Genome-Wide Analyses of Nkx2-1 Binding to Transcriptional Target Genes Uncover Novel Regulatory Patterns Conserved in Lung Development and Tumors

The homeodomain transcription factor Nkx2-1 is essential for normal lung development and homeostasis. In lung tumors, it is considered a lineage survival oncogene and prognostic factor depending on its expression levels. The target genes directly bound by Nkx2-1, that could be the primary effectors of its functions in the different cellular contexts where it is expressed, are mostly unknown. In embryonic day 11.5 (E11.5) mouse lung, epithelial cells expressing Nkx2-1 are predominantly expanding, and in E19.5 prenatal lungs, Nkx2-1-expressing cells are predominantly differentiating in preparation for birth. To evaluate Nkx2-1 regulated networks in these two cell contexts, we analyzed genome-wide binding of Nkx2-1 to DNA regulatory regions by chromatin immunoprecipitation followed by tiling array analysis, and intersected these data to expression data sets. We further determined expression patterns of Nkx2-1 developmental target genes in human lung tumors and correlated their expression levels to that of endogenous NKX2-1. In these studies we uncovered differential Nkx2-1 regulated networks in early and late lung development, and a direct function of Nkx2-1 in regulation of the cell cycle by controlling the expression of proliferation-related genes. New targets, validated in Nkx2-1 shRNA transduced cell lines, include E2f3, Cyclin B1, Cyclin B2, and c-Met. Expression levels of Nkx2-1 direct target genes identified in mouse development significantly correlate or anti-correlate to the levels of endogenous NKX2-1 in a dosage-dependent manner in multiple human lung tumor expression data sets, supporting alternative roles for Nkx2-1 as a transcriptional activator or repressor, and direct regulator of cell cycle progression in development and tumors

A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.)

<p>Abstract</p> <p>Background</p> <p>Cotton fiber length is an important quality attribute to the textile industry and longer fibers can be more efficiently spun into yarns to produce superior fabrics. There is typically a negative correlation between yield and fiber quality traits such as length. An understanding of the regulatory mechanisms controlling fiber length can potentially provide a valuable tool for cotton breeders to improve fiber length while maintaining high yields. The cotton (<it>Gossypium hirsutum </it>L.) fiber mutation Ligon lintless-2 is controlled by a single dominant gene (<it>Li₂</it>) that results in significantly shorter fibers than a wild-type. In a near-isogenic state with a wild-type cotton line, <it>Li₂</it>is a model system with which to study fiber elongation.</p> <p>Results</p> <p>Two near-isogenic lines of Ligon lintless-2 (<it>Li₂</it>) cotton, one mutant and one wild-type, were developed through five generations of backcrosses (BC₅). An F₂population was developed from a cross between the two <it>Li₂</it>near-isogenic lines and used to develop a linkage map of the <it>Li₂</it>locus on chromosome 18. Five simple sequence repeat (SSR) markers were closely mapped around the <it>Li₂</it>locus region with two of the markers flanking the <it>Li₂</it>locus at 0.87 and 0.52 centimorgan. No apparent differences in fiber initiation and early fiber elongation were observed between the mutant ovules and the wild-type ones. Gene expression profiling using microarrays suggested roles of reactive oxygen species (ROS) homeostasis and cytokinin regulation in the <it>Li₂</it>mutant phenotype. Microarray gene expression data led to successful identification of an EST-SSR marker (NAU3991) that displayed complete linkage to the <it>Li₂</it>locus.</p> <p>Conclusions</p> <p>In the field of cotton genomics, we report the first successful conversion of gene expression data into an SSR marker that is associated with a genomic region harboring a gene responsible for a fiber trait. The EST-derived SSR marker NAU3991 displayed complete linkage to the <it>Li₂</it>locus on chromosome 18 and resided in a gene with similarity to a putative plectin-related protein. The complete linkage suggests that this expressed sequence may be the <it>Li₂</it>gene.</p

Weakly nonlinear modelling of a forced turbulent axisymmetric wake

A theory is presented where the weakly nonlinear analysis of laminar g lobally unstable flows in the presence of external forcing is extended to the turbu lent regime. The analysis is demonstrated and validated using experimental results of an axis ymmetric bluff body wake at high Reynolds numbers, Re D ∼ 1 . 88 × 10 5 , where forcing is applied using a Zero-Net-Mass-Flux actuator located at the base of the blunt bo dy. In this study we focus on the response of antisymmetric coherent structures wit h azimuthal wavenumbers m = ± 1 at a frequency St D = 0 . 2, responsible for global vortex shedding. We found experimentally that axisymmetric forcing ( m = 0) couples nonlinearly with the global shedding mode when the flow is forced at twice the shedding frequen cy, resulting in parametric subharmonic resonance through a triadic interaction b etween forcing and shedding. We derive simple weakly nonlinear models from the phase-av eraged Navier- Stokes equations and show that they capture accurately the obs erved behaviour for this type of forcing. The unknown model coefficients are obtained e xperimentally by producing harmonic transients. This approach should be applicable in a variety of turbulent flows to describe the response of global modes to forcin g

Stability and coherent structures in the wake of axisymmetric Bluffbodies

The coherent structures observed in the turbulent wake of axisymmetric bluffbodies are investigated. Concepts from hydrodynamic stability are used to derive low-dimensional mathematical models based on a weakly nonlinear analysis of the governingNavier-Stokes equations that describe the temporal amplitude evolution of the coherent structures in the near wake. Forced experiments applying axisymmetric pulsed-jet blowing on the base of the body are performed to validate the models.Very good quantitative agreement between model predictions and experiments is obtained, showing for the first time that Landau-type models are capable of describing the dynamic behavior of a three-dimensional turbulent wake

Low-dimensional dynamics of a turbulent axisymmetric wake

The coherent structures of a turbulent wake generated behind a bluff three-dimensional axisymmetric body are investigated experimentally at a diameter-based Reynolds number of ∼2 × 105. Proper orthogonal decomposition of base pressure measurements indicates that the most energetic coherent structures retain the structure of the symmetry-breaking laminar instabilities and are manifested as unsteady vortex shedding with azimuthal wavenumber m=±1. In a rotating reference frame, the shedding preserves the reflectional symmetry and is linked with a reflectionally symmetric mean pressure distribution on the base. Due to a slow rotation of the symmetry plane of the turbulent wake around the axis of the body, statistical axisymmetry is recovered in the time average. The ratio of the time scales associated with the slow rotation of the symmetry plane and the vortex shedding is of order 100. © Cambridge University Press 2014

Diffusive dynamics and stochastic models of turbulent axisymmetric wakes

A modelling methodology to reproduce the experimental measurements of a turbulent flow in the presence of symmetry is presented. The flow is a three-dimensional wake generated by an axisymmetric body. We show that the dynamics of the turbulent wake flow can be assimilated by a nonlinear two-dimensional Langevin equation, the deterministic part of which accounts for the broken symmetries that occur in the laminar and transitional regimes at low Reynolds numbers and the stochastic part of which accounts for the turbulent fluctuations. Comparison between theoretical and experimental results allows the extraction of the model parameters

Prevalence of restless legs syndrome and associated factors in an otherwise healthy population: results from the Danish Blood Donor Study

$\textit{Objective}$ Restless legs syndrome (RLS) is a neurological sensorimotor disorder characterized by uncomfortable sensations in the legs. RLS often occurs as a comorbid condition. Besides an increased risk of iron deficiency, blood donors are considered to be generally healthy. Blood donors are therefore an ideal population for studying factors associated with RLS occurrence, herein the role of iron. It is suggested that RLS is linked to sex, age, low socioeconomic status, unhealthy lifestyle, and iron deficiency. The objective of this study is therefore to estimate the RLS prevalence and identify associated biological, sociodemographic, economic, and lifestyle factors in a population of blood donors. $\textit{Methods}$ A total of 13,448 blood donors enrolled in the Danish Blood Donor Study from May 2015 to May 2016. RLS cases were identified using the validated Cambridge–Hopkins RLS-questionnaire. Logistic regression models were applied to assess the relationship between RLS and data on socially related factors collected using questionnaires and population registers. $\textit{Results}$ In this study, 7.2% women and 4.5% men were classified with RLS. RLS was associated with: female sex, high age, smoking, frequent alcohol consumption, and low education. RLS-related symptoms were associated with obesity, parity and donation intensity 3 years prior to inclusion among women. RLS was not related to: reduced plasma ferritin, employment status, and income. $\textit{Conclusions}$ RLS is a frequent disorder in otherwise healthy individuals. The associations discovered in this study can be utilized in preventing or reducing RLS symptoms.The Danish Council for Independent Research - Medical Sciences, The Danish Administrative Regions, The Danish Blood Donor Research Foundation, The Danish Bio- and Genome bank, and The Brothers Hartmann Foundation