Biochemical Functions of Geophagy in Parrots: Detoxification of Dietary Toxins and Cytoprotective Effects

This study tests hypotheses on the biochemical functions of geophagy in parrots: mechanical enhancement of digestion, acid buffering capacity, mineral supplementation, adsorption of dietary toxins, and gastrointestinal cytoprotection. Parrots showed clear preferences for specific soil horizons. Comparisons of preferred and nonpreferred soils from several sites suggest that soils have little ability to enhance grinding and no measurable ability to buffer gastric pH. Soils offered insignificant mineral supplementation since most minerals occurred at similar levels in samples regardless of preference, and the minerals were generally more plentiful in the birds' diets. Sodium was available in moderate levels at some sites (>1000 ppm), but was well below sodium detection thresholds of parrots. X-ray diffraction, cation exchange capacity, and in vitro adsorptive trials showed that the preferred soils are capable of exchanging substantial quantities of cations and are capable of adsorbing low-molecular-weight secondary compounds. In captive Amazona parrots, orally administered clay reduced the bioavailability of the alkaloid quinidine by roughly 60%, demonstrating that in vivo adsorption of potentially toxic compounds may be a biologically important function of geophagy. Labeled clay remained in the lower gastrointestinal tract of captive parrots for >12 hr, which along with high adsorptive capacities, further suggests a potential role in protecting the gastrointestinal lining from various biological and chemical insults. Detoxification and cytoprotection are the most likely functions of geophagy for parrots and herbivores with similar ecologies. Given the variety of chemically defended seeds consumed by these herbivores, geophagy likely protects consumers from dietary toxins, allowing increased diet breadth and/or enhancing digestibility.     

Human DDX3X Unwinds Japanese Encephalitis and Zika Viral 5′ Terminal Regions

Flavivirus genus includes many deadly viruses such as the Japanese encephalitis virus (JEV) and Zika virus (ZIKV). The 5′ terminal regions (TR) of flaviviruses interact with human proteins and such interactions are critical for viral replication. One of the human proteins identified to interact with the 5′ TR of JEV is the DEAD-box helicase, DDX3X. In this study, we in vitro transcribed the 5′ TR of JEV and demonstrated its direct interaction with recombinant DDX3X (K_d of 1.66 ± 0.21 µM) using microscale thermophoresis (MST). Due to the proposed structural similarities of 5′ and 3′ TRs of flaviviruses, we investigated if the ZIKV 5′ TR could also interact with human DDX3X. Our MST studies suggested that DDX3X recognizes ZIKV 5′ TR with a K_d of 7.05 ± 0.75 µM. Next, we performed helicase assays that suggested that the binding of DDX3X leads to the unwinding of JEV and ZIKV 5′ TRs. Overall, our data indicate, for the first time, that DDX3X can directly bind and unwind in vitro transcribed flaviviral TRs. In summary, our work indicates that DDX3X could be further explored as a therapeutic target to inhibit Flaviviral replication     

Human DDX17 Unwinds Rift Valley Fever Virus Non-Coding RNAs

Rift Valley fever virus (RVFV) is a mosquito-transmitted virus from the Bunyaviridae family that causes high rates of mortality and morbidity in humans and ruminant animals. Previous studies indicated that DEAD-box helicase 17 (DDX17) restricts RVFV replication by recognizing two primary non-coding RNAs in the S-segment of the genome: the intergenic region (IGR) and 5′ non-coding region (NCR). However, we lack molecular insights into the direct binding of DDX17 with RVFV non-coding RNAs and information on the unwinding of both non-coding RNAs by DDX17. Therefore, we performed an extensive biophysical analysis of the DDX17 helicase domain (DDX17_135–555) and RVFV non-coding RNAs, IGR and 5’ NCR. The homogeneity studies using analytical ultracentrifugation indicated that DDX17_135–555, IGR, and 5’ NCR are pure. Next, we performed small-angle X-ray scattering (SAXS) experiments, which suggested that DDX17 and both RNAs are homogenous as well. SAXS analysis also demonstrated that DDX17 is globular to an extent, whereas the RNAs adopt an extended conformation in solution. Subsequently, microscale thermophoresis (MST) experiments were performed to investigate the direct binding of DDX17 to the non-coding RNAs. The MST experiments demonstrated that DDX17 binds with the IGR and 5’ NCR with a dissociation constant of 5.77 ± 0.15 µM and 9.85 ± 0.11 µM, respectively. As DDX17_135–555 is an RNA helicase, we next determined if it could unwind IGR and NCR. We developed a helicase assay using MST and fluorescently-labeled oligos, which suggested DDX17_135–555 can unwind both RNAs. Overall, our study provides direct evidence of DDX17_135–555 interacting with and unwinding RVFV non-coding regions.     

Antioxidant Activity of Osage Orange Extract in Soybean Oil and Fish Oil during Storage

The food industry is seeking natural antioxidants for edible oils that have comparable activity to synthetic counterparts. In this study, Osage orange extract (OOE) rich in osajin (42.9%) and pomiferin (30.0%) was obtained after hexane extraction of the fruit, and its antioxidant activity was examined in stripped soybean oil (SBO) and fish oil (FO), in which antioxidants and polar compounds were removed. The antioxidant activity of OOE was compared with commercial natural antioxidants (i.e., rosemary extract and mixed tocopherols) and a synthetic antioxidant, butylated hydroxytoluene (BHT), during storage at 25 and 40 °C. The 0.1% OOE had stronger antioxidant activity than 0.1% rosemary extract and 0.1% mixed tocopherols in both oils at 25 and 40 °C. Its activity was similar to 0.02% BHT in SBO and was similar or slightly stronger than 0.02% BHT in FO. When OOE was studied at 0.05, 0.1, and 0.2%, there was a weak dose–response in SBO but a stronger dose–response in FO. Headspace volatile analysis using solid phase micro-extraction (SPME) combined with GC–MS indicated that 0.1% OOE was very effective in preventing the formation of volatile oxidation products in both oils. Although it should be further tested for safety before the actual use, this study shows that OOE can be developed as an antioxidant for edible oils.     

An Engineered Biliverdin-Compatible Cyanobacteriochrome Enables a Unique Ultrafast Reversible Photoswitching Pathway

Cyanobacteriochromes (CBCRs) are promising optogenetic tools for their diverse absorption properties with a single compact cofactor-binding domain. We previously uncovered the ultrafast reversible photoswitching dynamics of a red/green photoreceptor AnPixJg2, which binds phycocyanobilin (PCB) that is unavailable in mammalian cells. Biliverdin (BV) is a mammalian cofactor with a similar structure to PCB but exhibits redder absorption. To improve the AnPixJg2 feasibility in mammalian applications, AnPixJg2_BV4 with only four mutations has been engineered to incorporate BV. Herein, we implemented femtosecond transient absorption (fs-TA) and ground state femtosecond stimulated Raman spectroscopy (GS-FSRS) to uncover transient electronic dynamics on molecular time scales and key structural motions responsible for the photoconversion of AnPixJg2_BV4 with PCB (Bpcb) and BV (Bbv) cofactors in comparison with the parent AnPixJg2 (Apcb). Bpcb adopts the same photoconversion scheme as Apcb, while BV4 mutations create a less bulky environment around the cofactor D ring that promotes a faster twist. The engineered Bbv employs a reversible clockwise/counterclockwise photoswitching that requires a two-step twist on ~5 and 35 picosecond (ps) time scales. The primary forward P_fr → P_o transition displays equal amplitude weights between the two processes before reaching a conical intersection. In contrast, the primary reverse P_o → P_fr transition shows a 2:1 weight ratio of the ~35 ps over 5 ps component, implying notable changes to the D-ring-twisting pathway. Moreover, we performed pre-resonance GS-FSRS and quantum calculations to identify the Bbv vibrational marker bands at ~659,797, and 1225 cm⁻¹. These modes reveal a stronger H-bonding network around the BV cofactor A ring with BV4 mutations, corroborating the D-ring-dominant reversible photoswitching pathway in the excited state. Implementation of BV4 mutations in other PCB-binding GAF domains like AnPixJg4, AM1_1870g3, and NpF2164g5 could promote similar efficient reversible photoswitching for more directional bioimaging and optogenetic applications, and inspire other bioengineering advances.     

The Effects of Insulin-Like Growth Factor I and BTP-2 on Acute Lung Injury

Acute lung injury (ALI) afflicts approximately 200,000 patients annually and has a 40% mortality rate. The COVID-19 pandemic has massively increased the rate of ALI incidence. The pathogenesis of ALI involves tissue damage from invading microbes and, in severe cases, the overexpression of inflammatory cytokines such as tumor necrosis factor-α (TNF-α) and interleukin-1β (IL-1β). This study aimed to develop a therapy to normalize the excess production of inflammatory cytokines and promote tissue repair in the lipopolysaccharide (LPS)-induced ALI. Based on our previous studies, we tested the insulin-like growth factor I (IGF-I) and BTP-2 therapies. IGF-I was selected, because we and others have shown that elevated inflammatory cytokines suppress the expression of growth hormone receptors in the liver, leading to a decrease in the circulating IGF-I. IGF-I is a growth factor that increases vascular protection, enhances tissue repair, and decreases pro-inflammatory cytokines. It is also required to produce anti-inflammatory 1,25-dihydroxyvitamin D. BTP-2, an inhibitor of cytosolic calcium, was used to suppress the LPS-induced increase in cytosolic calcium, which otherwise leads to an increase in proinflammatory cytokines. We showed that LPS increased the expression of the primary inflammatory mediators such as toll like receptor-4 (TLR-4), IL-1β, interleukin-17 (IL-17), TNF-α, and interferon-γ (IFN-γ), which were normalized by the IGF-I + BTP-2 dual therapy in the lungs, along with improved vascular gene expression markers. The histologic lung injury score was markedly elevated by LPS and reduced to normal by the combination therapy. In conclusion, the LPS-induced increases in inflammatory cytokines, vascular injuries, and lung injuries were all improved by IGF-I + BTP-2 combination therapy.     

Regulating the geological sequestration of CO2

Governments worldwide should provide incentives for initial large-scale GS projects to help build the knowledge base for a mature, internationally harmonized GS regulatory framework. Health, safety, and environmental risks of these early projects can be managed through modifications of existing regulations in the EU, Australia, Canada, and the U.S. An institutional mechanism, such as the proposed Federal Carbon Sequestration Commission in the U.S., should gather data from these early projects and combine them with factors such as GS industrial organization and climate regime requirements to create an efficient and adaptive regulatory framework suited to large-scale deployment. Mechanisms to structure long-term liability and fund long-term postclosure care must be developed, most likely at the national level, to equitably balance the risks and benefits of this important climate change mitigation technology. We need to do this right. During the initial field experiences, a single major accident, resulting from inadequate regulatory oversight, anywhere in the world, could seriously endanger the future viability of GS. That, in turn, could make it next to impossible to achieve the needed dramatic global reductions in CO2 emissions over the next several decades. We also need to do it quickly. Emissions are going up, the climate is changing, and impacts are growing. The need for safe and effective CO2 capture with deep GS is urgent.     

Anaerobic oxidation of methane: mechanisms, bioenergetics, and the ecology of associated microorganisms

Microbially mediated anaerobic oxidation of methane (AOM) moderates the input of methane, an important greenhouse gas, to the atmosphere by consuming methane produced in various marine, terrestrial, and subsurface environments. AOM coupled to sulfate reduction has been most extensively studied because of the abundance of sulfate in marine systems, but electron acceptors otherthan sulfate are more energetically favorable. Phylogenetic trees based on 16S rRNA gene clone libraries derived from microbial communities where AOM occurs show evidence of diverse, methanotrophic archaea (ANME) closely associated with sulfate-reducing bacteria, but these organisms have not yet been isolated as pure cultures. Several biochemical pathways for AOM have been proposed, including reverse methanogenesis, acetogenesis, and methylogenesis, and both culture-dependent and independent techniques have provided some clues to howthese communities function. Still, questions remain regarding the diversity, physiology, and metabolic restrictions of AOM-related organisms.     

A study of stabilization of P3HT/PCBM organic solar cells by photochemical active TiOx layer

We describe a study of the stabilization behavior of P3HT/PCBM organic solar cells under air and UV irradiation using a 20 nm thin TiO_x protection layer made by partial hydrolysis of a Ti-alkoxide and spin coating in air. Data on the degradation of solar cell performance under air and under UV exposure are presented indicating that significant improvements are observed with TiO_x layer protection. The protection mechanism has been investigated by transmission IR and UV spectroscopy and by ESR spectroscopy. The results of this study suggest how sol-gel derived TiO_x films containing organic functionalities serve as effective passivation films for protection from oxygen when excited by photons, where the photooxidation of the bound organic moieties causes oxygen gas scavenging.