The significance of subsurface chlorophyll, nitrite and ammonium maxima in relation to nitrogen for phytoplankton growth in stratified waters of the Gulf of Maine

Data on the distributions in summer of phytoplankton and inorganic nutrients in the Gulf of Maine and across Georges Bank are presented. The chlorophyll maximum represents a phytoplankton biomass maximum and occurs at a depth where both light and nitrate availability allow net growth of the population. The dominant species were generally flagellates and included the toxic dinoflagellate, Gonyaulax tamarensis var. excavata, at some stations. The ammonium and nitrite profiles suggest that nitrification is occurring at the base of the pycnocline below the chlorophyll maximum, and this may be an important source of nitrate during the summer months. The highest levels of nitrite and ammonium were found over the slopes of Georges Bank

Analyzing the Effects of Coccolithophore Concentration on the Relationship Between Vertical Absorption Coefficient and Secchi Disk Depth

The study of how light passes through water, known as ocean optics, is useful in determining the constituents suspended at the surface of a water body. Understanding the composition of the water over time can answer questions about how the oceans have changed with global climate change and ocean acidification. The vertical absorption coefficient in ocean waters is an indicator characterizing how deeply light penetrates the water column. Using this information, scientists can better understand and predict the amount of primary productivity occurring in the area. Here we examine the relationship between vertical absorption coefficient and Secchi disk depth to determine if the concentration of a type of calcifying phytoplankton, coccolithophores, causes the relationship to deviate from the findings of a pivotal historical study conducted in 1929 by Poole and Atkins. Data was collected during July 2018 aboard the R/V Endeavor on the EN616 “Cocco-Mix” cruise in the Northwest Atlantic Ocean. Diffuse attenuation was determined using downwelling irradiance measurements gathered from a HyperPro that measures electromagnetic energy through the water column. Diffuse attenuation values were compared with Secchi disk depth measurements taken at the same time and location as the HyperPro casts. Results will contribute to our understanding of how the relationship between light extinction and Secchi disk depth changes between water bodies. This knowledge can be used to relate light extinction and Secchi disk depth in historical studies in the Northwest Atlantic that did not have access to more modern equipment to measure light extinction

Quantitating the epigenetic transformation contributing to cholesterol homeostasis using Gaussian process.

To understand the impact of epigenetics on human misfolding disease, we apply Gaussian-process regression (GPR) based machine learning (ML) (GPR-ML) through variation spatial profiling (VSP). VSP generates population-based matrices describing the spatial covariance (SCV) relationships that link genetic diversity to fitness of the individual in response to histone deacetylases inhibitors (HDACi). Niemann-Pick C1 (NPC1) is a Mendelian disorder caused by >300 variants in the NPC1 gene that disrupt cholesterol homeostasis leading to the rapid onset and progression of neurodegenerative disease. We determine the sequence-to-function-to-structure relationships of the NPC1 polypeptide fold required for membrane trafficking and generation of a tunnel that mediates cholesterol flux in late endosomal/lysosomal (LE/Ly) compartments. HDACi treatment reveals unanticipated epigenomic plasticity in SCV relationships that restore NPC1 functionality. GPR-ML based matrices capture the epigenetic processes impacting information flow through central dogma, providing a framework for quantifying the effect of the environment on the healthspan of the individual

Chalk-Ex—fate of CaCO3 particles in the mixed layer : evolution of patch optical properties

Author Posting. © American Geophysical Union, 2009. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research 114 (2009): C07020, doi:10.1029/2008JC004902.The fate of particles in the mixed layer is of great relevance to the global carbon cycle as well as to the propagation of light in the sea. We conducted four manipulative field experiments called “Chalk-Ex” in which known quantities of uniform, calcium carbonate particles were injected into the surface mixed layer. Since the production term for these patches was known to high precision, the experimental design allowed us to focus on terms associated with particle loss. The mass of chalk in the patches was evaluated using the well-calibrated light-scattering properties of the chalk plus measurements from a variety of optical measurements and platforms. Patches were surveyed with a temporal resolution of hours over spatial scales of tens of kilometers. Our results demonstrated exponential loss of the chalk particles with time from the patches. There was little evidence for rapid sinking of the chalk. Instead, horizontal eddy diffusion appeared to be the major factor affecting the dispersion of the chalk to concentrations below the limits of detection. There was unequivocal evidence of subduction of the chalk along isopycnals and subsequent formation of thin layers. Shear dispersion is the most likely mechanism to explain these results. Calculations of horizontal eddy diffusivity were consistent with other mixed layer patch experiments. Our results provide insight into the importance of physics in the formation of subsurface particle maxima in the sea, as well as the importance of rapid coccolith production and critical patch size for maintenance of natural coccolithophore blooms in nature.We would like to thank the Office of Naval Research/Optical and Biological Oceanography Program for their support of Chalk-Ex with awards N000140110042 (WMB) and N00014-01-1-0141 (AJP). Additional funding for this work came from ONR (N00014-05-1- 0111) and NASA (NNG04Gl11G, NNX08AC27G, NNG04HZ25C) to W.M.B

The proteostasis boundary in misfolding diseases of membrane traffic

AbstractProtein function is regulated by the proteostasis network (PN) [Balch, W.E., Morimoto, R.I., Dillin, A. and Kelly, J.W. (2008) Adapting proteostasis for disease intervention. Science 319, 916–919], an integrated biological system that generates and protects the protein fold. The composition of the PN is regulated by signaling pathways including the unfolded protein response (UPR), the heat-shock response (HSR), the ubiquitin proteasome system (UPS) and epigenetic programs. Mismanagement of protein folding and function during membrane trafficking through the exocytic and endocytic pathways of eukaryotic cells by the PN is responsible for a wide range of diseases that include, among others, lysosomal storage diseases, myelination diseases, cystic fibrosis, systemic amyloidoses such as light chain myeloma, and neurodegenerative diseases including Alzheimer’s. Toxicity from misfolding can be cell autonomous (affect the producing cell) or cell non-autonomous (affect a non-producing cell) or both, and have either a loss-of-function or gain-of-toxic function phenotype. Herein, we review the role of the PN and its regulatory transcriptional circuitry likely to be operational in managing the protein fold and function during membrane trafficking. We emphasize the enabling principle of a ‘proteostasis boundary (PB)’ [Powers, E.T., Morimoto, R.T., Dillin, A., Kelly, J.W., and Balch, W.E. (2009) Biochemical and chemical approaches to diseases of proteostasis deficiency. Annu. Rev. Biochem. 78, 959–991]. The PB is defined by the combined effects of the kinetics and thermodynamics of folding and the kinetics of misfolding, which are linked to the variable and adjustable PN capacity found different cell types. Differences in the PN account for the versatility of protein folding and function in health, and the cellular and tissue response to mutation and environmental challenges in disease. We discuss how manipulation of the folding energetics or the PB through metabolites and pharmacological intervention provides multiple routes for restoration of biological function in trafficking disease

Along track temperature, salinity, backscatter, chlorophyll fluorescence, CDOM fluorescence, Es, Lt and Li, absorption and attenuation from R/V Endeavor cruise EN616 in July 2018

Dataset: EN616 UnderwayAlong track temperature, salinity, backscatter, chlorophyll fluorescence, CDOM fluorescence, Es, Lt and Li, absorption and attenuation from R/V Endeavor cruise EN616 in July 2018. For a complete list of measurements, refer to the full dataset description in the supplemental file 'Dataset_description.pdf'. The most current version of this dataset is available at: https://www.bco-dmo.org/dataset/843506NSF Division of Ocean Sciences (NSF OCE) OCE-163574

Hormone replacement therapy after surgery for stage 1 or 2 cutaneous melanoma

A total of 206 women were followed for a minimum of 5 years after primary melanoma surgery to establish if hormone replacement therapy (HRT) adversely affected prognosis. In all, 123 had no HRT and 22 have died of melanoma; 83 had HRT for varying periods and one has died of melanoma. After controlling for known prognostic factors, we conclude that HRT after melanoma does not adversely affect prognosis

Investigation Into the Reproducibility of the Association of Cord Blood Magnesium Concentration and Cerebral Palsy or Death in Children

Objective: To evaluate the association of cord blood magnesium concentrations at the time of birth with cerebral palsy (CP) and neonatal death. Study Design: A secondary analysis of a randomized controlled trial that randomized women at imminent risk of delivery between 24 and 31 weeks of gestation to receive magnesium sulfate or placebo. This ‘study’s primary outcome was a composite of either moderate to severe CP or death. Secondary outcomes included CP, moderate to severe CP, neonatal death, and neonatal head ultrasound findings. We used a logistic regression model to evaluate the relationship between the concentration of magnesium in cord blood and study outcomes. Results: A total of 668 women were included in this analysis and were randomized to magnesium sulfate at 28 ± 2.5 ‘weeks’ gestation. Cord blood magnesium concentrations were not associated with the primary outcome of infant death by 1 year of age or moderate or severe cerebral palsy, as assessed at or beyond 2 years of age (aOR 0.95 (0.67, 1.36), p = 0.79). Cord blood magnesium concentrations were not associated with any of the secondary outcome measurements. Conclusion: Cord blood magnesium concentrations were not associated with moderate to severe cerebral palsy or death, or other neurodevelopmental or sonographic outcomes

Simulation Approach for Timing Analysis of Genetic Logic Circuits

Constructing genetic logic circuits is an application of synthetic biology in which parts of the DNA of a living cell are engineered to perform a dedicated Boolean function triggered by an appropriate concentration of certain proteins or by different genetic components. These logic circuits work in a manner similar to electronic logic circuits, but they are much more stochastic and hence much harder to characterize. In this article, we introduce an approach to analyze the threshold value and timing of genetic logic circuits. We show how this approach can be used to analyze the timing behavior of single and cascaded genetic logic circuits. We further analyze the timing sensitivity of circuits by varying the degradation rates and concentrations. Our approach can be used not only to characterize the timing behavior but also to analyze the timing constraints of cascaded genetic logic circuits, a capability that we believe will be important for design automation in synthetic biology