Alternative N-Terminal Domains of PSD-95 and SAP97 Govern Activity-Dependent Regulation of Synaptic AMPA Receptor Function

SummaryPSD-95 and SAP97 are scaffolding proteins that have been implicated in regulating AMPA receptor incorporation and function at synapses. Gain- and loss-of-function approaches, however, have generated conflicting results. To minimize adaptations during development and potential dominant-negative effects of overexpression, we have combined silencing of endogenous PSD-95 in mature neurons with heterologous expression of specific SAP97 or PSD-95 isoforms. We find that both PSD-95 and SAP97 contain alternative N termini expressing either double cysteines that normally are palmitoylated (α-isoforms) or an L27 domain (β-isoforms). Whereas α-isoforms of PSD-95 and SAP97 influence AMPA receptor-mediated synaptic strength independent of activity, the effects of β-isoforms are regulated by activity in a CaMKII-dependent manner. Importantly, the synaptic effects of the β-isoforms are masked by the endogenous α-isoform of PSD-95. These results demonstrate that the different N termini of the predominant endogenous forms of PSD-95 (α-isoform) and SAP97 (β-isoform) govern their role in regulating synaptic function

An Improved Shortcut Design Method of Divided Wall Columns Exemplified by a Liquefied Petroleum Gas Process

Designing a sustainable and economical distillation system is a big global challenge in the industrial chemical field. To address this issue, one of most promising solutions is the so-called dividing wall columns addressed in this work, which not only can cut energy cost but also use limited installation space. An improved shortcut design approach is developed in this work to provide accurate models for each section of dividing wall columns; meanwhile Underwood’s and Gilliland’s equations are employed to determine minimum reflux ratio and total number of stages in different column sections in terms of corresponding design specifications and operating conditions. This proposed approach has been applied to separations of mixtures of hydrocarbons and alcohol with different values on the ease of separation index. To test its effectiveness, the preliminary design parameters obtained through the improved proposed shortcut method are further validated by a rigorous simulation in Aspen HYSYS. Furthermore, the results indicate that this method could provide much more accuracy of average interconnecting stream composition of the prefractionator and main column than those of other methods. In practice, this method has been applied to a case of liquefied petroleum gas (LPG) separation with three targeted products in an industrial liquefied petroleum gas plant. The applications and efficiency of the shortcut method in this study lay a theoretical foundation for designing the separation of ideal mixtures involving dividing wall columns

Modeling characterization of the vertical and temporal variability of environmental DNA in the mesopelagic ocean

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Allan, E. A., DiBenedetto, M. H., Lavery, A. C., Govindarajan, A. F., & Zhang, W. G. Modeling characterization of the vertical and temporal variability of environmental DNA in the mesopelagic ocean. Scientific Reports, 11(1), (2021): 21273, https://doi.org/10.1038/s41598-021-00288-5.Increasingly, researchers are using innovative methods to census marine life, including identification of environmental DNA (eDNA) left behind by organisms in the water column. However, little is understood about how eDNA is distributed in the ocean, given that organisms are mobile and that physical and biological processes can transport eDNA after release from a host. Particularly in the vast mesopelagic ocean where many species vertically migrate hundreds of meters diurnally, it is important to link the location at which eDNA was shed by a host organism to the location at which eDNA was collected in a water sample. Here, we present a one-dimensional mechanistic model to simulate the eDNA vertical distribution after its release and to compare the impact of key biological and physical parameters on the eDNA vertical and temporal distribution. The modeled vertical eDNA profiles allow us to quantify spatial and temporal variability in eDNA concentration and to identify the most important parameters to consider when interpreting eDNA signals. We find that the vertical displacement by advection, dispersion, and settling has limited influence on the eDNA distribution, and the depth at which eDNA is found is generally within tens of meters of the depth at which the eDNA was originally shed from the organism. Thus, using information about representative vertical migration patterns, eDNA concentration variability can be used to answer ecological questions about migrating organisms such as what depths species can be found in the daytime and nighttime and what percentage of individuals within a species diurnally migrate. These findings are critical both to advance the understanding of the vertical distribution of eDNA in the water column and to link eDNA detection to organism presence in the mesopelagic ocean as well as other aquatic environments.This research is part of the Woods Hole Oceanographic Institution’s Ocean Twilight Zone project, funded as part of The Audacious Project housed at TED

The Antiviral RNA Interference Response Provides Resistance to Lethal Arbovirus Infection and Vertical Transmission in Caenorhabditis elegans

The recent discovery of the positive-sense single-stranded RNA (ssRNA) Orsay virus (OV) as a natural pathogen of the nematode Caenorhabditis elegans has stimulated interest in exploring virus-nematode interactions. However, OV infection is restricted to a small number of intestinal cells, even in nematodes defective in their antiviral RNA interference (RNAi) response, and is neither lethal nor vertically transmitted. Using a fluorescent reporter strain of the negative-sense ssRNA vesicular stomatitis virus (VSV), we show that microinjection of VSV particles leads to a dose-dependent, muscle tissue-tropic, lethal infection in C. elegans. Furthermore, we find nematodes deficient for components of the antiviral RNAi pathway, such as Dicer-related helicase 1 (DRH-1), to display hypersusceptibility to VSV infection as evidenced by elevated infection rates, virus replication in multiple tissue types, and earlier mortality. Strikingly, infection of oocytes and embryos could also be observed in drh-1 mutants. Our results suggest that the antiviral RNAi response not only inhibits vertical VSV transmission but also promotes transgenerational inheritance of antiviral immunity. Our study introduces a new, in vivo virus-host model system for exploring arbovirus pathogenesis and provides the first evidence for vertical pathogen transmission in C. elegans

Neuronal pentraxins mediate synaptic refinement in the developing visual system

Peer reviewedPublisher PD

PFAS and their substitutes in groundwater: Occurrence, transformation and remediation

Poly- and perfluoroalkyl substances (PFAS) are increasingly investigated due to their global occurrence and potential human health risk. The ban on PFOA and PFOS has led to the use of novel substitutes such as GenX, F-53B and OBS. This paper reviews the studies on the occurrence, transformation and remediation of major PFAS i.e. PFOA, PFNA, PFBA, PFOS, PFHxS, PFBS and the three substitutes in groundwater. The data indicated that PFOA, PFBA, PFOS and PFBS were present at high concentrations up to 21,200 ng L−1 while GenX and F-53B were found up to 30,000 ng L−1 and 0.18–0.59 ng L−1, respectively. PFAS in groundwater are from direct sources e.g. surface water and soil. PFAS remediation methods based on membrane, redox, sorption, electrochemical and photocatalysis are analyzed. Overall, photocatalysis is considered to be an ideal technology with low cost and high degradation efficacy for PFAS removal. Photocatalysis could be combined with electrochemical or membrane filtration to become more advantageous. GenX, F-53B and OBS in groundwater treatment by UV/sulfite system and electrochemical oxidation proved effective. The review identified gaps such as the immobilization and recycling of materials in groundwater treatment, and recommended visible light photocatalysis for future studies

Enzymatic glucosylation of polyphenols using glucansucrases and branching sucrases of glycoside hydrolase family 70

Polyphenols exhibit various beneficial biological activities and represent very promising candidates as active compounds for food industry. However, the low solubility, poor stability and low bioavailability of polyphenols have severely limited their industrial applications. Enzymatic glycosylation is an effective way to improve the physicochemical properties of polyphenols. As efficient transglucosidases, glycoside hydrolase family 70 (GH70) glucansucrases naturally catalyze the synthesis of polysaccharides and oligosaccharides from sucrose. Notably, GH70 glucansucrases show broad acceptor substrate promiscuity and catalyze the glucosylation of a wide range of non-carbohydrate hydroxyl group-containing molecules, including benzenediol, phenolic acids, flavonoids and steviol glycosides. Branching sucrase enzymes, a newly established subfamily of GH70, are shown to possess a broader acceptor substrate binding pocket that acts efficiently for glucosylation of larger size polyphenols such as flavonoids. Here we present a comprehensive review of glucosylation of polyphenols using GH70 glucansucrase and branching sucrases. Their catalytic efficiency, the regioselectivity of glucosylation and the structure of generated products are described for these reactions. Moreover, enzyme engineering is effective for improving their catalytic efficiency and product specificity. The combined information provides novel insights on the glucosylation of polyphenols by GH70 glucansucrases and branching sucrases, and may promote their applications.</p

Exploring the use of environmental DNA (eDNA) to detect animal taxa in the Mesopelagic Zone

© The Author(s), 2021. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Govindarajan, A. F., Francolini, R. D., Jech, J. M., Lavery, A. C., Llopiz, J. K., Wiebe, P. H., & Zhang, W. Exploring the use of environmental DNA (eDNA) to detect animal taxa in the Mesopelagic Zone. Frontiers in Ecology and Evolution, 9, (2021): 574877, https://doi.org/10.3389/fevo.2021.574877.Animal biodiversity in the ocean’s vast mesopelagic zone is relatively poorly studied due to technological and logistical challenges. Environmental DNA (eDNA) analyses show great promise for efficiently characterizing biodiversity and could provide new insight into the presence of mesopelagic species, including those that are missed by traditional net sampling. Here, we explore the utility of eDNA for identifying animal taxa. We describe the results from an August 2018 cruise in Slope Water off the northeast United States. Samples for eDNA analysis were collected using Niskin bottles during five CTD casts. Sampling depths along each cast were selected based on the presence of biomass as indicated by the shipboard Simrad EK60 echosounder. Metabarcoding of the 18S V9 gene region was used to assess taxonomic diversity. eDNA metabarcoding results were compared with those from net-collected (MOCNESS) plankton samples. We found that the MOCNESS sampling recovered more animal taxa, but the number of taxa detected per liter of water sampled was significantly higher in the eDNA samples. eDNA was especially useful for detecting delicate gelatinous animals which are undersampled by nets. We also detected eDNA changes in community composition with depth, but not with sample collection time (day vs. night). We provide recommendations for applying eDNA-based methods in the mesopelagic including the need for studies enabling interpretation of eDNA signals and improvement of barcode reference databases.This research was part of the Woods Hole Oceanographic Institution’s Ocean Twilight Zone Project, funded as part of The Audacious Project housed at TED. Funding for the NOAA Ship Henry B Bigelow was provided by NOAA’s Office of Marine and Aviation Operations (OMAO)

Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF

Approximately 75% of the human genome is transcribed, the majority of which does not encode protein. However, many noncoding RNAs (ncRNAs) are rapidly degraded after transcription, and relatively few have established functions, questioning the significance of this observation. Here we show that esBAF, a SWI/SNF family nucleosome remodeling factor, suppresses transcription of ncRNAs from approximately 57,000 nucleosome-depleted regions (NDRs) throughout the genome of mouse embryonic stem cells (ESCs). We show that esBAF functions to both keep NDRs nucleosome-free and promote elevated nucleosome occupancy adjacent to NDRs. Reduction of adjacent nucleosome occupancy upon esBAF depletion is strongly correlated with ncRNA expression, suggesting that flanking nucleosomes form a barrier to pervasive transcription. Upon forcing nucleosome occupancy near two NDRs using a nucleosome-positioning sequence, we found that esBAF is no longer required to silence transcription. Therefore, esBAF\u27s function to enforce nucleosome occupancy adjacent to NDRs, and not its function to maintain NDRs in a nucleosome-free state, is necessary for silencing transcription over ncDNA. Finally, we show that the ability of a strongly positioned nucleosome to repress ncRNA depends on its translational positioning. These data reveal a novel role for esBAF in suppressing pervasive transcription from open chromatin regions in ESCs