The CEBPA gene is down-regulated in acute promyelocytic leukemia and its upstream promoter, but not the core promoter, is highly methylated

impairment of CCAAT Enhancer Binding Protein alpha (CEBPA) function is a common finding in acute myeloid leukemia; nevertheless, its relevance for acute promyelocytic leukemia pathogenesis is unclear. We analyzed the expression and assessed the methylation status of the core and upstream promoters of CEBPA in acute promyelocytic leukemia at diagnosis. Patients with acute promyelocytic leukemia (n=18) presented lower levels of CEBPA expression compared to healthy controls (n=5), but higher levels than those in acute myeloid leukemia with t(8;21) (n=9) and with inv(16) (n=5). Regarding the core promoter, we detected no methylation in 39 acute promyelocytic leukemia samples or in 8 samples from controls. In contrast, analysis of the upstream promoter showed methylation in 37 of 39 samples, with 17 patients showing methylation levels over 30%. Our results corroborate data obtained in animal models showing that CEBPA is down-regulated in acute promyelocytic leukemia stem cells and suggest that epigenetic mechanisms may be involved.

Single nucleotide polymorphism C/T-13910, located upstream of the lactase gene, associated with adult-type hypolactasia: Validation for clinical practice

Objectives: To validate C/T-13910 polymorphism associated with primary hypolactasia for clinical practice. Design and methods: Lactose breath test and PCR-RFLP for the C/T-13910 polymorphism were performed. Results: Twenty-seven of 28 patients with genotype CC had positive breath tests, all twenty-two patients with genotypes CT or TT had negative breath tests. Agreement of tests was high (p<0.0001; Kappa Index 0.96). Conclusion: C/T-13910 polymorphism detection may be a new tool for primary hypolactasia diagnosis. (C) 2008 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Upstream porthole injection in a 2-D scramjet model

Injection from portholes upstream of the combustion chamber was investigated as a method of delivering fuel into a scramjet. This method reduces the viscous drag on a model by allowing a reduction in the length of the combustion chamber. At experimental enthalpies of 3.0 MJ/kg in the T4 shock tunnel, there was no evidence of combustion in the intake, either by shadowgraph or pressure measurements. Combustion was observed in the combustion chamber. A theoretical extension of these results is made to a hot wall scenario.

HLA-C cell surface expression and control of HIV/AIDS correlate with a variant upstream of HLA-C.

A variant 35 kb upstream of the HLA-C gene (-35C/T) was previously shown to associate with HLA-C mRNA expression level and steady-state plasma HIV RNA levels. We genotyped this variant in 1,698 patients of European ancestry with HIV. Individuals with known seroconversion dates were used for disease progression analysis and those with longitudinal viral load data were used for viral load analysis. We further tested cell surface expression of HLA-C in normal donors using an HLA-C-specific antibody. We show that the -35C allele is a proxy for high HLA-C cell surface expression, and that individuals with high-expressing HLA-C alleles progress more slowly to AIDS and control viremia significantly better than individuals with low HLA-C expressing alleles. These data strongly implicate high HLA-C expression levels in more effective control of HIV-1, potentially through better antigen presentation to cytotoxic T lymphocytes or recognition and killing of infected cells by natural killer cells.

Loss-of-function mutations of an inhibitory upstream ORF in the human hairless transcript cause Marie Unna hereditary hypotrichosis.

Marie Unna hereditary hypotrichosis (MUHH) is an autosomal dominant form of genetic hair loss. In a large Chinese family carrying MUHH, we identified a pathogenic initiation codon mutation in U2HR, an inhibitory upstream ORF in the 5' UTR of the gene encoding the human hairless homolog (HR). U2HR is predicted to encode a 34-amino acid peptide that is highly conserved among mammals. In 18 more families from different ancestral groups, we identified a range of defects in U2HR, including loss of initiation, delayed termination codon and nonsense and missense mutations. Functional analysis showed that these classes of mutations all resulted in increased translation of the main HR physiological ORF. Our results establish the link between MUHH and U2HR, show that fine-tuning of HR protein levels is important in control of hair growth, and identify a potential mechanism for preventing hair loss or promoting hair removal.

Identification of Novel Craniofacial Regulatory Domains Located far Upstream of SOX9 and Disrupted in Pierre Robin Sequence.

Mutations in the coding sequence of SOX9 cause campomelic dysplasia (CD), a disorder of skeletal development associated with 46,XY disorders of sex development (DSDs). Translocations, deletions, and duplications within a ∼2 Mb region upstream of SOX9 can recapitulate the CD-DSD phenotype fully or partially, suggesting the existence of an unusually large cis-regulatory control region. Pierre Robin sequence (PRS) is a craniofacial disorder that is frequently an endophenotype of CD and a locus for isolated PRS at ∼1.2-1.5 Mb upstream of SOX9 has been previously reported. The craniofacial regulatory potential within this locus, and within the greater genomic domain surrounding SOX9, remains poorly defined. We report two novel deletions upstream of SOX9 in families with PRS, allowing refinement of the regions harboring candidate craniofacial regulatory elements. In parallel, ChIP-Seq for p300 binding sites in mouse craniofacial tissue led to the identification of several novel craniofacial enhancers at the SOX9 locus, which were validated in transgenic reporter mice and zebrafish. Notably, some of the functionally validated elements fall within the PRS deletions. These studies suggest that multiple noncoding elements contribute to the craniofacial regulation of SOX9 expression, and that their disruption results in PRS.

Conformity, upstream reciprocity and social diversity: secondary mechanisms for the evolution of cooperation

Cooperation is ubiquitous in nature: genes cooperate in genomes, cells in muti- cellular organims, and individuals in societies. In humans, division of labor and trade are key elements of most known societies, where social life is regulated by- moral systems specifying rights and duties often enforced by third party punish¬ment. Over the last decades, several primary mechanisms, such as kin selection, direct and indirect reciprocity, have been advanced to explain the evolution of cooperation from a naturalistic approach. In this thesis, I focus on the study of three secondary mechanisms which, although insufficient to allow for the evo¬lution of cooperation, have been hypothesized to further promote it when they are linked to proper primary mechanisms: conformity (the tendency to imitate common behaviors), upstream reciprocity (the tendency to help somebody once help has been received from somebody else) and social diversity (heterogeneous social contexts). I make use of mathematical and computational models in the formal framework of evolutionary game theory in order to investigate the theoret¬ical conditions under which conformity, upstream reciprocity and social diversity are able to raise the levels of cooperation attained in evolving populations. - La coopération est ubiquitaire dans la nature: les gènes coopèrent dans les génomes, les cellules dans les organismes muticellulaires, et les organismes dans les sociétés. Chez les humains, la division du travail et le commerce sont des éléments centraux de la plupart des sociétés connues, où la vie sociale est régie par des systèmes moraux établissant des droits et des devoirs, souvent renforcés par la punition. Au cours des dernières décennies, plusieurs mécanismes pri¬maires, tels que la sélection de parentèle et les réciprocités directe et indirecte, ont été avancés pour expliquer l'évolution de la coopération d'un point de vue nat¬uraliste. Dans cette thèse, nous nous concentrons sur l'étude de trois mécanismes secondaires qui, bien qu'insuffisants pour permettre l'évolution de la coopération, sont capables de la promouvoir davantage s'ils sont liés aux mécanismes primaires appropriés: la conformité (tendance à imiter des comportements en commun), la 'réciprocité en amont' (tendance à aider quelqu'un après avoir reçu l'aide de quelqu'un d'autre) et la diversité sociale (contextes sociaux hétérogènes). Nous faisons usage de modèles mathématiques et informatiques dans le cadre formel de la théorie des jeux évolutionnaires afin d'examiner les conditions théoriques dans lesquelles la conformité, la 'réciprocité en amont' et la diversité sociale sont capables d'élever le niveau de coopération des populations en évolution.

Ribosome profiling reveals the rhythmic liver translatome and circadian clock regulation by upstream open reading frames.

Mammalian gene expression displays widespread circadian oscillations. Rhythmic transcription underlies the core clock mechanism, but it cannot explain numerous observations made at the level of protein rhythmicity. We have used ribosome profiling in mouse liver to measure the translation of mRNAs into protein around the clock and at high temporal and nucleotide resolution. We discovered, transcriptome-wide, extensive rhythms in ribosome occupancy and identified a core set of approximately 150 mRNAs subject to particularly robust daily changes in translation efficiency. Cycling proteins produced from nonoscillating transcripts revealed thus-far-unknown rhythmic regulation associated with specific pathways (notably in iron metabolism, through the rhythmic translation of transcripts containing iron responsive elements), and indicated feedback to the rhythmic transcriptome through novel rhythmic transcription factors. Moreover, estimates of relative levels of core clock protein biosynthesis that we deduced from the data explained known features of the circadian clock better than did mRNA expression alone. Finally, we identified uORF translation as a novel regulatory mechanism within the clock circuitry. Consistent with the occurrence of translated uORFs in several core clock transcripts, loss-of-function of Denr, a known regulator of reinitiation after uORF usage and of ribosome recycling, led to circadian period shortening in cells. In summary, our data offer a framework for understanding the dynamics of translational regulation, circadian gene expression, and metabolic control in a solid mammalian organ.

Swimming upstream: navigating ethical practices in the creation of a participatory youth media workshop

Despite the growing popularity of participatory video as a tool for facilitating youth empowerment, the methodology and impacts of the practice are extremely understudied. This paper describes a study design created to examine youth media methodology and the ethical dilemmas that arose in its attempted implementation. Specifically, elements that added “rigor” to the study (i.e., randomization, pre- and post-measures, and an intensive interview) conflicted with the fundamental tenets of youth participation. The paper concludes with suggestions for studying participatory media methodologies that are more in line with an ethics of participation.

A TVD finite difference scheme with non-uniform meshes and without upstream weighting

We present a finite difference scheme, with the TVD (total variation diminishing) property, for scalar conservation laws. The scheme applies to non-uniform meshes, allowing for variable mesh spacing, and is without upstream weighting. When applied to systems of conservation laws, no scalar decomposition is required, nor are any artificial tuning parameters, and this leads to an efficient, robust algorithm.

Upstream control of Agulhas Ring shedding

Rings shed in the Agulhas Retroflection region play an important role in the global thermohaline circulation. The shedding of these rings has been considered very irregular. In this paper, we present evidence for remote control of the timing and frequency of the ring shedding events. This turns out to be a far more regular process, at a frequency of 4–5 cycles per year. The movement of the Agulhas Retroflection, and thereby the shedding of rings, is timed by incoming eddies from the upstream regions. Eddies from the Mozambique Channel, and from the East Madagascar current reach the retroflection region at the frequency of 4–5 times per year. The existence of these eddies can be related to incoming Rossby waves that cross the Indian Ocean and reach the Agulhas Current system. These may in turn be part of a basin-wide oscillation. The irregularity found in ring shedding statistics can be ascribed to processes occurring between the actual shedding and the first unambiguous observation of a separated ring.