Parasitic plants in the genus Cuscuta (dodders) make their living by extracting resources from other plants. While relatively few dodder species are agricultural pests, those that are can be challenging to control, in part due to their intimate physical and physiological association with host plants. Consequently, dodders remain pervasive and economically damaging pests in a variety of crop systems. The development of improved management strategies would be facilitated by greater understanding of the ecological and environmental factors that influence the establishment and perpetuation of dodder infestations. Light cues play an important role in dodder host location and attachment. To better understand the influence of light conditions on parasite ecology, and potential implications for management, we examined how manipulating the ratio of red to far-red wavelengths (R:FR), via both passive filtering of natural sunlight and active spectral manipulation using LEDs, affects host location and host attachment by two dodder species (C. campestris on tomato hosts and C. gronovii on jewelweed). For both host-parasite combinations, host location and subsequent attachment by dodder parasites was dramatically reduced in high R:FR environments compared to control conditions (with R:FR characteristic of sunlight) and low R:FR conditions. Circumnutation by dodder seedlings was also significantly faster under high R:FR. We observed short-term effects of high R:FR on the height and dry mass of tomato host plants (immediately following 7-day exposure), as well as changes in tomato volatile emissions. However, preliminary investigation of long-term effects on host plants suggests that short-term exposure to high R:FR (i.e. during the critical period when dodder seedlings emerge and attach to hosts) has little or no effect on host plant size or fruit yield at the time of harvest. Synthesis and applications. Our findings suggest that spectral manipulation during the early stages of crop plant growth (e.g. via light-filtering row covers), may have significant potential to augment existing methods for managing or preventing dodder infestations in agricultural crops. We discuss potential obstacles to the realization of its potential, as well as next steps toward the development and optimization of spectral manipulation methods for use in agroecosystems.

While the opportunities available for targeting RNA with small molecules have been widely appreciated, the challenges associated with achieving specific RNA recognition in biological systems have hindered progress and prevented many researchers from entering the field. To facilitate the discovery of RNA-targeted chemical probes and their subsequent applications, we curated the RNA-targeted BIoactive ligaNd Database (R-BIND). This collection contains an array of information on reported chemical probes that target non-rRNA and have biological activity, and analysis has led to the discovery of RNA-privileged properties. Herein, we developed an online platform to make this information freely available to the community, offering search options, a suite of tools for probe development, and an updated R-BIND data set with detailed experimental information for each probe. We repeated the previous cheminformatics analysis on the updated R-BIND list and found that the distinguishing physicochemical, structural, and spatial properties remained unchanged, despite an almost 50% increase in the database size. Further, we developed several user-friendly tools, including queries based on cheminformatic parameters, experimental details, functional groups, and substructures. In addition, a nearest neighbor algorithm can assess the similarity of user-uploaded molecules to R-BIND ligands. These tools and resources can be used to design small molecule libraries, optimize lead ligands, or select targets, probes, assays, and control experiments. Chemical probes are critical to the study and discovery of novel functions for RNA, and we expect this resource to greatly assist researchers in exploring and developing successful RNA-targeted probes.

Discoveries of RNA roles in cellular physiology and pathology are increasing the need for new tools that modulate the structure and function of these biomolecules, and small molecules are proving useful. In 2017, we curated the RNA-targeted BIoactive ligaNd Database (R-BIND) and discovered distinguishing physicochemical properties of RNA-targeting ligands, leading us to propose the existence of an “RNA-privileged” chemical space. Biennial updates of the database and the establishment of a website platform (rbind.chem.duke.edu) have provided new insights and tools to design small molecules based on the analyzed physicochemical and spatial properties. In this report and R-BIND 2.0 update, we refined the curation approach and ligand classification system as well as conducted analyses of RNA structure elements for the first time to identify new targeting strategies. Specifically, we curated and analyzed RNA target structural motifs to determine the properties of small molecules that may confer selectivity for distinct RNA secondary and tertiary structures. Additionally, we collected sequences of target structures and incorporated an RNA structure search algorithm into the website that outputs small molecules targeting similar motifs without a priori secondary structure knowledge. Cheminformatic analyses revealed that, despite the 50% increase in small molecule library size, the distinguishing properties of R-BIND ligands remained significantly different from that of proteins and are therefore still relevant to RNA-targeted probe discovery. Combined, we expect these novel insights and website features to enable the rational design of RNA-targeted ligands and to serve as a resource and inspiration for a variety of scientists interested in RNA targeting.

AE1918 was a cruise of opportunity on which two oceanographic sampling activities were conducted: a CTD cast and a MOCNESS net tow. These are the net data from the MOCNESS tow. access_formats=.htmlTable,.csv,.json,.mat,.nc,.tsv acquisition_description=Standard MOCNESS procedure. It was observed filtered volumes to be too high (and speeds too high), so flowmeter was "recalibrated"\u00a0using deployments and files reanalyzed. It is likely that, since the flowmeter was too new, after several recent deployments has finally "broken-in" and now goes faster. Flow calibration was done by running the LVpki software for several profiles looking at average CF values.

Refer to the cruise report for more information. See also: the xmlcon and hdr files under Supplemental Files. awards_0_award_nid=764113 awards_0_award_number=OCE-1829318 awards_0_data_url=http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1829318 awards_0_funder_name=NSF Division of Ocean Sciences awards_0_funding_acronym=NSF OCE awards_0_funding_source_nid=355 awards_0_program_manager=David L. Garrison awards_0_program_manager_nid=50534 awards_1_award_nid=764119 awards_1_award_number=OCE-1829378 awards_1_data_url=http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1829378 awards_1_funder_name=NSF Division of Ocean Sciences awards_1_funding_acronym=NSF OCE awards_1_funding_source_nid=355 awards_1_program_manager=David L. Garrison awards_1_program_manager_nid=50534 cdm_data_type=Other comment=MOCNESS Net Data from R/V Atlantic Explorer cruise AE1918 PI: Amy Maas (BIOS) Co-PIs: Leocadio Blanco-Bercial (BIOS) & Ann Tarrant (WHOI) Version date: 13-Nov-2019 Noted after the cruise: original volumes (VOL) were wrong.
New column (NewVol) was added with real values after changing the calibration to 2.7.
The incorrect VOL column has been removed. Please notice that, contrary to regular mocness net numbering (0 to 8) the net count starts at 1 (1 to 9). Conventions=COARDS, CF-1.6, ACDD-1.3 data_source=extract_data_as_tsv version 2.3 19 Dec 2019 defaultDataQuery=&time<now doi=10.1575/1912/bco-dmo.781508.1 infoUrl=https://www.bco-dmo.org/dataset/781508 institution=BCO-DMO instruments_0_acronym=MOC1 instruments_0_dataset_instrument_description=Seabird 9/11 unit attached to a 1 m MOCNESS, 150 micron mesh nets instruments_0_dataset_instrument_nid=781517 instruments_0_description=The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. The MOCNESS-1 carries nine 1-m2 nets usually of 335 micrometer mesh and is intended for use with the macrozooplankton. All nets are black to reduce contrast with the background. A motor/toggle release assembly is mounted on the top portion of the frame and stainless steel cables with swaged fittings are used to attach the net bar to the toggle release. A stepping motor in a pressure compensated case filled with oil turns the escapement crankshaft of the toggle release which sequentially releases the nets to an open then closed position on command from the surface. -- from the MOCNESS Operations Manual (1999 + 2003). instruments_0_instrument_external_identifier=https://vocab.nerc.ac.uk/collection/L22/current/NETT0097/ instruments_0_instrument_name=MOCNESS1 instruments_0_instrument_nid=437 instruments_0_supplied_name=MOCNESS keywords_vocabulary=GCMD Science Keywords metadata_source=https://www.bco-dmo.org/api/dataset/781508 param_mapping={'781508': {'ISO_DateTime_UTC_start': 'flag - time'}} parameter_source=https://www.bco-dmo.org/mapserver/dataset/781508/parameters people_0_affiliation=Bermuda Institute of Ocean Sciences people_0_affiliation_acronym=BIOS people_0_person_name=Amy Maas people_0_person_nid=51589 people_0_role=Principal Investigator people_0_role_type=originator people_1_affiliation=Bermuda Institute of Ocean Sciences people_1_affiliation_acronym=BIOS people_1_person_name=Leocadio Blanco-Bercial people_1_person_nid=51108 people_1_role=Co-Principal Investigator people_1_role_type=originator people_2_affiliation=Woods Hole Oceanographic Institution people_2_affiliation_acronym=WHOI people_2_person_name=Ann M. Tarrant people_2_person_nid=51430 people_2_role=Co-Principal Investigator people_2_role_type=originator people_3_affiliation=Woods Hole Oceanographic Institution people_3_affiliation_acronym=WHOI BCO-DMO people_3_person_name=Shannon Rauch people_3_person_nid=51498 people_3_role=BCO-DMO Data Manager people_3_role_type=related project=Zooplankton Diel Rhythm projects_0_acronym=Zooplankton Diel Rhythm projects_0_description=NSF Award Abstract: The daily vertical migration (DMV) of zooplankton and fish across hundreds of meters between shallow and deep waters is a predominant pattern in pelagic ecosystems. This migration has consequences for biogeochemical cycling as it moves a substantial portion of fixed carbon and nitrogen (an estimated 15 to 40 % of the total global organic export) from the surface directly to depth where it feeds the midwater food chain and sequesters nutrients away from atmospheric mixing. Estimates and predictions of these fluxes are, however, poorly understood at present. New observations have shown that one source of uncertainty is due to the assumption that metabolic rates and processes do not vary over the course of the day, except based on changes in temperature and oxygen availability. Rates are, however, also driven by differences in feeding, swimming behavior, and underlying circadian cycles. The objective of this project is to improve the ability of scientists to understand and predict zooplankton contributions to the movement of carbon and nitrogen in the ocean by detailing daily changes in physiological processes of these organisms. By producing a set of respiration and excretion measurements over a daily time series, paired with simultaneously collected gene and protein expression patterns for an abundant vertically migratory species, the investigators will provide unprecedented and predictive insight into how changes in the environment affect the contribution of zooplankton to biogeochemical fluxes. The sampling design of the project will advance discovery and understanding by providing hands-on training opportunities to at least two undergraduate researchers. The project will broaden dissemination of the research via development of an educational module, focusing on rhythms in the ocean. The module will initially be piloted with the Bermuda Institute of Ocean Sciences (BIOS) summer camp students and then disseminated through the BIOS Explorer program, the Teacher Resources Page on the BIOS website, and published in a peer-reviewed educational journal. This project will characterize the metabolic consequences of daily physiological rhythms and DVM for a model zooplankton species, the abundant subtropical copepod Pleuromamma xiphias. Flux processes (oxygen consumption, carbon dioxide production, production of ammonium and fecal pellet production) will be interrogated using directed experiments testing the effects of temperature, feeding and circadian cycle. Circadian cycling will further be examined using transcriptomic and proteomic profiling. These experiments will be related to field samples taken at 6-h intervals over the course of the diel migration using an integrated suite of molecular and organismal metrics. Combined organismal, transcriptomic and proteomic profiles will provide an understanding of which metabolic pathways and associated flux products vary in relation to particular environmental variables (food, light cycle, temperature). Diel variation in metabolic rates will also be assessed across seasons and species using other important migratory groups (pteropod, euphausiid, and another copepod). The metabolic data will then be contextualized with abundance estimates from archived depth-stratified tows to allow scaling to community-level patterns and will be used to improve calculations of zooplankton contribution to particulate organic carbon, nitrogen and respiratory active flux. The results of this study will both improve our flux estimates and provide predictive insight into how various environmental variables influence the underlying physiological pathways generating carbon and nitrogen flux. Cruise reports are available from the completed cruises:SD031019AE1910AE1918 projects_0_end_date=2021-09 projects_0_geolocation=Bermuda projects_0_name=Collaborative Research: Diel physiological rhythms in a tropical oceanic copepod projects_0_project_nid=764114 projects_0_start_date=2018-10 sourceUrl=(local files) standard_name_vocabulary=CF Standard Name Table v55 subsetVariables=tow,date_start,time_start,time,cruise,Date time_coverage_end=2019-07-25T14:20:08Z time_coverage_start=2019-07-25T14:20:08Z version=1 xml_source=osprey2erddap.update_xml() v1.3

Georges Bank Fish larvae collected in MOCNESS tows from R/V Albatross IV, R/V Endeavor, and R/V Oceanus broadscale cruises in the Gulf of Maine and Georges Bank from 1995-1999 access_formats=.htmlTable,.csv,.json,.mat,.nc,.tsv,.esriCsv,.geoJson acquisition_description=GLOBEC Fish Larvae collected by MOCNESS nets, Standard Haul Factor: numerical factor (multiplier) used to standardize catches to be expressed as number caught per 10m^2 of sea surface area. Most haul factors range from 1 to 10. awards_0_award_nid=54610 awards_0_award_number=unknown GB NSF awards_0_funder_name=National Science Foundation awards_0_funding_acronym=NSF awards_0_funding_source_nid=350 awards_0_program_manager=David L. Garrison awards_0_program_manager_nid=50534 awards_1_award_nid=54626 awards_1_award_number=unknown GB NOAA awards_1_funder_name=National Oceanic and Atmospheric Administration awards_1_funding_acronym=NOAA awards_1_funding_source_nid=352 cdm_data_type=Other comment=GLOBEC Fish Larvae collected by MOCNESS nets Donna Johnson (NMFS) Conventions=COARDS, CF-1.6, ACDD-1.3 data_source=extract_data_as_tsv version 2.3 19 Dec 2019 defaultDataQuery=&time<now doi=10.1575/1912/bco-dmo.2324.1 Easternmost_Easting=-65.645 geospatial_lat_max=42.327 geospatial_lat_min=40.278 geospatial_lat_units=degrees_north geospatial_lon_max=-65.645 geospatial_lon_min=-69.038 geospatial_lon_units=degrees_east geospatial_vertical_max=281.0 geospatial_vertical_min=-0.8 geospatial_vertical_positive=down geospatial_vertical_units=m infoUrl=https://www.bco-dmo.org/dataset/2324 institution=BCO-DMO instruments_0_acronym=MOC1 instruments_0_dataset_instrument_description=MOCNESS 1 meter square nets (150 and 335 micrometer mesh). instruments_0_dataset_instrument_nid=4102 instruments_0_description=The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. The MOCNESS-1 carries nine 1-m2 nets usually of 335 micrometer mesh and is intended for use with the macrozooplankton. All nets are black to reduce contrast with the background. A motor/toggle release assembly is mounted on the top portion of the frame and stainless steel cables with swaged fittings are used to attach the net bar to the toggle release. A stepping motor in a pressure compensated case filled with oil turns the escapement crankshaft of the toggle release which sequentially releases the nets to an open then closed position on command from the surface. -- from the MOCNESS Operations Manual (1999 + 2003). instruments_0_instrument_external_identifier=https://vocab.nerc.ac.uk/collection/L22/current/NETT0097/ instruments_0_instrument_name=MOCNESS1 instruments_0_instrument_nid=437 instruments_0_supplied_name=MOCNESS1 metadata_source=https://www.bco-dmo.org/api/dataset/2324 Northernmost_Northing=42.327 param_mapping={'2324': {'lat': 'master - latitude', 'lon': 'master - longitude', 'depth_close': 'flag - depth'}} parameter_source=https://www.bco-dmo.org/mapserver/dataset/2324/parameters people_0_affiliation=National Marine Fisheries Service people_0_affiliation_acronym=NMFS people_0_person_name=Dr Donna L. Johnson people_0_person_nid=50416 people_0_role=Principal Investigator people_0_role_type=originator people_1_affiliation=Woods Hole Oceanographic Institution people_1_affiliation_acronym=WHOI BCO-DMO people_1_person_name=Ms Dicky Allison people_1_person_nid=50382 people_1_role=BCO-DMO Data Manager people_1_role_type=related project=GB projects_0_acronym=GB projects_0_description=The U.S. GLOBEC Georges Bank Program is a large multi- disciplinary multi-year oceanographic effort. The proximate goal is to understand the population dynamics of key species on the Bank - Cod, Haddock, and two species of zooplankton (Calanus finmarchicus and Pseudocalanus) - in terms of their coupling to the physical environment and in terms of their predators and prey. The ultimate goal is to be able to predict changes in the distribution and abundance of these species as a result of changes in their physical and biotic environment as well as to anticipate how their populations might respond to climate change. The effort is substantial, requiring broad-scale surveys of the entire Bank, and process studies which focus both on the links between the target species and their physical environment, and the determination of fundamental aspects of these species' life history (birth rates, growth rates, death rates, etc). Equally important are the modelling efforts that are ongoing which seek to provide realistic predictions of the flow field and which utilize the life history information to produce an integrated view of the dynamics of the populations. The U.S. GLOBEC Georges Bank Executive Committee (EXCO) provides program leadership and effective communication with the funding agencies. projects_0_geolocation=Georges Bank, Gulf of Maine, Northwest Atlantic Ocean projects_0_name=U.S. GLOBEC Georges Bank projects_0_project_nid=2037 projects_0_project_website=http://globec.whoi.edu/globec_program.html projects_0_start_date=1991-01 sourceUrl=(local files) Southernmost_Northing=40.278 standard_name_vocabulary=CF Standard Name Table v55 subsetVariables=inst version=1 Westernmost_Easting=-69.038 xml_source=osprey2erddap.update_xml() v1.3

The dissolution of the nuclear membrane marks the beginning of the prometaphase. Kinetochores are created when proteins attach to the centromeres. Microtubules then attach at the kinetochores, and the chromosomes begin to move to the metaphase plate.

R-loops are non-canonical, three-stranded nucleic acid structures composed of a DNA:RNA hybrid, a displaced single-stranded (ss)DNA, and a trailing ssRNA overhang. R-loops perform critical biological functions under both normal and disease conditions. To elucidate their cellular functions, we need to understand the mechanisms underlying R-loop formation, recognition, signaling, and resolution. Previous high-throughput screens identified multiple proteins that bind R-loops, with many of these proteins containing folded nucleic acid processing and binding domains that prevent (e.g., topoisomerases), resolve (e.g., helicases, nucleases), or recognize (e.g., KH, RRMs) R-loops. However, a significant number of these R-loop interacting Enzyme and Reader proteins also contain long stretches of intrinsically disordered regions (IDRs). The precise molecular and structural mechanisms by which the folded domains and IDRs synergize to recognize and process R-loops or modulate R-loop-mediated signaling have not been fully explored. While studying one such modular R-loop Reader, the Fragile X Protein (FMRP), we unexpectedly discovered that the C-terminal IDR (C-IDR) of FMRP is the predominant R-loop binding site, with the three N-terminal KH domains recognizing the trailing ssRNA overhang. Interestingly, the C-IDR of FMRP has recently been shown to undergo spontaneous Liquid-Liquid Phase Separation (LLPS) assembly by itself or in complex with another non-canonical nucleic acid structure, RNA G-quadruplex. Furthermore, we have recently shown that FMRP can suppress persistent R-loops that form during transcription, a process that is also enhanced by LLPS via the assembly of membraneless transcription factories. These exciting findings prompted us to explore the role of IDRs in R-loop processing and signaling proteins through a comprehensive bioinformatics and computational biology study. Here, we evaluated IDR prevalence, sequence composition and LLPS propensity for the known R-loop interactome. We observed that, like FMRP, the majority of the R-loop interactome, especially Readers, contains long IDRs that are highly enriched in low complexity sequences with biased amino acid composition, suggesting that these IDRs could directly interact with R-loops, rather than being “mere flexible linkers” connecting the “functional folded enzyme or binding domains”. Furthermore, our analysis shows that several proteins in the R-loop interactome are either predicted to or have been experimentally demonstrated to undergo LLPS or are known to be associated with phase separated membraneless organelles. Thus, our overall results present a thought-provoking hypothesis that IDRs in the R-loop interactome can provide a functional link between R-loop recognition via direct binding and downstream signaling through the assembly of LLPS-mediated membrane-less R-loop foci. The absence or dysregulation of the function of IDR-enriched R-loop interactors can potentially lead to severe genomic defects, such as the widespread R-loop-mediated DNA double strand breaks that we recently observed in Fragile X patient-derived cells.