A multi-omic survey of black cottonwood tissues highlights coordinated transcriptomic and metabolomic mechanisms for plant adaptation to phosphorus deficiency.

Introduction: Phosphorus (P) deficiency in plants creates a variety of metabolic perturbations that decrease photosynthesis and growth. Phosphorus deficiency is especially challenging for the production of bioenergy feedstock plantation species, such as poplars (Populus spp.), where fertilization may not be practically or economically feasible. While the phenotypic effects of P deficiency are well known, the molecular mechanisms underlying whole-plant and tissue-specific responses to P deficiency, and in particular the responses of commercially valuable hardwoods, are less studied. Methods: We used a multi-tissue and multi-omics approach using transcriptomic, proteomic, and metabolomic analyses of the leaves and roots of black cottonwood (Populus trichocarpa) seedlings grown under P-deficient (5 µM P) and replete (100 µM P) conditions to assess this knowledge gap and to identify potential gene targets for selection for P efficiency. Results: In comparison to seedlings grown at 100 µM P, P-deficient seedlings exhibited reduced dry biomass, altered chlorophyll fluorescence, and reduced tissue P concentrations. In line with these observations, growth, C metabolism, and photosynthesis pathways were downregulated in the transcriptome of the P-deficient plants. Additionally, we found evidence of strong lipid remodeling in the leaves. Metabolomic data showed that the roots of P-deficient plants had a greater relative abundance of phosphate ion, which may reflect extensive degradation of P-rich metabolites in plants exposed to long-term P-deficiency. With the notable exception of the KEGG pathway for Starch and Sucrose Metabolism (map00500), the responses of the transcriptome and the metabolome to P deficiency were consistent with one another. No significant changes in the proteome were detected in response to P deficiency. Discussion and conclusion: Collectively, our multi-omic and multi-tissue approach enabled the identification of important metabolic and regulatory pathways regulated across tissues at the molecular level that will be important avenues to further evaluate for P efficiency. These included stress-mediating systems associated with reactive oxygen species maintenance, lipid remodeling within tissues, and systems involved in P scavenging from the rhizosphere.

A compendium of multi-omics data illuminating host responses to lethal human virus infections.

Human infections caused by viral pathogens trigger a complex gamut of host responses that limit disease, resolve infection, generate immunity, and contribute to severe disease or death. Here, we present experimental methods and multi-omics data capture approaches representing the global host response to infection generated from 45 individual experiments involving human viruses from the Orthomyxoviridae, Filoviridae, Flaviviridae, and Coronaviridae families. Analogous experimental designs were implemented across human or mouse host model systems, longitudinal samples were collected over defined time courses, and global multi-omics data (transcriptomics, proteomics, metabolomics, and lipidomics) were acquired by microarray, RNA sequencing, or mass spectrometry analyses. For comparison, we have included transcriptomics datasets from cells treated with type I and type II human interferon. Raw multi-omics data and metadata were deposited in public repositories, and we provide a central location linking the raw data with experimental metadata and ready-to-use, quality-controlled, statistically processed multi-omics datasets not previously available in any public repository. This compendium of infection-induced host response data for reuse will be useful for those endeavouring to understand viral disease pathophysiology and network biology.

Environment-specific virocell metabolic reprogramming.

Viruses impact microbial systems through killing hosts, horizontal gene transfer, and altering cellular metabolism, consequently impacting nutrient cycles. A virus-infected cell, a "virocell", is distinct from its uninfected sister cell as the virus commandeers cellular machinery to produce viruses rather than replicate cells. Problematically, virocell responses to the nutrient-limited conditions that abound in nature are poorly understood. Here we used a systems biology approach to investigate virocell metabolic reprogramming under nutrient limitation. Using transcriptomics, proteomics, lipidomics, and endo- and exo-metabolomics, we assessed how low phosphate (low-P) conditions impacted virocells of a marine Pseudoalteromonas host when independently infected by two unrelated phages (HP1 and HS2). With the combined stresses of infection and nutrient limitation, a set of nested responses were observed. First, low-P imposed common cellular responses on all cells (virocells and uninfected cells), including activating the canonical P-stress response, and decreasing transcription, translation, and extracellular organic matter consumption. Second, low-P imposed infection-specific responses (for both virocells), including enhancing nitrogen assimilation and fatty acid degradation, and decreasing extracellular lipid relative abundance. Third, low-P suggested virocell-specific strategies. Specifically, HS2-virocells regulated gene expression by increasing transcription and ribosomal protein production, whereas HP1-virocells accumulated host proteins, decreased extracellular peptide relative abundance, and invested in broader energy and resource acquisition. These results suggest that although environmental conditions shape metabolism in common ways regardless of infection, virocell-specific strategies exist to support viral replication during nutrient limitation, and a framework now exists for identifying metabolic strategies of nutrient-limited virocells in nature.

Recent advances in the application of magnetic materials for the management of perfluoroalkyl substances in aqueous phases.

Perfluoroalkyl substances (PFASs) are a class of artificially synthesised organic compounds extensively used in both industrial and consumer products owing to their unique characteristics. However, their persistence in the environment and potential risk to health have raised serious global concerns. Therefore, developing effective techniques to identify, eliminate, and degrade these pollutants in water are crucial. Owing to their high surface area, magnetic responsiveness, redox sensitivity, and ease of separation, magnetic materials have been considered for the treatment of PFASs from water in recent years. This review provides a comprehensive overview of the recent use of magnetic materials for the detection, removal, and degradation of PFASs in aqueous solutions. First, the use of magnetic materials for sensitive and precise detection of PFASs is addressed. Second, the adsorption of PFASs using magnetic materials is discussed. Several magnetic materials, including iron oxides, ferrites, and magnetic carbon composites, have been explored as efficient adsorbents for PFASs removal from water. Surface modification, functionalization, and composite fabrication have been employed to improve the adsorption effectiveness and selectivity of magnetic materials for PFASs. The final section of this review focuses on the advanced oxidation for PFASs using magnetic materials. This review suggests that magnetic materials have demonstrated considerable potential for use in various environmental remediation applications, as well as in the treatment of PFASs-contaminated water.

Utilizing sludge-based activated carbon for targeted leachate mitigation in wastewater treatment.

Activated carbon (AC) based adsorbents derived from waste sludge were utilized to remediate mixed contaminants in wastewater as an integrated waste-to-resource approach promoting a paradigm shift in management of refuse sludge and wastewater. This review specifically focuses on the remediation of constituents of landfill leachate by sludge-based activated carbon (SBAC). The adsorption effectiveness of SBAC for the exclusion of leachate characters including heavy metals, phenols, dyes, phosphates, and phosphorus were explored with regard to modifiers such as pH, temperature, properties of the adsorbent including functional groups, initial doses of absorbent and adsorbate, and duration of exposure to note the impact of each parameter on the efficiency of adsorption of the sludge adsorbent. Through the works of various researchers, it was noted that the properties of the adsorbent, pH and temperature impact the working of SBACs. The pH of the adsorbent by influencing the functional groups. Temperature was expected to have a paramount effect on the adsorption efficiency of the SBACs. The importance of the regeneration and recycling of the adsorbents as well as their leachability is highlighted. Sludge based activated carbon is recommended as a timely, resource-efficient, and sustainable approach for the remediation of wastewater.

Dynamic nitrogen fixation in an aerobic endophyte of Populus.

Biological nitrogen fixation by microbial diazotrophs can contribute significantly to nitrogen availability in non-nodulating plant species. In this study of molecular mechanisms and gene expression relating to biological nitrogen fixation, the aerobic nitrogen-fixing endophyte Burkholderia vietnamiensis, strain WPB, isolated from Populus trichocarpa served as a model for endophyte-poplar interactions. Nitrogen-fixing activity was observed to be dynamic on nitrogen-free medium with a subset of colonies growing to form robust, raised globular like structures. Secondary ion mass spectrometry (NanoSIMS) confirmed that N-fixation was uneven within the population. A fluorescent transcriptional reporter (GFP) revealed that the nitrogenase subunit nifH is not uniformly expressed across genetically identical colonies of WPB and that only ~11% of the population was actively expressing the nifH gene. Higher nifH gene expression was observed in clustered cells through monitoring individual bacterial cells using single-molecule fluorescence in situ hybridization. Through 15N2 enrichment, we identified key nitrogenous metabolites and proteins synthesized by WPB and employed targeted metabolomics in active and inactive populations. We cocultivated WPB Pnif-GFP with poplar within a RhizoChip, a synthetic soil habitat, which enabled direct imaging of microbial nifH expression within root epidermal cells. We observed that nifH expression is localized to the root elongation zone where the strain forms a unique physical interaction with the root cells. This work employed comprehensive experimentation to identify novel mechanisms regulating both biological nitrogen fixation and beneficial plant-endophyte interactions.

Characteristics of biological manganese oxides produced by manganese-oxidizing bacteria H38 and its removal mechanism of oxytetracycline.

Oxytetracycline (OTC) is widely used in clinical medicine and animal husbandry. Residual OTC can affect the normal life activities of microorganisms, animals, and plants and affect human health. Microbial remediation has become a research hotspot in the environmental field. Manganese oxidizing bacteria (MnOB) exist in nature, and the biological manganese oxides (BMO) produced by them have the characteristics of high efficiency, low cost, and environmental friendliness. However, the effect and mechanism of BMO in removing OTC are still unclear. In this study, Bacillus thuringiensis strain H38 of MnOB was obtained, and the conditions for its BMO production were optimized. The optimal conditions were determined as follows: optimal temperature = 35 °C, optimal pH = 7.5, optimal Mn(Ⅱ) initial concentration = 10 mmol/L. The results show that BMO are irregular or massive, mainly containing MnCO3, Mn2O3, and MnO2, with rich functional groups and chemical bonds. They have the characteristics of small particle size and large specific surface area. OTC (2.5 mg/L) was removed when the BMO dosage was 75 µmol/L and the solution pH was 5.0. The removal ratio was close to 100 % after 12 h of culture at 35 °C and 150 r/min. BMO can adsorb and catalyze the oxidation of OTC and can produce ·O2-, ·OH, 1O2, and Mn(Ⅲ) intermediate. Fifteen products and degradation pathways were identified, and the toxicity of most intermediates is reduced compared to OTC. The removal mechanism was preliminarily clarified. The results of this study are convenient for the practical application of BMO in OTC pollution in water and for solving the harm caused by antibiotic pollution.

Rhizosphere bacteria G-H27 significantly promoted the degradation of chlorpyrifos and fosthiazate.

Microbial remediation of polluted environments is the most promising and significant research direction in the field of bioremediation. In this study, chlorpyrifos and fosthiazate were selected as representative organophosphorus pesticides, wheat was the tested plant, and fluorescently labeled degrading Bacillus cereus G-H27 were the film-forming bacteria. Exogenous strengthening technology was used to establish degrading bacterial biofilms on the root surface of wheat. The influence of root surface-degrading bacterial biofilms on the enrichment of chlorpyrifos and fosthiazate in wheat was comprehensively evaluated. First, the fluorescently-labeled degrading bacteria G-H27 was constructed, and its film-forming ability was investigated. Second, the growth- promoting characteristics and degradation ability of the bacteria G-H27 were investigated. Finally, the degradation effect of the root surface-degrading bacterial biofilm on chlorpyrifos and fosthiazate was determined. The above research provides an important material basis and method for the bioremediation of pesticide-contaminated soil.

Oligosaccharide production and signaling correlate with delayed flowering in an Arabidopsis genotype grown and selected in high [CO2].

Since industrialization began, atmospheric CO2 ([CO2]) has increased from 270 to 415 ppm and is projected to reach 800-1000 ppm this century. Some Arabidopsis thaliana (Arabidopsis) genotypes delayed flowering in elevated [CO2] relative to current [CO2], while others showed no change or accelerations. To predict genotype-specific flowering behaviors, we must understand the mechanisms driving flowering response to rising [CO2]. [CO2] changes alter photosynthesis and carbohydrates in plants. Plants sense carbohydrate levels, and exogenous carbohydrate application influences flowering time and flowering transcript levels. We asked how organismal changes in carbohydrates and transcription correlate with changes in flowering time under elevated [CO2]. We used a genotype (SG) of Arabidopsis that was selected for high fitness at elevated [CO2] (700 ppm). SG delays flowering under elevated [CO2] (700 ppm) relative to current [CO2] (400 ppm). We compared SG to a closely related control genotype (CG) that shows no [CO2]-induced flowering change. We compared metabolomic and transcriptomic profiles in these genotypes at current and elevated [CO2] to assess correlations with flowering in these conditions. While both genotypes altered carbohydrates in response to elevated [CO2], SG had higher levels of sucrose than CG and showed a stronger increase in glucose and fructose in elevated [CO2]. Both genotypes demonstrated transcriptional changes, with CG increasing genes related to fructose 1,6-bisphosphate breakdown, amino acid synthesis, and secondary metabolites; and SG decreasing genes related to starch and sugar metabolism, but increasing genes involved in oligosaccharide production and sugar modifications. Genes associated with flowering regulation within the photoperiod, vernalization, and meristem identity pathways were altered in these genotypes. Elevated [CO2] may alter carbohydrates to influence transcription in both genotypes and delayed flowering in SG. Changes in the oligosaccharide pool may contribute to delayed flowering in SG. This work extends the literature exploring genotypic-specific flowering responses to elevated [CO2].

Metabolomic, photoprotective, and photosynthetic acclimatory responses to post-flowering drought in sorghum.

Climate change is globally affecting rainfall patterns, necessitating the improvement of drought tolerance in crops. Sorghum bicolor is a relatively drought-tolerant cereal. Functional stay-green sorghum genotypes can maintain green leaf area and efficient grain filling during terminal post-flowering water deprivation, a period of ~10 weeks. To obtain molecular insights into these characteristics, two drought-tolerant genotypes, BTx642 and RTx430, were grown in replicated control and terminal post-flowering drought field plots in California's Central Valley. Photosynthetic, photoprotective, and water dynamics traits were quantified and correlated with metabolomic data collected from leaves, stems, and roots at multiple timepoints during control and drought conditions. Physiological and metabolomic data were then compared to longitudinal RNA sequencing data collected from these two genotypes. The unique metabolic and transcriptomic response to post-flowering drought in sorghum supports a role for the metabolite galactinol in controlling photosynthetic activity through regulating stomatal closure in post-flowering drought. Additionally, in the functional stay-green genotype BTx642, photoprotective responses were specifically induced in post-flowering drought, supporting a role for photoprotection in the molecular response associated with the functional stay-green trait. From these insights, new pathways are identified that can be targeted to maximize yields under growth conditions with limited water.

Tripogon loliiformis tolerates rapid desiccation after metabolic and transcriptional priming during initial drying.

Crop plants and undomesticated resilient species employ different strategies to regulate their energy resources and growth. Most crop species are sensitive to stress and prioritise rapid growth to maximise yield or biomass production. In contrast, resilient plants grow slowly, are small, and allocate their resources for survival in challenging environments. One small group of plants, termed resurrection plants, survive desiccation of their vegetative tissue and regain full metabolic activity upon watering. However, the precise molecular mechanisms underlying this extreme tolerance remain unknown. In this study, we employed a transcriptomics and metabolomics approach, to investigate the mechanisms of desiccation tolerance in Tripogon loliiformis, a modified desiccation-tolerant plant, that survives gradual but not rapid drying. We show that T. loliiformis can survive rapid desiccation if it is gradually dried to 60% relative water content (RWC). Furthermore, the gene expression data showed that T. loliiformis is genetically predisposed for desiccation in the hydrated state, as evidenced by the accumulation of MYB, NAC, bZIP, WRKY transcription factors along with the phytohormones, abscisic acid, salicylic acid, amino acids (e.g., proline) and TCA cycle sugars during initial drying. Through network analysis of co-expressed genes, we observed differential responses to desiccation between T. loliiformis shoots and roots. Dehydrating shoots displayed global transcriptional changes across broad functional categories, although no enrichment was observed during drying. In contrast, dehydrating roots showed distinct network changes with the most significant differences occurring at 40% RWC. The cumulative effects of the early stress responses may indicate the minimum requirements of desiccation tolerance and enable T. loliiformis to survive rapid drying. These findings potentially hold promise for identifying biotechnological solutions aimed at developing drought-tolerant crops without growth and yield penalties.

Elucidating regulatory processes of intense physical activity by multi-omics analysis.

BACKGROUND: Physiological and biochemical processes across tissues of the body are regulated in response to the high demands of intense physical activity in several occupations, such as firefighting, law enforcement, military, and sports. A better understanding of such processes can ultimately help improve human performance and prevent illnesses in the work environment. METHODS: To study regulatory processes in intense physical activity simulating real-life conditions, we performed a multi-omics analysis of three biofluids (blood plasma, urine, and saliva) collected from 11 wildland firefighters before and after a 45 min, intense exercise regimen. Omics profiles post- versus pre-exercise were compared by Student's t-test followed by pathway analysis and comparison between the different omics modalities. RESULTS: Our multi-omics analysis identified and quantified 3835 proteins, 730 lipids and 182 metabolites combining the 3 different types of samples. The blood plasma analysis revealed signatures of tissue damage and acute repair response accompanied by enhanced carbon metabolism to meet energy demands. The urine analysis showed a strong, concomitant regulation of 6 out of 8 identified proteins from the renin-angiotensin system supporting increased excretion of catabolites, reabsorption of nutrients and maintenance of fluid balance. In saliva, we observed a decrease in 3 pro-inflammatory cytokines and an increase in 8 antimicrobial peptides. A systematic literature review identified 6 papers that support an altered susceptibility to respiratory infection. CONCLUSION: This study shows simultaneous regulatory signatures in biofluids indicative of homeostatic maintenance during intense physical activity with possible effects on increased infection susceptibility, suggesting that caution against respiratory diseases could benefit workers on highly physical demanding jobs.

Identification of a specific exporter that enables high production of aconitic acid in Aspergillus pseudoterreus.

Aconitic acid is an unsaturated tricarboxylic acid that is attractive for its potential use in manufacturing biodegradable and biocompatible polymers, plasticizers, and surfactants. Previously Aspergillus pseudoterreus was engineered as a platform to produce aconitic acid by deleting the cadA (cis-aconitic acid decarboxylase) gene in the itaconic acid biosynthetic pathway. In this study, the aconitic acid transporter gene (aexA) was identified using comparative global discovery proteomics analysis between the wild-type and cadA deletion strains. The protein AexA belongs to the Major Facilitator Superfamily (MFS). Deletion of aexA almost abolished aconitic acid secretion, while its overexpression led to a significant increase in aconitic acid production. Transportation of aconitic acid across the plasma membrane is a key limiting step in its production. In vitro, proteoliposome transport assay further validated AexA's function and substrate specificity. This research provides new approaches to efficiently pinpoint and characterize exporters of fungal organic acids and accelerate metabolic engineering to improve secretion capability and lower the cost of bioproduction.

Postoperative change in the joint-line convergence angle is associated with inaccurate correction in open-wedge high tibial osteotomy.

OBJECTIVE: Accurate correction is a prerequisite for the favorable outcomes of open-wedge high tibial osteotomy (OWHTO). However, previous studies have reported disappointing results regarding correction accuracy despite the use of intra-operative navigation, which implies that a certain factor other than bony components is involved in the inaccurate correction (mainly overcorrection). The joint-line convergence angle (JLCA) can represent soft tissue effects in OWHTO. This study tried to determine whether the postoperative change in the JLCA (∆JLCA) led to inaccurate correction. METHODS: Medical records of 78 OWHTO patients from 2005 to 2021 were retrospectively reviewed. The hip-knee-ankle angle (HKA) was measured with a positive value indicating varus alignment. Inaccurate correction was defined as postoperative HKA < - 3°. The JLCA was measured before and 6 months after surgery on long-standing hip-to-ankle radiographs, and ∆JLCA was defined as the difference between the preoperative and 6-month postoperative JLCAs. ∆JLCA was compared between the accurate correction group and the inaccurate correction group, and a receiver operating characteristic (ROC) curve was used to obtain the cutoff ∆JLCA at which the sensitivity and the specificity for inaccurate correction were maximized. Clinical outcomes were also compared between the groups using the knee injury and osteoarthritis outcome score (KOOS) at final follow-up (60.9 ± 53.3 months postoperatively). RESULTS: Of the 78 patients, inaccurate correction was noted in 10 patients. The overall preoperative and postoperative HKAs were 7.0 ± 3.1° and - 0.4 ± 1.5°, respectively. The accurate correction group and the inaccurate correction group had a difference in ∆JLCA (p = 0.010). However, no significant difference was found in the preoperative HKA (p = 0.529). An ROC curve showed that the cutoff ∆JLCA was 1.9°. In the patients having ∆JLCA ≥ 1.9°, the mean JLCA was 4.9 ± 1.6° preoperatively and 1.7 ± 1.2° postoperatively. In the other patients having ∆JLCA < 1.9°, the mean preoperative and postoperative JLCA were 2.5 ± 1.8° and 2.3 ± 1.8°, respectively. The difference in the preoperative JLCA was significant (p < 0.001). The postoperative KOOS subscales did not differ according to correction accuracy. CONCLUSION: Inaccurate correction in OWHTO, specifically valgus overcorrection, is associated with large ∆JLCA which represents the postoperative change of soft tissue effects. Overcorrection should be checked in cases of large preoperative JLCAs.

Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites.

Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome-focused studies and may result in confounding microbial signals and host-filtering across different root microbiome compartments. Using a 26-year-old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root-microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.

Single-cell isotope tracing reveals functional guilds of bacteria associated with the diatom Phaeodactylum tricornutum.

Bacterial remineralization of algal organic matter fuels algal growth but is rarely quantified. Consequently, we cannot currently predict whether some bacterial taxa may provide more remineralized nutrients to algae than others. Here, we quantified bacterial incorporation of algal-derived complex dissolved organic carbon and nitrogen and algal incorporation of remineralized carbon and nitrogen in fifteen bacterial co-cultures growing with the diatom Phaeodactylum tricornutum at the single-cell level using isotope tracing and nanoSIMS. We found unexpected strain-to-strain and cell-to-cell variability in net carbon and nitrogen incorporation, including non-ubiquitous complex organic nitrogen utilization and remineralization. We used these data to identify three distinct functional guilds of metabolic interactions, which we termed macromolecule remineralizers, macromolecule users, and small-molecule users, the latter exhibiting efficient growth under low carbon availability. The functional guilds were not linked to phylogeny and could not be elucidated strictly from metabolic capacity as predicted by comparative genomics, highlighting the need for direct activity-based measurements in ecological studies of microbial metabolic interactions.

Effects of magnesium-modified biochar on antibiotic resistance genes and microbial communities in chicken manure composting.

Abatement of antibiotic resistance genes (ARGs) in livestock manure by composting has attracted attention. This study investigated the effect of adding magnesium-modified biochar (MBC) on ARGs and microbial communities in chicken manure composting. Twelve genes for tetracyclines, sulfonamides, and macrolides, and mobile genetic elements were measured in the compost pile. The results showed that after 45 days of the composting, the treatment groups of MBC had longer high temperature periods, significantly higher germination indices (GI) and lower phytotoxicity. There were four major dominant phyla (Firmicutes, Actinobacteriota, Proteobacteria, and Bacteroidota) in the compost. The abundance of Firmicutes decreased significantly during the compost cooling period; tetracycline resistance genes demonstrated an extremely significant positive correlation with Firmicutes, showing a trend of the same increase and decrease with composting time; tetT, tetO, tetM, tetW, ermB, and intI2 were reduced in the MBC group; the total abundance of resistance genes in the 2% MBC addition group was 0.67 times that of the control; Proteobacteria and Chloroflexi were also significantly lower than the other treatment groups. Most ARGs were significantly associated with mobile genetic elements (MGEs); MBC can reduce the spread and diffusion of ARGs by reducing the abundance of MGEs and inhibiting horizontal gene transfer (HGT).

Engineering transcriptional regulation of pentose metabolism in Rhodosporidium toruloides for improved conversion of xylose to bioproducts.

Efficient conversion of pentose sugars remains a significant barrier to the replacement of petroleum-derived chemicals with plant biomass-derived bioproducts. While the oleaginous yeast Rhodosporidium toruloides (also known as Rhodotorula toruloides) has a relatively robust native metabolism of pentose sugars compared to other wild yeasts, faster assimilation of those sugars will be required for industrial utilization of pentoses. To increase the rate of pentose assimilation in R. toruloides, we leveraged previously reported high-throughput fitness data to identify potential regulators of pentose catabolism. Two genes were selected for further investigation, a putative transcription factor (RTO4_12978, Pnt1) and a homolog of a glucose transceptor involved in carbon catabolite repression (RTO4_11990). Overexpression of Pnt1 increased the specific growth rate approximately twofold early in cultures on xylose and increased the maximum specific growth by 18% while decreasing accumulation of arabitol and xylitol in fast-growing cultures. Improved growth dynamics on xylose translated to a 120% increase in the overall rate of xylose conversion to fatty alcohols in batch culture. Proteomic analysis confirmed that Pnt1 is a major regulator of pentose catabolism in R. toruloides. Deletion of RTO4_11990 increased the growth rate on xylose, but did not relieve carbon catabolite repression in the presence of glucose. Carbon catabolite repression signaling networks remain poorly characterized in R. toruloides and likely comprise a different set of proteins than those mainly characterized in ascomycete fungi.

Characterization of Bioactivity of Selective Molecules in Fruit Wines by FTIR and NMR Spectroscopies, Fluorescence and Docking Calculations.

Fourier transform infrared (FTIR) and proton nuclear magnetic resonance (1H NMR) spectroscopies were applied to characterize and compare the chemical shifts in the polyphenols' regions of some fruit wines. The obtained results showed that FTIR spectra (1800-900 cm-1) and 1H NMR (δ 6.5-9.3 ppm) of different fruit wines can be used as main indices of the year of vintage and quality of fruit wines. In addition to the classical determination of antioxidant profiles and bioactive substances in wines, fluorometric measurements were used to determine the interactions of wine substances with the main human serum proteins. The results showed relatively high binding properties of wines with the highest one for pomegranate, followed by kiwifruit and persimmon wines. The interactions of vitamin C, catechin and gallic acid with human serum albumin (HSA) were also examined by docking studies. The docking calculations showed that gallic acid has a stronger binding affinity compared to catechin and vitamin C. The stronger binding affinity of gallic acid may be due to three hydrogen bonds and pi-pi interactions. The fluorescence and docking studies proved that only the bioactive compounds of wines and not the amount of alcohol have high binding properties to human serum proteins. The emphasis in this report was made on the utility of FTIR, NMR and fluorescence of wines as a mean of wine authentication and its fingerprint. The findings, based on polyphenols from fruits and fruit wines, their bioactivity and health properties, offer valuable insights for future endeavours focused on designing healthy food products.

An Unusual Case of Erdheim Chester Disease (ECD) with Knee Pain: A Case Report.

Background: Erdheim Chester disease (ECD) is a rare, non-Langerhans cell histiocytosis of unknown etiology that occurs in multiple organs. The clinical characteristics of ECD are unknown, making it difficult to diagnose. Case presentation: A 61-year-old woman presented with left knee pain and contracture. She had recent medical problems such as recurrent urinary tract infection, pericardial effusion, and pleural effusion. Simple radiography and magnetic resonance imaging of the knee revealed an osteosclerotic lesion. Under suspicion of malignancy, other radiologic modalities were performed, but there were no significant results showing malignancy. A bone biopsy of the knee lesion led to a final diagnosis of ECD. The patient was treated with systemic steroids and was ultimately tried on PEG-interferon. Conclusion: This report describes an unusual presentation of ECD involving the skeletal system and multiple extraskeletal organs. Owing to its non-specific nature, ECD was notably difficult to diagnose. Therefore, if a patient has knee pain and other multiorgan presentations without malignancy, clinicians should suspect ECD.