Gene regulatory networks in lactation: identification of global principles using bioinformatics

<p>Abstract</p> <p>Background</p> <p>The molecular events underlying mammary development during pregnancy, lactation, and involution are incompletely understood.</p> <p>Results</p> <p>Mammary gland microarray data, cellular localization data, protein-protein interactions, and literature-mined genes were integrated and analyzed using statistics, principal component analysis, gene ontology analysis, pathway analysis, and network analysis to identify global biological principles that govern molecular events during pregnancy, lactation, and involution.</p> <p>Conclusion</p> <p>Several key principles were derived: (1) nearly a third of the transcriptome fluctuates to build, run, and disassemble the lactation apparatus; (2) genes encoding the secretory machinery are transcribed prior to lactation; (3) the diversity of the endogenous portion of the milk proteome is derived from fewer than 100 transcripts; (4) while some genes are differentially transcribed near the onset of lactation, the lactation switch is primarily post-transcriptionally mediated; (5) the secretion of materials during lactation occurs not by up-regulation of novel genomic functions, but by widespread transcriptional suppression of functions such as protein degradation and cell-environment communication; (6) the involution switch is primarily transcriptionally mediated; and (7) during early involution, the transcriptional state is partially reverted to the pre-lactation state. A new hypothesis for secretory diminution is suggested – milk production gradually declines because the secretory machinery is not transcriptionally replenished. A comprehensive network of protein interactions during lactation is assembled and new regulatory gene targets are identified. Less than one fifth of the transcriptionally regulated nodes in this lactation network have been previously explored in the context of lactation. Implications for future research in mammary and cancer biology are discussed.</p

Salt marsh ecosystem biogeochemical responses to nutrient enrichment : a paired 15N tracer study

Author Posting. © Ecological Society of America, 2009. This article is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecology 90 (2009): 2535-2546, doi:10.1890/08-1051.1.We compared processing and fate of dissolved NO3− in two New England salt marsh ecosystems, one receiving natural flood tide concentrations of 1–4 μmol NO3−/L and the other receiving experimentally fertilized flood tides containing 70–100 μmol NO3−/L. We conducted simultaneous 15NO3− (isotope) tracer additions from 23 to 28 July 2005 in the reference (8.4 ha) and fertilized (12.4 ha) systems to compare N dynamics and fate. Two full tidal cycles were intensively studied during the paired tracer additions. Resulting mass balances showed that essentially 100% (0.48–0.61 mol NO3-N·ha−1·h−1) of incoming NO3− was assimilated, dissimilated, sorbed, or sedimented (processed) within a few hours in the reference system when NO3− concentrations were 1.3–1.8 μmol/L. In contrast, only 50–60% of incoming NO3− was processed in the fertilized system when NO3− concentrations were 84–96 μmol/L; the remainder was exported in ebb tidewater. Gross NO3− processing was 40 times higher in the fertilized system at 19.34–24.67 mol NO3-N·ha−1·h−1. Dissimilatory nitrate reduction to ammonium was evident in both systems during the first 48 h of the tracer additions but <1% of incoming 15NO3− was exported as 15NH4+. Nitrification rates calculated by 15NO3− dilution were 6.05 and 4.46 mol·ha−1·h−1 in the fertilized system but could not be accurately calculated in the reference system due to rapid (<4 h) NO3− turnover. Over the five-day paired tracer addition, sediments sequestered a small fraction of incoming NO3−, although the efficiency of sequestration was 3.8% in the reference system and 0.7% in the fertilized system. Gross sediment N sequestration rates were similar at 13.5 and 12.6 mol·ha−1·d−1, respectively. Macrophyte NO3− uptake efficiency, based on tracer incorporation in aboveground tissues, was considerably higher in the reference system (16.8%) than the fertilized system (2.6%), although bulk uptake of NO3− by plants was lower in the reference system (1.75 mol NO3−·ha−1·d−1) than the fertilized system (10 mol NO3−·ha−1·d−1). Nitrogen processing efficiency decreased with NO3− load in all pools, suggesting that the nutrient processing capacity of the marsh ecosystem was exceeded in the fertilized marsh.This work was funded by National Science Foundation Grant DEB 0213767 and OCE 9726921

Lactation and neonatal nutrition: defining and refining the critical questions.

This paper resulted from a conference entitled "Lactation and Milk: Defining and refining the critical questions" held at the University of Colorado School of Medicine from January 18-20, 2012. The mission of the conference was to identify unresolved questions and set future goals for research into human milk composition, mammary development and lactation. We first outline the unanswered questions regarding the composition of human milk (Section I) and the mechanisms by which milk components affect neonatal development, growth and health and recommend models for future research. Emerging questions about how milk components affect cognitive development and behavioral phenotype of the offspring are presented in Section II. In Section III we outline the important unanswered questions about regulation of mammary gland development, the heritability of defects, the effects of maternal nutrition, disease, metabolic status, and therapeutic drugs upon the subsequent lactation. Questions surrounding breastfeeding practice are also highlighted. In Section IV we describe the specific nutritional challenges faced by three different populations, namely preterm infants, infants born to obese mothers who may or may not have gestational diabetes, and infants born to undernourished mothers. The recognition that multidisciplinary training is critical to advancing the field led us to formulate specific training recommendations in Section V. Our recommendations for research emphasis are summarized in Section VI. In sum, we present a roadmap for multidisciplinary research into all aspects of human lactation, milk and its role in infant nutrition for the next decade and beyond

Susceptibility of salt marshes to nutrient enrichment and predator removal

Author Posting. © The Author(s), 2007. This is the author's version of the work. It is posted here by permission of Ecological Society of America for personal use, not for redistribution. The definitive version was published in Ecological Applications 17, Suppl. (2007): S42–S63, doi:10.1890/06-0452.1.The sustainability of coastal ecosystems in the face of widespread environmental change is an issue of pressing concern throughout the world (Emeis et al. 2001). Coastal ecosystems form a dynamic interface between terrestrial and oceanic systems and are one of the most productive ecosystems in the world. Coastal systems probably serve more human uses than any other ecosystem and they have always been valued for their rich bounty of fish and shellfish. Coastal areas are also the sites of the nation’s and the world’s most intense commercial activity and population growth; worldwide, approximately 75% of the human population now lives in coastal regions (Emeis et al. 2001). Over the past three decades nutrient enrichment of coastal and estuarine waters has become the premier issue for both scientists and managers (National Research Council 2000). Our understanding of coastal eutrophication has been developed principally through monitoring of estuaries, with a focus on pelagic or subtidal habitats (National Research Council 2000, Cloern 2001). Because estuarine systems are usually nitrogen limited, NO3- is the most common nutrient responsible for cultural nutrient enrichment (Cloern 2001). Increased nitrogen delivery to pelagic habitats of estuaries produces the classic response of ecosystems to stress (altered primary producers and nutrient cycles and loss of secondary producer species and production; Nixon 1995, Rapport and Whitford 1999, Deegan et al. 2002). Salt marsh ecosystems have been thought of as not susceptible to nitrogen over-loading because early studies found added nitrogen increased marsh grass production (primarily Spartina spp., cordgrass) and concluded that salt marshes can adsorb excess nutrients in plants and salt marsh plant-derived organic matter as peat (Verhoeven et al. 2006). Detritus from Spartina is important in food webs (Deegan et al. 2000) and in creating peat that forms the physical structure of the marsh platform (Freidrichs and Perry 2001). However, the accumulation of peat and inputs of sediments and loss of peat through decomposition and sediment through erosion may be altered under high nutrient regimes and threaten the long-term stability of marsh systems. Nitrogen addition may lead to either net gain or loss of the marsh depending on the balance between increased marsh plant production and increased decomposition. Absolute change in marsh surface elevation is determined by marsh plant species composition, production and allocation to above- and belowground biomass, microbial decomposition, sedimentation, erosion and compaction (Friedrichs and Perry 2001). Levine et al. (1998) suggested that competitive dynamics among plants might be affected by nutrient enrichment, potentially altering relative abundance patterns favoring species with less belowground storage and thus lowering rates of peat formation. When combined with the observation that nutrient additions may also stimulate microbial respiration and decomposition (Morris and Bradley 1999), the net effect on the salt marsh under conditions of chronic nitrogen loading is a critical unknown. Although most research treats nutrient enrichment as a stand-alone stress, it never occurs in isolation from other perturbations. The effect of nutrient loading on species composition (both plants and animals) and the resultant structure and function of wetlands has been largely ignored when considering their ability to adsorb nutrients (Verhoeven et al. 2006). Recent studies suggest the response of estuaries to stress may depend on animal species composition (Silliman et al. 2005). Animal species composition may alter the balance between marsh gain and loss as animals may increase or decrease primary production, decomposition or N recycling (Pennings and Bertness 2001). Failure to understand interactions between nutrient loading and change in species composition may lead to underestimating the impacts of these stresses. The 'bottom up or top down' theory originated from the observation that nutrient availability (bottom up)sets the quantity of primary productivity, while other studies have shown that species composition (top down), particularly of top consumers, has a marked and cascading effect on ecosystems, including controlling species composition and nutrient cycling (Matson and Price 1992, Pace et al. 1999). Most examples of trophic cascades are in aquatic ecosystems with fairly simple, algal grazing pelagic food webs (Strong 1992). The rarity of trophic cascades in terrestrial systems has been attributed to the importance of detrital food webs (Polis 1999). Detritus-based aquatic ecosystems, such as salt marshes, bogs, and swamps, have classically been considered bottom-up or physically controlled ecosystems. Recent experiments, however, suggest that salt marshes may exhibit top-down control at several trophic levels (Silliman and Zeiman. 2001, Silliman and Bertness 2002, Quiñones-Rivera and Fleeger 2005). One abundant, ubiquitous predator, a small (<10 cm total length) killifish (Fundulus heteroclitus, mummichog) has been suggested to control benthic algal through a trophic cascade because they prey on the invertebrates that graze on the benthic algae (Kneib 1997, Sarda et al. 1998). In late summer, killifish are capable of consuming 3-10 times the creek meiofauna production and meiofauna in the absence of predators appear capable of grazing over 60% of the microalgal community per day (Carman et al. 1997). Strong top-down control by grazers is considered a moderating influence on the negative effects of elevated nutrients on algae (Worm et al. 2000). Small-scale nutrient additions and predator community exclusion experiments have demonstrated bottom-up and top-down control of macroinfauna in mudflats associated with salt marsh creeks (Posey et al. 1999, Posey et al. 2002). Together, these observations suggest mummichogs are at the top of a trophic cascade that controls benthic algae (Sarda et al. 1998). Mummichogs are also omnivorous and ingest algae, bulk detritus and the attached microbial community (D’Avanzo and Valiela 1990). As a result, marsh decomposition rates may be limited by top-down controls through trophic pathways or by release from competition with algae for nutrients. Whole-ecosystem experiments have shown that responses to stress are often not predictable from studies of the individual components (Schindler 1998). Developing the information needed to predict the interacting impacts of nutrient loading and species composition change requires experiments with realistic alterations carried out at scales of space and time that include the complexities of real ecosystems. Whole ecosystem manipulation experiments have been used effectively in other ecosystems (Bormann and Likens 1979, Carpenter et al. 1995), but they are rare in coastal research. Experiments in salt marshes have traditionally been less than a few m2. Our understanding of the response of salt marsh plants to nutrient enrichment is from small ( 1000 g N m-2 y-1) are sprinkled on the marsh surface at low tide. Dry fertilizer additions were usually made every two weeks or monthly and the duration of elevated nutrient levels after these additions was usually not determined. Tidal water is the primary vector for N delivery to coastal marshes, suggesting that dry fertilizer addition to the marsh surface may not be the best basis for determining if Spartina production responds to nutrient enrichment of tidal waters. Similarly, our understanding of top-down controls in salt marshes also relies on small (1 - 4 m2) exclusion experiments that use cages to isolate communities from top consumers. While the design of these cage experiments has improved, there are some remaining drawbacks. For example, it is impossible to selectively exclude single species using cages, and recruitment or size-selective movement into or out of the cages may obscure interpretations. In addition, while these small-scale experiments provide insight into controls on isolated ecosystem processes, they do not allow for interaction among different parts of the ecosystem which may buffer or alter the impacts and are not appropriate for determining the effects of populations of larger more motile animals on whole-ecosystems or the effects of ecosystem changes on populations. For example, interactions may be caused when a motile species alters its distribution among the habitats available to it because of an experimental treatment. Small-scale experiments generally do not allow such events to happen. Complex feedbacks among physical and biological processes can alter accumulation rates and affect marsh elevation relative to sea level rise making extrapolation of small plot level experiments to whole marsh ecosystems problematic. We are conducting an ecosystem-scale, multi-year field experiment including both nutrient and biotic manipulations to coastal salt marsh ecosystems. We are testing, for the first time at the ecosystem level, the hypothesis that nutrient enrichment and species composition change have interactive effects across multiple levels of biological organization and a range of biogeochemical processes. We altered whole salt marsh creek watersheds (~60,000 m2 of saltmarsh) by addition of nutrients (15x ambient) in flooding waters and by a 60% reduction of a key fish species, the mummichog. Small marsh creek watersheds provide an ideal experimental setting because they have the spatial complexity, species composition and processes characteristic of the larger salt marsh ecosystem, which are often hundreds of thousands of m2. Manipulating entire salt marsh creeksheds allowed us to examine effects on large motile animals and the interactive effects of motile species changes on ecosystem processes without cage artifacts. Because our manipulations were done on whole-marsh ecosystems, we are able to evaluate the integrated and interactive effects on all habitats (e.g., water column, tidal creeks and marsh) and on populations. These experiments are similar in many respects to the small watershed experiments carried out in forested catchments. Our nutrient enrichment is novel compared to past studies in two important ways. We added nutrients (N and P) directly to the flooding tidal creek waters to mimic the way in which anthropogenic nutrients reach marsh ecosystems. All previous experimental salt marsh nutrient enrichment studies used a dose-response design with spatially uniform dry fertilizer loading on small plots (<10 m2). Nutrients carried in water will interact and reach parts of the ecosystem differently than dry fertilizer. Our enrichment method also creates a spatial gradient of nutrient loading across the landscape that is proportional to the frequency and depth of inundation in the marsh. Spatial gradients in loading within an ecosystem are typical in real world situations in many terrestrial and aquatic ecosystems. Because of our enrichment method, at any location in the ecosystem, nutrient load will be a function of the nutrient concentration in the water, the frequency and depth of tidal flooding and the reduction of nutrients from the flooding waters by other parts of the ecosystem. Uniform loading misses important aspects of the spatial complexity of ecosystem exposure and response. This work is organized around two questions that are central to understanding the long-term fate of coastal marshes: 1. Does chronic nutrient enrichment via flooding water increase primary production more than it stimulates microbial decomposition? 2. Do top-down controls change the response of the salt marsh ecosystem to nutrient enrichment? Here we present findings on the first 2 years of these experiments including 1) water chemistry, 2) standing stocks and species composition of benthic microalgae, 3) microbial production, 4) species composition and ecophysiology of macrophytes, 5) invertebrates, and 6) nekton. Because even highly eutrophic waters result in nutrient loading that is an order of magnitude less than most plot level experiments, we expected little stimulation of salt marsh vascular plant growth. However, moderate levels of nutrient enrichment in the water column were expected to increase benthic algal biomass and to stimulate bacterial activity and detrital decomposition throughout the ecosystem because of direct uptake of nitrogen from the water column and availability of more high quality organic matter from increased algal production. We predicted nutrient enrichment would increase invertebrate production because of an increase of high quality microalgal and microbial production at the base of the food web. Finally, we predicted that fish reduction would reduce predation on benthic invertebrates resulting in increased abundance of benthic invertebrates that would graze down the benthic algae.The National Science Foundation (Grant DEB 0213767, OCE 9726921, and OCE 0423565) supported this work. Additional funding was provided by the National Science Foundation postdoctoral fellowship in Microbial Biology (DBI-0400819), the NOAA Coastal Intern grant (NA04NOS4780182), the Office of Environmental Education of Louisiana, Middlebury College and Connecticut College

Change in maternal body mass index is associated with offspring body mass index: a 21-year prospective study

High body-mass index (BMI; defined as 25 kg/m(2) or greater) is associated with increased risk of cancer. To inform public health policy and future research, we estimated the global burden of cancer attributable to high BMI in 2012

The Influence of Spatial Registration on Detection of Cerebral Asymmetries Using Voxel-Based Statistics of Fractional Anisotropy Images and TBSS

The sensitivity of diffusion tensor imaging (DTI) for detecting microstructural white matter alterations has motivated the application of voxel-based statistics (VBS) to fractional anisotropy (FA) images (FA-VBS). However, detected group differences may depend on the spatial registration method used. The objective of this study was to investigate the influence of spatial registration on detecting cerebral asymmetries in FA-VBS analyses with reference to data obtained using Tract-Based Spatial Statistics (TBSS). In the first part of this study we performed FA-VBS analyses using three single-contrast and one multi-contrast registration: (i) whole-brain registration based on T2 contrast, (ii) whole-brain registration based on FA contrast, (iii) individual-hemisphere registration based on FA contrast, and (iv) a combination of (i) and (iii). We then compared the FA-VBS results with those obtained from TBSS. We found that the FA-VBS results depended strongly on the employed registration approach, with the best correspondence between FA-VBS and TBSS results when approach (iv), the “multi-contrast individual-hemisphere” method was employed. In the second part of the study, we investigated the spatial distribution of residual misregistration for each registration approach and the effect on FA-VBS results. For the FA-VBS analyses using the three single-contrast registration methods, we identified FA asymmetries that were (a) located in regions prone to misregistrations, (b) not detected by TBSS, and (c) specific to the applied registration approach. These asymmetries were considered candidates for apparent FA asymmetries due to systematic misregistrations associated with the FA-VBS approach. Finally, we demonstrated that the “multi-contrast individual-hemisphere” approach showed the least residual spatial misregistrations and thus might be most appropriate for cerebral FA-VBS analyses

Insulated molecular wires: inhibiting orthogonal contacts in metal complex based molecular junctions

Metal complexes are receiving increased attention as molecular wires in fundamental studies of the transport properties of metal|molecule|metal junctions. In this context we report the single-molecule conductance of a systematic series of d8 square-planar platinum(II) trans-bis(alkynyl) complexes with terminal trimethylsilylethynyl (C[triple bond, length as m-dash]CSiMe3) contacting groups, e.g. trans-Pt{C[triple bond, length as m-dash]CC6H4C[triple bond, length as m-dash]CSiMe3}2(PR3)2 (R = Ph or Et), using a combination of scanning tunneling microscopy (STM) experiments in solution and theoretical calculations using density functional theory and non-equilibrium Green's function formalism. The measured conductance values of the complexes (ca. 3–5 × 10−5G0) are commensurate with similarly structured all-organic oligo(phenylene ethynylene) and oligo(yne) compounds. Based on conductance and break-off distance data, we demonstrate that a PPh3 supporting ligand in the platinum complexes can provide an alternative contact point for the STM tip in the molecular junctions, orthogonal to the terminal C[triple bond, length as m-dash]CSiMe3 group. The attachment of hexyloxy side chains to the diethynylbenzene ligands, e.g. trans-Pt{C[triple bond, length as m-dash]CC6H2(Ohex)2C[triple bond, length as m-dash]CSiMe3}2(PPh3)2 (Ohex = OC6H13), hinders contact of the STM tip to the PPh3 groups and effectively insulates the molecule, allowing the conductance through the full length of the backbone to be reliably measured. The use of trialkylphosphine (PEt3), rather than triarylphosphine (PPh3), ancillary ligands at platinum also eliminates these orthogonal contacts. These results have significant implications for the future design of organometallic complexes for studies in molecular junctions

Sensory Communication

Contains table of contents for Section 2, an introduction and reports on twelve research projects.National Institutes of Health Grant 5 R01 DC00117National Institutes of Health Contract 2 P01 DC00361National Institutes of Health Grant 5 R01 DC00126National Institutes of Health Grant R01-DC00270U.S. Air Force - Office of Scientific Research Contract AFOSR-90-0200National Institutes of Health Grant R29-DC00625U.S. Navy - Office of Naval Research Grant N00014-88-K-0604U.S. Navy - Office of Naval Research Grant N00014-91-J-1454U.S. Navy - Office of Naval Research Grant N00014-92-J-1814U.S. Navy - Naval Training Systems Center Contract N61339-93-M-1213U.S. Navy - Naval Training Systems Center Contract N61339-93-C-0055U.S. Navy - Naval Training Systems Center Contract N61339-93-C-0083U.S. Navy - Office of Naval Research Grant N00014-92-J-4005U.S. Navy - Office of Naval Research Grant N00014-93-1-119

Sensory Communication

Contains table of contents for Section 2 and reports on five research projects.National Institutes of Health Contract 2 R01 DC00117National Institutes of Health Contract 1 R01 DC02032National Institutes of Health Contract 2 P01 DC00361National Institutes of Health Contract N01 DC22402National Institutes of Health Grant R01-DC001001National Institutes of Health Grant R01-DC00270National Institutes of Health Grant 5 R01 DC00126National Institutes of Health Grant R29-DC00625U.S. Navy - Office of Naval Research Grant N00014-88-K-0604U.S. Navy - Office of Naval Research Grant N00014-91-J-1454U.S. Navy - Office of Naval Research Grant N00014-92-J-1814U.S. Navy - Naval Air Warfare Center Training Systems Division Contract N61339-94-C-0087U.S. Navy - Naval Air Warfare Center Training System Division Contract N61339-93-C-0055U.S. Navy - Office of Naval Research Grant N00014-93-1-1198National Aeronautics and Space Administration/Ames Research Center Grant NCC 2-77

Sensory Communication

Contains table of contents for Section 2, an introduction and reports on fifteen research projects.National Institutes of Health Grant RO1 DC00117National Institutes of Health Grant RO1 DC02032National Institutes of Health Contract P01-DC00361National Institutes of Health Contract N01-DC22402National Institutes of Health/National Institute on Deafness and Other Communication Disorders Grant 2 R01 DC00126National Institutes of Health Grant 2 R01 DC00270National Institutes of Health Contract N01 DC-5-2107National Institutes of Health Grant 2 R01 DC00100U.S. Navy - Office of Naval Research/Naval Air Warfare Center Contract N61339-94-C-0087U.S. Navy - Office of Naval Research/Naval Air Warfare Center Contract N61339-95-K-0014U.S. Navy - Office of Naval Research/Naval Air Warfare Center Grant N00014-93-1-1399U.S. Navy - Office of Naval Research/Naval Air Warfare Center Grant N00014-94-1-1079U.S. Navy - Office of Naval Research Subcontract 40167U.S. Navy - Office of Naval Research Grant N00014-92-J-1814National Institutes of Health Grant R01-NS33778U.S. Navy - Office of Naval Research Grant N00014-88-K-0604National Aeronautics and Space Administration Grant NCC 2-771U.S. Air Force - Office of Scientific Research Grant F49620-94-1-0236U.S. Air Force - Office of Scientific Research Agreement with Brandeis Universit