados, afastadas, dentro do possível, as ingerências políticas e formas de captura. A regulação previdenciária, desde adequadamente disciplinada e executada, permitirá que os pilares propostos funcionem em harmonia.