The rockefeller university

Organizing data about patterning and morphogenesis into a coherent framework remains a challenge in developmental biology. Reporting in Science, Corson et al. (2017) apply innovative analysis to an old problem of bristle patterns in Drosophila, reducing the nonlinear interactions among tens of cells to a succinct model with quantitative predictions.

Tissue stem cells contribute to tissue regeneration and wound repair through cellular programs that can be hijacked by cancer cells. Here, we investigate such a phenomenon in skin, where during homeostasis, stem cells of the epidermis and hair follicle fuel their respective tissues. We find that breakdown of stem cell lineage confinement-granting privileges associated with both fates-is not only hallmark but also functional in cancer development. We show that lineage plasticity is critical in wound repair, where it operates transiently to redirect fates. Investigating mechanism, we discover that irrespective of cellular origin, lineage infidelity occurs in wounding when stress-responsive enhancers become activated and override homeostatic enhancers that govern lineage specificity. In cancer, stress-responsive transcription factor levels rise, causing lineage commanders to reach excess. When lineage and stress factors collaborate, they activate oncogenic enhancers that distinguish cancers from wounds.

Understanding the biologic role of N-6-methyladenosine (m(6)A) RNA modifications in mRNA requires an understanding of when and where in the life of a pre-mRNA transcript the modifications are made. We found that HeLa cell chromatin-associated nascent pre-mRNA (CA-RNA) contains many unspliced introns and m(6)A in exons but very rarely in introns. The m(6)A methylation is essentially completed upon the release of mRNA into the nucleoplasm. Furthermore, the content and location of each m(6)A modification in steady-state cytoplasmic mRNA are largely indistinguishable from those in the newly synthesized CA-RNA or nucleoplasmic mRNA. This result suggests that quantitatively little methylation or demethylation occurs in cytoplasmic mRNA. In addition, only similar to 10% of m(6)As in CA-RNA are within 50 nucleotides of 5' or 3' splice sites, and the vast majority of exons harboring m(6)A in wild-type mouse stem cells is spliced the same in cells lacking the major m(6)A methyltransferase Mettl3. Both HeLa and mouse embryonic stem cell mRNAs harboring m(6)As have shorter half-lives, and thousands of these mRNAs have increased half-lives (twofold or more) in Mettl3 knockout cells compared with wild type. In summary, m(6)A is added to exons before or soon after exon definition in nascent pre-mRNA, and while m(6)A is not required for most splicing, its addition in the nascent transcript is a determinant of cytoplasmic mRNA stability.

Mice produce ultrasonic vocalizations (USVs) in a variety of social contexts throughout development and adulthood. These USVs are used for mother-pup retrieval(1), juvenile interactions(2), opposite and same sex interactions(3,4,5), and territorial interactions(6). For decades, the USVs have been used by investigators as proxies to study neuropsychiatric and developmental or behavioral disorders(7,8,9), and more recently to understand mechanisms and evolution of vocal communication among vertebrates(10). Within the sexual interactions, adult male mice produce USV songs, which have some features similar to courtship songs of songbirds(11). The use of such multisyllabic repertoires can increase potential flexibility and information they carry, as they can be varied in how elements are organized and recombined, namely syntax. In this protocol a reliable method to elicit USV songs from male mice in various social contexts, such as exposure to fresh female urine, anesthetized animals, and estrus females is described. This includes conditions to induce a large amount of syllables from the mice. We reduce recording of ambient noises with inexpensive sound chambers, and present a quantification method to automatically detect, classify and analyze the USVs. The latter includes evaluation of call-rate, vocal repertoire, acoustic parameters, and syntax. Various approaches and insight on using playbacks to study an animal's preference for specific song types are described. These methods were used to describe acoustic and syntax changes across different contexts in male mice, and song preferences in female mice.

Osteoporosis is characterized by low bone density, and osteopenia is responsible for 1.5 million fractures in the United States annually.(1) In order to identify regions of the genome which are likely to contain genes predisposing to osteopenia, we genotyped 149 members of seven large pedigrees having recurrence of low bone mineral density (BMD) with 330 DNA markers spread throughout the autosomal genome. Linkage analysis for this quantitative trait was carried out using spine and hip BMD values by the classical lod-score method using a genetic model with parameters estimated from the seven families. In addition, non parametric analysis was performed using the traditional Haseman-Elston approach in 74 independent sib pairs from the same pedigrees. The maximum lod score obtained by parametric analysis in all families combined was +2.08 (theta = 0.05) for the marker CD3D on chromosome 11q. All other combined lod scores from the parametric analysis were less than +1.90, the threshold for suggestive linkage. Non-parametric analysis suggested linkage of low BMD to chromosomes 1p36 (Z(max) = +3.51 for D1S450) and 2p23-24 (Z(max) = +2.07 for D2S149). Maximum multi-point lod scores for these regions were +2.29 and +2.25, respectively. A third region with associated lod scores above the threshold of suggestive linkage in both single-point and multi point non-parametric analysis was on chromosome 4qter (Z(max) = +2.95 for D4S1539 and Z(max) = +2.48 for D4S1554). Our data suggest the existence of multiple genes involved in controlling spine and hip BMD, and indicate several candidate regions for further screening in this and other independent samples.

Mud is a porous medium containing a high density of diverse microorganisms. It is out of equilibrium as the energy from a photon flux is dissipated by a cascade of biochemical reactions, mediated by the metabolisms of the constituent organisms. Despite its complexity, microbes in nature self-organize into simple reproducible patterns. We present two experiments in which the dynamics of natural mud coming to steady state are observed and modeled. In the first, the oxygen gradient produced by cyanobacteria in an imposed light gradient is measured. In the second, a thin front of oxygen-consuming microbes forms at the penetration depth of oxygen and moves with the changing oxygen gradient.

Vascular abnormalities and inflammation are found in many Alzheimer disease (AD) patients, but whether these changes play a causative role in AD is not clear. The factor XII (FXII)-initiated contact system can trigger both vascular pathology and inflammation and is activated in AD patients and AD mice. We have investigated the role of the contact system in AD pathogenesis. Cleavage of high-molecular-weight kininogen (HK), a marker for activation of the inflammatory arm of the contact system, is increased in a mouse model of AD, and this cleavage is temporally correlated with the onset of brain inflammation. Depletion of FXII in AD mice inhibited HK cleavage in plasma and reduced neuroinflammation, fibrinogen deposition, and neurodegeneration in the brain. Moreover, FXII-depleted AD mice showed better cognitive function than untreated AD mice. These results indicate that FXII-mediated contact system activation contributes to AD pathogenesis, and therefore this system may offer novel targets for AD treatment.

The mechanisms by which early chronic low-level lead (Pb) exposure disrupts the developing brain are not yet understood. Rodent models have provided promising results however behavioral tests sensitive to effects at lowest levels of exposure during development are needed. Preadolescent animals (N = 52) exposed to low and higher levels of Pb via lactation from birth to PND 28 completed the Object-in-Place Task of visual spatial and visual object memory retrieval (at PND 28). Generalized linear mixed models were used, controlling for sex and litter as a random effect. As compared with controls, global vertical exploratory behavior (rearing) markedly increased during memory retrieval. The findings suggested that early chronic Pb exposure altered the development of critical exploratory functions needed for learning and survival. Behaviors exhibited in novel spatial and novel object zone perimeters suggested that the Object-in-Place task is a valid measure of visual spatial and visual object memory in pre-adolescent C57BL/6J mice. Additional studies are needed to understand how early chronic low-level lead exposure disrupts the trajectory and possible linkages of critical exploratory and perceptual systems during development. (C) 2017 Elsevier Inc. All rights reserved.

The bulk of studies of coupled oscillators use, as is appropriate in Physics, a global coupling constant controlling all individual interactions. However, because as the coupling is increased, the number of relevant degrees of freedom also increases, this setting conflates the strength of the coupling with the effective dimensionality of the resulting dynamics. We propose a coupling more appropriate to neural circuitry, where synaptic strengths are under biological, activity-dependent control and where the coupling strength and the dimensionality can be controlled separately. Here we study a set of N -> infinity strongly- and nonsymmetrically-coupled, dissipative, powered, rotational dynamical systems, and derive the equations of motion of the reduced system for dimensions 2 and 4. Our setting highlights the statistical structure of the eigenvectors of the connectivity matrix as the fundamental determinant of collective behavior, inheriting from this structure symmetries and singularities absent from the original microscopic dynamics.

Meso-scale turbulence is an innate phenomenon, distinct from inertial turbulence, that spontaneously occurs at low Reynolds number in fluidized biological systems. This spatiotemporal disordered flow radically changes nutrient and molecular transport in living fluids and can strongly affect the collective behaviour in prominent biological processes, including biofilm formation, morphogenesis and cancer invasion. Despite its crucial role in such physiological processes, understanding meso-scale turbulence and any relation to classical inertial turbulence remains obscure. Here we show how the motion of active matter along a micro-channel transitions to meso-scale turbulence through the evolution of locally disordered patches (active puffs) from an ordered vortex-lattice flow state. We demonstrate that the stationary critical exponents of this transition to meso-scale turbulence in a channel coincide with the directed percolation universality class. This finding bridges our understanding of the onset of low-Reynolds-number meso-scale turbulence and traditional scale-invariant turbulence in confinement.