UV Photo-Oxidation of Polybenzimidazole (PBI)

Since polybenzimidazole (PBI) is often used in the aerospace industry and in high temperature fuel cells, this research investigated the surface modification of PBI film with 253.7 and 184.9 nm UV photo-oxidation. As observed by X-ray photoelectron spectroscopy (XPS), the oxygen concentration on the surface increased up to a saturation level of 20.2 ± 0.7 at %. With increasing treatment time, there were significant decreases in the concentrations of C-C sp2 and C=N groups and increases in the concentration of C=O, O-C=O, O-(C=O)-O, C-N, N-O, and N-C=O containing moieties due to 253.7 nm photo-oxidation of the aromatic groups of PBI and reaction with ozone produced by 184. 9 nm photo-dissociation of oxygen. Because no significant changes in surface topography were detected by AFM and SEM measurements, the observed decrease in the water contact angle down to ca. 44°, i.e., increase in hydrophilic, was due to the chemical changes on the surface

Pol II phosphorylation regulates a switch between transcriptional and splicing condensates

The synthesis of pre-mRNA by RNA polymerase II (Pol II) involves the formation of a transcription initiation complex, and a transition to an elongation complex. The large subunit of Pol II contains an intrinsically disordered C-terminal domain that is phosphorylated by cyclin-dependent kinases during the transition from initiation to elongation, thus influencing the interaction of the C-terminal domain with different components of the initiation or the RNA-splicing apparatus. Recent observations suggest that this model provides only a partial picture of the effects of phosphorylation of the C-terminal domain. Both the transcription-initiation machinery and the splicing machinery can form phase-separated condensates that contain large numbers of component molecules: hundreds of molecules of Pol II and mediator are concentrated in condensates at super-enhancers, and large numbers of splicing factors are concentrated in nuclear speckles, some of which occur at highly active transcription sites. Here we investigate whether the phosphorylation of the Pol II C-terminal domain regulates the incorporation of Pol II into phase-separated condensates that are associated with transcription initiation and splicing. We find that the hypophosphorylated C-terminal domain of Pol II is incorporated into mediator condensates and that phosphorylation by regulatory cyclin-dependent kinases reduces this incorporation. We also find that the hyperphosphorylated C-terminal domain is preferentially incorporated into condensates that are formed by splicing factors. These results suggest that phosphorylation of the Pol II C-terminal domain drives an exchange from condensates that are involved in transcription initiation to those that are involved in RNA processing, and implicates phosphorylation as a mechanism that regulates condensate preference

Coactivator condensation at super-enhancers links phase separation and gene control

Super-enhancers (SEs) are clusters of enhancers that cooperatively assemble a high density of the transcriptional apparatus to drive robust expression of genes with prominent roles in cell identity. Here we demonstrate that the SE-enriched transcriptional coactivators BRD4 and MED1 form nuclear puncta at SEs that exhibit properties of liquid-like condensates and are disrupted by chemicals that perturb condensates. The intrinsically disordered regions (IDRs) of BRD4 and MED1 can form phase-separated droplets, and MED1-IDR droplets can compartmentalize and concentrate the transcription apparatus from nuclear extracts. These results support the idea that coactivators form phase-separated condensates at SEs that compartmentalize and concentrate the transcription apparatus, suggest a role for coactivator IDRs in this process, and offer insights into mechanisms involved in the control of key cell-identity genes.National Institutes of Health (U.S.) (Grant GM123511)National Institutes of Health (U.S.) (Grant P01-CA042063)National Science Foundation (U.S.) (Grant PHY-1743900)National Cancer Institute (U.S.) (Grant P30-CA14051

Coactivator condensation at super-enhancers links phase separation and gene control

Super-enhancers (SEs) are clusters of enhancers that cooperatively assemble a high density of the transcriptional apparatus to drive robust expression of genes with prominent roles in cell identity. Here we demonstrate that the SE-enriched transcriptional coactivators BRD4 and MED1 form nuclear puncta at SEs that exhibit properties of liquid-like condensates and are disrupted by chemicals that perturb condensates. The intrinsically disordered regions (IDRs) of BRD4 and MED1 can form phase-separated droplets, and MED1-IDR droplets can compartmentalize and concentrate the transcription apparatus from nuclear extracts. These results support the idea that coactivators form phase-separated condensates at SEs that compartmentalize and concentrate the transcription apparatus, suggest a role for coactivator IDRs in this process, and offer insights into mechanisms involved in the control of key cell-identity genes

Global urban environmental change drives adaptation in white clover

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations in 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense that also affects tolerance to abiotic stressors. Urban-rural gradients were associated with the evolution of clines in defense in 47% of cities throughout the world. Variation in the strength of clines was explained by environmental changes in drought stress and vegetation cover that varied among cities. Sequencing 2074 genomes from 26 cities revealed that the evolution of urban-rural clines was best explained by adaptive evolution, but the degree of parallel adaptation varied among cities. Our results demonstrate that urbanization leads to adaptation at a global scale

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Utilisation of wastewater for fuel and fodder production and environmental and social benefits in semi-arid, peri-urban zones of sub-Saharan Africa. Final Report 1/12/2002 - 30/11/2007 Contract number ICA4-CT-2002-10017

The overall objective was to develop low-tech water treatment and irrigation systems and test their use for the production of fuel wood and fodder in semi-arid sub-Saharan Africa. Sites for waste water treatment plants and irrigation systems were identified and the systems were constructed in Burkina Faso, Mali and Niger. Project partners were trained in how to use and maintain the systems. The irrigation sites were characterised in advance of tree planting, and soil and water analyses are being conducted regularly. Tree species with potential for use in irrigated conditions in each country were identified and experimental designs for the trials produced. Some species were used in common in all three countries. Nursery screening trials were conducted and plants were then planted at the irrigation sites. Trees grew quickly under the irrigated conditions and many species performed well. Species which were selected for their good performance in the nursery were not necessarily the best performers in the field. Biomass production was determined and the effects of different coppicing treatments on regrowth were assessed. Parameters of planting stock quality were assessed and incidence of pest attacks determined. Partners were also trained in the use of sap flow and associated equipment. Considerable variation between tree species in water use was noted, together with differential effects according to the inoculation history of the plants. Working in controlled glasshouse conditions, using sterilised soil media, considerable variation in effectiveness of different mycorrhizal strains on different tree species was detected. When plant response to simulated irrigation water was measured, uninoculated plants grew very poorly irrespective of whether they are receiving the simulated irrigation water or not. Thus mycorrhizal infection enabled plants to make use of the nutrients in the irrigation water. Initially, nursery and field studies gave much less clear results. However, assessments during the final year of the project demonstrated positive effects of inoculation on tree growth in Mali and Niger. These observations were reinforced on the rhizobial side by molecular studies, using strain-specific probes for nodule analysis. In Ouagadougou it was estimated that 225,004 tons of fuel wood and 6708 tons of charcoal per year are transported to the city. The average price of firewood was approximately 21 F CFA per kg, and charcoal was 60 – 110 F CFA per kg. Sellers can achieve a substantial income from sales. The large quantities of fuel imported into Ouagadougou highlight the pressure on fuel resources. This is further indicated by the observations in Niger and Mali. Dissemination to stakeholders has been conducted and is continuing. The irrigation sites are continuing to be run. An important development is the formation of a partnership with representative farmers’ organizations regrouped under the umbrella of ROPPA (Réseau des Organisations Paysannes et des Producteurs Agricoles d’Afrique de l’Ouest, who federates millions of farmers through twelve west African countries, with the objective of bringing symbionts to farmers