Distinct roles of DBHS family members in the circadian transcriptional feedback loop

Factors interacting with core circadian clock components are essential to achieve transcriptional feedback necessary for metazoan clocks. Here we show that all three members of the Drosophila Behavior Human Splicing (DBHS) family of RNA-binding proteins play a role in the mammalian circadian oscillator, abrogating or altering clock function when overexpressed or depleted in cells. Although these proteins are members of so-called nuclear paraspeckles, depletion of paraspeckles themselves via silencing of the structural non-coding RNA (ncRNA) Neat1 did not affect overall clock function, suggesting that paraspeckles are not required for DBHS-mediated circadian effects. Instead, we show that the proteins bound to circadian promoter DNA in a fashion that required the PERIOD (PER) proteins, and potently repressed E box-mediated transcription but not CMV promoter-mediated transcription when exogenously recruited. Nevertheless, mice with one or both copies of these genes deleted show only small changes in period length or clock gene expression in vivo. Data from transient transfections show that each of these proteins can either repress or activate depending on the context. Taken together, our data suggest that all of the DBHS family members serve overlapping or redundant roles as transcriptional cofactors at circadian clock-regulated genes

Building block libraries and structural considerations in the self-assembly of polyoxometalate and polyoxothiometalate systems

Inorganic metal-oxide clusters form a class of compounds that are unique in their topological and electronic versatility and are becoming increasingly more important in a variety of applications. Namely, Polyoxometalates (POMs) have shown an unmatched range of physical properties and the ability to form structures that can bridge several length scales. The formation of these molecular clusters is often ambiguous and is governed by self-assembly processes that limit our ability to rationally design such molecules. However, recent years have shown that by considering new building block principles the design and discovery of novel complex clusters is aiding our understanding of this process. Now with current progress in thiometalate chemistry, specifically polyoxothiometalates (POTM), the field of inorganic molecular clusters has further diversified allowing for the targeted development of molecules with specific functionality. This chapter discusses the main differences between POM and POTM systems and how this affects synthetic methodologies and reactivities. We will illustrate how careful structural considerations can lead to the generation of novel building blocks and further deepen our understanding of complex systems

Silicate weathering and carbon cycle controls on the Oligocene-Miocene transition glaciation

Changes in both silicate weathering rates and organic carbon burial have been proposed as drivers of the transient “Mi-1” glaciation event at the Oligocene-Miocene transition (OMT; ~23 Ma). However detailed geochemical proxy data are required to test these hypotheses. Here we present records of Li/Ca, Mg/Ca, Cd/Ca, U/Ca, δ18O, δ13C, and shell weight in planktonic foraminifera from marine sediments spanning the OMT in the equatorial Atlantic Ocean. Li/Ca values increase by 1 μmol/mol across this interval. We interpret this to indicate a ~20% increase in silicate weathering rates, which would have lowered atmospheric CO2, potentially forcing the Antarctic glaciation circa 23 Ma. δ13C of thermocline dwelling planktonic foraminifera track the global increase in seawater δ13C across the OMT and during the Mi-1 event, hence supporting a hypothesized global increase in organic carbon burial rates. High δ13C previously measured in epipelagic planktonic foraminifera and high Cd/Ca ratios during Mi-1 are interpreted to represent locally enhanced primary productivity, stimulated by increased nutrients supply to surface waters. The fingerprint of high export production and associated organic carbon burial at this site is found in reduced bottom water oxygenation (inferred from high foraminiferal U/Ca), and enhanced respiratory dissolution of carbonates, characterised by reduced foraminiferal shell weight. Replication of our results elsewhere would strengthen the case that weathering-induced CO2 sequestration preconditioned climate for Antarctic ice sheet growth across the OMT and increased burial of organic carbon acted as a feedback that intensified cooling at this time

Withanolides and related steroids

Since the isolation of the first withanolides in the mid-1960s, over 600 new members of this group of compounds have been described, with most from genera of the plant family Solanaceae. The basic structure of withaferin A, a C28 ergostane with a modified side chain forming a δ-lactone between carbons 22 and 26, was considered for many years the basic template for the withanolides. Nowadays, a considerable number of related structures are also considered part of the withanolide class; among them are those containing γ-lactones in the side chain that have come to be at least as common as the δ-lactones. The reduced versions (γ and δ-lactols) are also known. Further structural variations include modified skeletons (including C27 compounds), aromatic rings and additional rings, which may coexist in a single plant species. Seasonal and geographical variations have also been described in the concentration levels and types of withanolides that may occur, especially in the Jaborosa and Salpichroa genera, and biogenetic relationships among those withanolides may be inferred from the structural variations detected. Withania is the parent genus of the withanolides and a special section is devoted to the new structures isolated from species in this genus. Following this, all other new structures are grouped by structural types. Many withanolides have shown a variety of interesting biological activities ranging from antitumor, cytotoxic and potential cancer chemopreventive effects, to feeding deterrence for several insects as well as selective phytotoxicity towards monocotyledoneous and dicotyledoneous species. Trypanocidal, leishmanicidal, antibacterial, and antifungal activities have also been reported. A comprehensive description of the different activities and their significance has been included in this chapter. The final section is devoted to chemotaxonomic implications of withanolide distribution within the Solanaceae. Overall, this chapter covers the advances in the chemistry and biology of withanolides over the last 16 years.Fil: Misico, Rosana Isabel. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Orgánica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad de Microanálisis y Métodos Físicos Aplicados a la Química Orgánica (i); ArgentinaFil: Nicotra, V.. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal (p); Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Orgánica; ArgentinaFil: Oberti, Juan Carlos María. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal (p); Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Química Orgánica; ArgentinaFil: Barboza, Gloria Estela. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Córdoba. Instituto Multidisciplinario de Biología Vegetal (p); Argentina. Universidad Nacional de Córdoba. Facultad de Ciencias Químicas. Departamento de Farmacia; ArgentinaFil: Gil, Roberto Ricardo. University Of Carnegie Mellon; Estados UnidosFil: Burton, Gerardo. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Química Orgánica; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Ciudad Universitaria. Unidad de Microanálisis y Métodos Físicos Aplicados a la Química Orgánica (i); Argentin

Affinity-restricted memory B cells dominate recall responses to heterologous flaviviruses

Memory B cells (MBCs) can respond to heterologous antigens either by molding new specificities through secondary germinal centers (GCs) or selecting pre-existing clones without further affinity maturation. To distinguish these mechanisms in flavivirus infections and immunizations, we studied recall responses to envelope protein domain III (DIII). Conditional deletion of activation induced cytidine deaminase (AID) between heterologous challenges of West Nile, Japanese encephalitis, Zika, and Dengue viruses did not affect recall responses. DIII-specific MBCs were contained mostly within the plasma cell-biased CD80(+) subset and few GCs arose following heterologous boosters, demonstrating that recall responses are confined by pre-existing clonal diversity. Measurement of monoclonal antibody binding affinity to DIII proteins, timed AID deletion, single cell RNA-sequencing, and lineage tracing experiments point to selection of relatively low affinity MBCs as a mechanism to promote diversity. Engineering immunogens to avoid this MBC diversity may facilitate flavivirus type-specific vaccines with minimized potential for infection enhancement

Validation of GEMS tropospheric NO2 columns and their diurnal variation with ground-based DOAS measurements

Instruments for air quality observations on geostationary satellites provide multiple observations per day and allow for the analysis of the diurnal variation in important air pollutants such as nitrogen dioxide (NO2). The South Korean instrument GEMS (Geostationary Environmental Monitoring Spectrometer), launched in February 2020, is the first geostationary instrument that is able to observe the diurnal variation in NO2. The measurements have a spatial resolution of 3.5 km × 8 km and cover a large part of Asia. This study compares 1 year of tropospheric NO2 vertical column density (VCD) observations from the operational GEMS L2 product, the scientific GEMS IUP-UB (Institute of Environmental Physics at the University of Bremen) product, the operational TROPOspheric Monitoring Instrument (TROPOMI) product, and ground-based differential optical absorption spectroscopy (DOAS) measurements in South Korea. The GEMS L2 tropospheric NO2 VCDs overestimate the ground-based tropospheric NO2 VCDs with a median relative difference of +61 % and a correlation coefficient of 0.76. The median relative difference is −2 % for the GEMS IUP-UB product and −16 % for the TROPOMI product, with correlation coefficients of 0.83 and 0.89, respectively. The scatter in the GEMS products can be reduced when observations are limited to the TROPOMI overpass time. Diurnal variations in tropospheric NO2 VCDs differ by the pollution level of the analyzed site but with good agreement between the GEMS IUP-UB and ground-based observations. Low-pollution sites show weak or almost no diurnal variation. In summer, the polluted sites show a minimum around noon, indicating the large influence of photochemical loss. Most variation is seen in spring and autumn, with increasing NO2 in the morning, a maximum close to noon, and a decrease towards the afternoon. Winter observations show rather flat or slightly decreasing NO2 throughout the day. Winter observations under low-wind-speed conditions at high-pollution sites show enhancements of NO2 throughout the day. This indicates that under calm conditions, dilution and the less effective chemical loss in winter do not balance the accumulating emissions. Diurnal variation observed at a low-pollution site follows seasonal wind patterns. A weekday–weekend effect analysis shows good agreement between the different products. However, the GEMS L2 product, while agreeing with the other data sets on weekdays, shows significantly less reduction on weekends. The influence of the stratospheric contribution and the surface reflectivity product on the satellite tropospheric NO2 VCD products is investigated. While the TM5 model's stratospheric VCDs, used in the TROPOMI product, are too high, resulting in tropospheric NO2 VCDs that are too low and even negative, when used in the GEMS IUP-UB retrieval, the GEMS L2 stratospheric VCD is too low. Surface reflectivity comparisons indicate that the GEMS L2 reflectivity makes a large contribution to the observed overestimation and scatter

Validation of GEMS operational v2.0 total column NO2 and HCHO during the GMAP/SIJAQ campaign

The Geostationary Environmental Monitoring Spectrometer (GEMS), the first geostationary air quality instrument, onboard the GEO-KOMPSAT-2B (GK2B) satellite, produces hourly observations over Asia with 3.5 km × 8 km spatial resolution. To evaluate the GEMS L2 products, the National Institute of Environmental Research (NIER) organized the GEMS Map of Air Pollutants 2021 (GMAP2021) and the Satellite Integrated Joint monitoring of Air Quality 2022 (SIJAQ2022) campaigns during October 2021 to November 2021 and from June 2022 to July 2022, respectively. While GMAP2021 mainly targeted the SMA (Seoul Metropolitan Area), the SIJAQ2022 campaign extended to the southeastern area of South Korea. In this study, a comparison between Pandora and Multi-AXis Differential Optical Absorption Spectroscopy (MAX-DOAS) products and an evaluation of the GEMS operational v2.0 total column NO2 and HCHO products are conducted. A comparative analysis between the Pandora (P189) and the IUP Bremen MAX-DOAS instrument at the Incheon NIER-ESC site was performed to analyze discrepancies between the retrieval processors (Pandora: PGN official processor, MAX-DOAS: MMF in FRM4DOAS framework). Aligning the viewing directions of both Pandora and MAX-DOAS leads to a significant increase in the slope and correlation coefficient from 0.87 to 0.96 and from 0.86 to 0.96, respectively, in the case of NO2 tropospheric columns. Similarly, for HCHO tropospheric columns, slope and correlation coefficient change from 0.94 to 1.09 and from 0.81 to 0.90 when matching the viewing geometries of both instruments. In contrast to tropospheric columns, total HCHO columns derived from Pandora (P189) direct-sun measurements show significantly larger values than the MAX-DOAS ones, with a mean relative difference (MRD) of 126 %. This bias can however be reduced to 33 % after suitable adjustment of the direct-sun retrieval settings. The GEMS v2.0 NO2 total column product, evaluated over 6 official PGN sites in South Korea, shows good agreement with a correlation coefficient of 0.87 and similar seasonal and diurnal NO2 variation. However, GEMS tends to report higher values than Pandora with a mean relative difference of +41 %. The magnitude of the GEMS overestimation is amplified in highly polluted conditions (i.e. during winter and at noontime). Compared to 6 MAX-DOAS stations and 6 Pandora stations, the GEMS HCHO product captures well the seasonal and diurnal variation of HCHO and shows good agreement both with MAX-DOAS and Pandora with slopes of 0.84 and 0.79, respectively, and correlation coefficients of 0.86 for both. Large columns, however, tend to be systematically underestimated

CHD1 Remodels Chromatin and Influences Transient DNA Methylation at the Clock Gene frequency

Circadian-regulated gene expression is predominantly controlled by a transcriptional negative feedback loop, and it is evident that chromatin modifications and chromatin remodeling are integral to this process in eukaryotes. We previously determined that multiple ATP–dependent chromatin-remodeling enzymes function at frequency (frq). In this report, we demonstrate that the Neurospora homologue of chd1 is required for normal remodeling of chromatin at frq and is required for normal frq expression and sustained rhythmicity. Surprisingly, our studies of CHD1 also revealed that DNA sequences within the frq promoter are methylated, and deletion of chd1 results in expansion of this methylated domain. DNA methylation of the frq locus is altered in strains bearing mutations in a variety of circadian clock genes, including frq, frh, wc-1, and the gene encoding the frq antisense transcript (qrf). Furthermore, frq methylation depends on the DNA methyltransferase, DIM-2. Phenotypic characterization of Δdim-2 strains revealed an approximate WT period length and a phase advance of approximately 2 hours, indicating that methylation plays only an ancillary role in clock-regulated gene expression. This suggests that DNA methylation, like the antisense transcript, is necessary to establish proper clock phasing but does not control overt rhythmicity. These data demonstrate that the epigenetic state of clock genes is dependent on normal regulation of clock components