Systems biology of gene regulation fulfills its promise

A report on the meeting 'Systems Biology: Global Regulation of Gene Expression' at Cold Spring Harbor, New York, USA, 23-26 March 2006

Plasminogen Activator Activity in Tears of Pregnant Women

Plasminogen activator activity (PAA) in tears of pregnant women was investigated at various gestation times to assess the availability of plasminogen activator for aiding potential corneal wound healing processes during pregnancy.PAA was measured by a spectrophotometric method. The analysis used 91 tear samples from pregnant and non-pregnant women, supplemented with 10 additional tear PAA measurements from non-pregnant women obtained in a previous study.Tear levels of PAA in pregnant women formed a bimodal distribution. Either the tear PAA level was zero or non-zero during pregnancy. When non-zero, the tear PAA level was dissociated from gestation time and not different than non-pregnant and post-pregnant levels. The frequency of occurrence of zero level tear PAA increased with gestation: 16%, 17% and 46% had zero tear PAA in samples taken from women in the first, second and third trimester, respectively.Overall, of the tear samples taken from women during pregnancy, a total of 26% were at zero tear PAA. The remaining tear samples had non-zero tear PAA values throughout gestation equivalent to non-pregnant tear PAA values, suggesting local control of the source of PAA in tears. Given the importance of the plasminogen activator system in tears to wound healing in the cornea, and the high occurrence of zero tear PAA in our sample of pregnant women, elective corneal surgery would be contraindicated. If corneal surgery is nevertheless necessary, the tear PAA level would be worth checking and patients with low level should be closely observed during the postoperative period

Interannual and seasonal asymmetries in gulf stream ring formations from 1980 to 2019

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Silver, A., Gangopadhyay, A., Gawarkiewicz, G., Silva, E. N. S., & Clark, J. Interannual and seasonal asymmetries in gulf stream ring formations from 1980 to 2019. Scientific Reports, 11(1), (2021): 2207, https://doi.org/10.1038/s41598-021-81827-y.As the Gulf Stream separates from the coast, it sheds both Warm and Cold Core Rings between 75∘ and 55∘W. We present evidence that this ring formation behavior has been asymmetric over both interannual and seasonal time-scales. After a previously reported regime-shift in 2000, 15 more Warm Core Rings have been forming yearly compared to 1980–1999. In contrast, there have been no changes in the annual formation rate of the Cold Core Rings. This increase in Warm Core Ring production leads to an excess heat transfer of 0.10 PW to the Slope Sea, amounting to 7.7–12.4% of the total Gulf Stream heat transport, or 5.4–7.3% of the global oceanic heat budget at 30∘N. Seasonally, more Cold Core Rings are produced in the winter and spring and more Warm Core Rings are produced in the summer and fall leading to more summertime heat transfer to the north of the Stream. The seasonal cycle of relative ring formation numbers is strongly correlated (r = 0.82) with that of the difference in upper layer temperatures between the Sargasso and Slope seas. This quantification motivates future efforts to understand the recent increasing influence of the Gulf Stream on the circulation and ecosystem in the western North Atlantic.The authors acknowledge financial supports from NOAA (NA11NOS0120038), NSF (OCE-1851242), SMAST and UMass Dartmouth. GG was supported by NSF under grant OCE-1851261 and ONR under grant N00014-19-1-2646

A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain

BACKGROUND: In eukaryotic cells, RNA-binding proteins (RBPs) contribute to gene expression by regulating the form, abundance, and stability of both coding and non-coding RNA. In the vertebrate brain, RBPs account for many distinctive features of RNA processing such as activity-dependent transcript localization and localized protein synthesis. Several RBPs with activities that are important for the proper function of adult brain have been identified, but how many RBPs exist and where these genes are expressed in the developing brain is uncharacterized. RESULTS: Here we describe a comprehensive catalogue of the unique RBPs encoded in the mouse genome and provide an online database of RBP expression in developing brain. We identified 380 putative RBPs in the mouse genome. Using in situ hybridization, we visualized the expression of 323 of these RBP genes in the brains of developing mice at embryonic day 13.5, when critical fate choice decisions are made and at P0, when major structural components of the adult brain are apparent. We demonstrate i) that 16 of the 323 RBPs examined show neural-specific expression at the stages we examined, and ii) that a far larger subset (221) shows regionally restricted expression in the brain. Of the regionally restricted RBPs, we describe one group that is preferentially expressed in the E13.5 ventricular areas and a second group that shows spatially restricted expression in post-mitotic regions of the embryonic brain. Additionally, we find a subset of RBPs that share the same complex pattern of expression, in proliferating regions of the embryonic and postnatal NS and peripheral tissues. CONCLUSION: Our data show that, in contrast to their proposed ubiquitous involvement in gene regulation, most RBPs are not uniformly expressed. Here we demonstrate the region-specific expression of RBPs in proliferating vs. post-mitotic brain regions as well as cell-type-specific RBP expression. We identify uncharacterized RBPs that exhibit neural-specific expression as well as novel RBPs that show expression in non-neural tissues. The data presented here and in an online database provide a visual filter for the functional analysis of individual RBPs

A census of the warm-core rings of the Gulf Stream: 1980-2017

Author Posting. © American Geophysical Union, 2020. 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: Oceans 125(8), (2020): e2019JC016033, doi:10.1029/2019JC016033.A census of Gulf Stream (GS) warm‐core rings (WCRs) is presented based on 38 years (1980–2017) of data. The census documents formation and demise times and locations, and formation size for all 961 WCRs formed in the study period that live for a week or more. A clear regime shift was observed around the Year 2000 and was reported by a subset of authors (Gangopadhyay et al., 2019, https://doi.org/10.1038/s41598-019-48661-9). The WCR formation over the whole region (75–55°W) increased from an average of 18 per year during Regime 1 (1980–1999) to 33 per year during Regime 2 (2000–2017). For geographic analysis formation locations were grouped in four 5° zones between 75°W and 55°W. Seasonally, WCR formations show a significant summer maxima and winter minima, a pattern that is consistent through all zones and both temporal regimes. The lifespan and size distribution show progressively more rings with higher longevity and greater size when formed to the east of 70°W. The average lifespan of the WCRs in all four zones decreased by 20–40% depending on zones and/or seasons from Regime 1 to Regime 2, while the size distribution remained unchanged across regimes. The ring footprint index, a first‐order signature of impact of the WCRs on the slope, increased significantly (26–90%) for all zones from Regime 1 to Regime 2, with the highest percent increase in Zone 2 (70–65°W). This observational study establishes critical statistical and dynamical benchmarks for validating numerical models and highlights the need for further dynamical understanding of the GS‐ring formation processes.The authors acknowledge financial support from NOAA (NA11NOS0120038), NSF (OCE‐0815679 and OCE‐1851242), and SMAST and UMass Dartmouth. G. G. was supported by NSF under Grant OCE‐1657853 as well as a Senior Scientist Chair from WHOI. We have benefitted from many discussions on Gulf Stream and WCR with Magdalena Andres, Andre Schmidt, Paula Fratantoni, Jon Hare, Wendell Brown, Kathy Donohue, Tom Rossby, Peter Cornillon, and Randy Watts.2020-12-2

Forecasting the Gulf Stream Path using buoyancy and wind forcing over the North Atlantic

Fluctuations in the path of the Gulf Stream (GS) have been previously studied by primarily connecting to either the wind-driven subtropical gyre circulation or buoyancy forcing via the subpolar gyre. Here we present a statistical model for 1 year predictions of the GS path (represented by the GS northern wall—GSNW) between urn:x-wiley:21699275:media:jgrc24667:jgrc24667-math-0001W and urn:x-wiley:21699275:media:jgrc24667:jgrc24667-math-0002W incorporating both mechanisms in a combined framework. An existing model with multiple parameters including the previous year's GSNW index, center location, and amplitude of the Icelandic Low and the Southern Oscillation Index was augmented with basin-wide Ekman drift over the Azores High. The addition of the wind is supported by a validation of the simpler two-layer Parsons-Veronis model of GS separation over the last 40 years. A multivariate analysis was carried out to compare 1-year-in-advance forecast correlations from four different models. The optimal predictors of the best performing model include: (a) the GSNW index from the previous year, (b) gyre-scale integrated Ekman Drift over the past 2 years, and (c) longitude of the Icelandic Low center lagged by 3 years. The forecast correlation over the 27 years (1994–2020) is 0.65, an improvement from the previous multi-parameter model's forecast correlation of 0.52. The improvement is attributed to the addition of the wind-drift component. The sensitivity of forecasting the GS path after extreme atmospheric years is quantified. Results indicate the possibility of better understanding and enhanced predictability of the dominant wind-driven variability of the Atlantic Meridional Overturning Circulation and of fisheries management models that use the GS path as a metric

Exon expression profiling reveals stimulus-mediated exon use in neural cells

Exon centric microarrays were used to resolve the calcium-modulated gene expression response into transcript-level an exon-level regulation

A survival analysis of the gulf stream warm core rings

Author Posting. © American Geophysical Union, 2020. 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: Oceans 125(10),(2020): e2020JC016507, https://doi.org/10.1029/2020JC016507.Survival of Gulf Stream (GS) warm core rings (WCRs) was investigated using a census consisting of a total of 961 rings formed during the period 1980–2017. Kaplan‐Meier survival probability and Cox hazard proportional models were used for the analysis. The survival analysis was performed for rings formed in four 5° zones between 75° W and 55° W. The radius, latitude, and distance from the shelf‐break of a WCR at formation all had a significant effect on the survival of WCRs. A pattern of higher survival was observed in WCRs formed in Zone 2 (70°–65° W) or Zone 3 (65°–60° W) and then demised in Zone 1 (75°–70° W). Survival probability of the WCRs increased to more than 70% for those formed within a latitude band from 39.5° to 41.5° N. Survival probability is reduced when the WCRs are formed near the New England Seamounts.We are grateful for financial supports from NOAA (NA11NOS0120038), NSF (OCE‐1851242), SMAST, and UMass Dartmouth. G. G. was supported by NSF under grant OCE‐1851261.2021-04-1