Miracle-dz/UniFAR-FTUs huggingface dataset:
Investigating the role of root exudates in recruiting Streptomyces bacteria to the Arabidopsis thaliana root microbiome

Streptomyces species are saprophytic soil bacteria that produce a diverse array of specialised metabolites, including half of all known antibiotics. They are also rhizobacteria and plant endophytes that can promote plant growth and protect against disease. Several studies have shown that streptomycetes are enriched in the rhizosphere and endosphere of the model plant Arabidopsis thaliana. Here, we set out to test the hypothesis that they are attracted to plant roots by root exudates, and specifically by the plant phytohormone salicylate, which they might use as a nutrient source. We confirmed a previously published report that salicylate over-producing cpr5 plants are colonised more readily by streptomycetes but found that salicylate-deficient sid2-2 and pad4 plants had the same levels of root colonisation by Streptomyces bacteria as the wild-type plants. We then tested eight genome sequenced Streptomyces endophyte strains in vitro and found that none were attracted to or could grow on salicylate as a sole carbon source. We next used 13CO2 DNA stable isotope probing to test whether Streptomyces species can feed off a wider range of plant metabolites but found that Streptomyces bacteria were outcompeted by faster growing proteobacteria and did not incorporate photosynthetically fixed carbon into their DNA. We conclude that, given their saprotrophic nature and under conditions of high competition, streptomycetes most likely feed on more complex organic material shed by growing plant roots. Understanding the factors that impact the competitiveness of strains in the plant root microbiome could have consequences for the effective application of biocontrol strains. Importance Streptomyces bacteria are ubiquitous in soil but their role as rhizobacteria is less well studied. Our recent work demonstrated that streptomycetes isolated from A. thaliana roots can promote growth and protect against disease across plant species and that plant growth hormones can modulate the production of bioactive specialised metabolites by these strains. Here we used 13CO2 DNA stable isotope probing to identify which bacteria feed on plant metabolites in the A. thaliana rhizosphere and, for the first time, in the endosphere. We found that Streptomyces species are outcompeted for these metabolites by faster growing proteobacteria and instead likely subsist on more complex organic material such as cellulose derived from plant cell material that is shed from the roots. This work thus reveals the “winners and losers” in the battle between soil bacteria for plant metabolites and could inform the development of methods to apply streptomycetes as plant growth-promoting agents.
Recent Advance of the Arctic Treeline Along the Eastern Coast of Hudson Bay

1 The very cold, wind-exposed coastal environment along the eastern Hudson Bay coast (northern Quebec, Canada) has resulted in a treeline which runs parallel to the coast (i.e. north-south). We have measured changes in the longitudinal position of the black spruce (Picea mariana (Mill.) B.S.P.) treeline during the last centuries, using tree ring analysis of spruce stem development. 2 Treeline trees () 2.5 m high) were sampled along transects in valley sites of four different rivers draining towards Hudson Bay, from the present treeline to the forest limit. The year of initiation of supranival stem growth (i.e. when stems first developed above the snowpack) was determined for trees, whorled growth forms and dead shrubs. Supranival tree stems developed synchronously in the valleys, from the late 1800s to the mid 1900s, in the area presently occupied by treeline trees, indicating that only krummholz (shrubby spruces) were present at these sites during the Little Ice Age. 3 A corresponding displacement of the treeline of about 12 km towards Hudson Bay has occurred in the area since the late 1 800s, most likely as a result of recent warming. The recent treeline shift also resulted from the development of vertical tree stems from pre-established krummholz, suggesting that stem growth was a direct response to favourable summer growth conditions and reduced wind-driven snow abrasion and supercold wind-chill. The absence of treeline trees originating from seeds indicates that the recent warming has not been of sufficient magnitude or duration to promote sexual reproduction.
Early Outcomes in an Emerging Facial Nerve Center: The Oregon Health and Science University (OHSU) Experience

Objectives: Nerve transfer (NT) and free gracilis muscle transfer (FGMT) are procedures for reanimation of the paralyzed face. Assessing the surgical outcomes of these procedures is imperative when evaluating the effectiveness of these interventions, especially when establishing a new center focused on the treatment of patients with facial paralysis. We desired to discuss the factors to consider when implementing a facial nerve center and the means by which the specialist can assess and analyze outcomes. Methods: Patients with facial palsy secondary to multiple etiologies, including cerebellopontine angle tumors, head and neck carcinoma, and trauma, who underwent NT or FGMT between 2014 and 2019 were included. Primary outcomes were facial symmetry and smile excursion, calculated using FACE-gram and Emotrics software. Subjective quality of life outcomes, including the Facial Clinimetric Evaluation (FaCE) Scale and Synkinesis Assessment Questionnaire (SAQ), were also assessed. Results: 14/22 NT and 6/6 FGMT patients met inclusion criteria having both pre-and postoperative photo documentation. NT increased oral commissure excursion from 0.4 mm (SD 5.3) to 2.9 mm (SD 6.8) (P = 0.05), and improved symmetry of excursion (P < 0.001) and angle (P < 0.001). FGMT increased oral commissure excursion from −1.4 mm (SD 3.9) to 2.1 mm (SD 3.7), (P = 0.02), and improved symmetry of excursion (P < 0.001). FaCE scores improved in NT patients postoperatively (P < 0.001). Conclusions: Measuring outcomes, critical analyses, and a multidisciplinary approach are necessary components when building a facial nerve center. At our emerging facial nerve center, we found NT and FGMT procedures improved smile excursion and symmetry, and improved QOL following NT in patients with facial palsy secondary to multiple etiologies.
Potent Small-Molecule Inhibitors Targeting Acetylated Microtubules as Anticancer Agents Against Triple-Negative Breast Cancer

Microtubules are one of the major targets for anticancer drugs because of their role in cell proliferation and migration. However, as anticancer drugs targeting microtubules have side effects, including the death of normal cells, it is necessary to develop anticancer agents that can target microtubules by specifically acting on cancer cells only. In this study, we identified chemicals that can act as anticancer agents by specifically binding to acetylated microtubules, which are predominant in triple-negative breast cancer (TNBC). The chemical compounds disrupted acetylated microtubule lattices by interfering with microtubule access to alpha-tubulin acetyltransferase 1 (αTAT1), a major acetyltransferase of microtubules, resulting in the increased apoptotic cell death of MDA-MB-231 cells (a TNBC cell line) compared with other cells, such as MCF-10A and MCF-7, which lack microtubule acetylation. Moreover, mouse xenograft experiments showed that treatment with the chemical compounds markedly reduced tumor growth progression. Taken together, the newly identified chemical compounds can be selective for acetylated microtubules and act as potential therapeutic agents against microtubule acetylation enrichment in TNBC.
The Water Flux Dynamic in a Hybrid Forward Osmosis-Membrane Distillation for Produced Water Treatment

Standalone membrane distillation (MD) and forward osmosis (FO) have been considered as promising technologies for produced water treatment. However, standalone MD is still vulnerable to membrane-wetting and scaling problems, while the standalone FO is energy-intensive, since it requires the recovery of the draw solution (DS). Thus, the idea of coupling FO and MD is proposed as a promising combination in which the MD facilitate DS recovery for FO—and FO acts as pretreatment to enhance fouling and wetting-resistance of the MD. This study was therefore conducted to investigate the effect of DS temperature on the dynamic of water flux of a hybrid FO–MD. First, the effect of the DS temperature on the standalone FO and MD was evaluated. Later, the flux dynamics of both units were evaluated when the FO and DS recovery (via MD) was run simultaneously. Results show that an increase in the temperature difference (from 20 to 60 °C) resulted in an increase of the FO and MD fluxes from 11.17 ± 3.85 to 30.17 ± 5.51 L m−2 h−1, and from 0.5 ± 0.75 to 16.08 L m−2 h−1, respectively. For the hybrid FO–MD, either MD or FO could act as the limiting process that dictates the equilibrium flux. Both the concentration and the temperature of DS affected the flux dynamic. When the FO flux was higher than MD flux, DS was diluted, and its temperature decreased; both then lowered the FO flux until reaching an equilibrium (equal FO and MD flux). When FO flux was lower than MD flux, the DS was concentrated which increased the FO flux until reaching the equilibrium. The overall results suggest the importance of temperature and concentration of solutes in the DS in affecting the water flux dynamic hybrid process.
Characterization of Hybrid Oil Palm Empty Fruit Bunch/Woven Kenaf Fabric-Reinforced Epoxy Composites

In this research, the physical, mechanical and morphological properties of oil palm empty fruit bunch (EFB) mat/woven kenaf fabric-reinforced epoxy composites have been investigated. The oil palm EFB/woven kenaf fabrics were varied, with weight ratios of 50/0 (T1), 35/15 (T2), 25/25 (T3), 15/35 (T4) and 0/50 (T5). The composites were fabricated using a simple hand lay-up technique followed by hot pressing. The result obtained shows that an increase in kenaf fiber content exhibited higher tensile and flexural properties. On the other hand, the opposite trend was observed in the impact strength of hybrid composites, where an increase in kenaf fiber content reduced the impact strength. This can be corroborated with the physical properties analysis, where a higher void content, water absorption and thickness swelling were observed for pure oil palm EFB (T1) composites compared to other samples. The scanning electron microscopy analysis results clearly show the different failure modes of the tensile fractured samples. Statistical analysis was performed using one-way ANOVA and shows significant differences between the obtained results.
Influence of SH2B3, MTHFD1L, GGCX, and ITGB3 Gene Polymorphisms on theVariability on Warfarin Dosage Requirements and Susceptibility to CVD in the Jordanian Population

The purpose of this study was to investigate the effects of the SH2B3, MTHFD1L, GGCX, and ITGB3 gene variants on the efficacy of warfarin treatment and its effects on the risk of cardiovascular disorders in Jordanian patients. The selected genes and their polymorphisms are involved in many Genome-Wide Association Study (GWAS) associated with cardiovascular disease and the variability of warfarin therapy. The current study conducted a genetic association and pharmacogenetics study in (212) Jordanian cardiovascular patients treated with warfarin and (213) healthy controls. DNA extraction and the Mass ARRAY™ system were used to genotype ten selected polymorphisms within four genes (SH2B3, MTHFD1L, GGCX, and ITGB3). This study confirmed a genetic association of MTHFD1L rs6922269 Single Nucleotide Polymorphism (SNP) with warfarin sensitivity during the initial and stabilization phases of treatment. Moreover, this SNP showed significant differences in the initial and maintenance doses of warfarin. This study also found an association between the genetic haplotypes (AGC and GAT) within the SH2B3 gene and responsiveness to warfarin. However, possession of an MTHFD1L rs491552 variant allele was found to affect the outcome measure of the international normalized ratio (INR) during the stabilization phase of warfarin treatment. In contrast, there was no association between all selected SNPs and susceptibility to cardiovascular disorders. This study extends the current understanding of the high variability of the warfarin response, including variability in dose requirements and susceptibility to cardiovascular disease in the Jordanian-Arab population. Other studies on a larger sample and in different ethnic groups could help to better understand the pharmacogenetics of warfarin and its application in personalized medicine.
Characterization of the CAZy Repertoire from the Marine-Derived Fungus Stemphylium lucomagnoense in Relation to Saline Conditions

Even if the ocean represents a large part of Earth’s surface, only a few studies describe marine-derived fungi compared to their terrestrial homologues. In this ecosystem, marine-derived fungi have had to adapt to the salinity and to the plant biomass composition. This articles studies the growth of five marine isolates and the tuning of lignocellulolytic activities under different conditions, including the salinity. A de novo transcriptome sequencing and assembly were used in combination with a proteomic approach to characterize the Carbohydrate Active Enzymes (CAZy) repertoire of one of these strains. Following these approaches, Stemphylium lucomagnoense was selected for its adapted growth on xylan in saline conditions, its high xylanase activity, and its improved laccase activities in seagrass-containing cultures with salt. De novo transcriptome sequencing and assembly indicated the presence of 51 putative lignocellulolytic enzymes. Its secretome composition was studied in detail when the fungus was grown on either a terrestrial or a marine substrate, under saline and non-saline conditions. Proteomic analysis of the four S. lucomagnoense secretomes revealed a minimal suite of extracellular enzymes for plant biomass degradation and highlighted potential enzyme targets to be further studied for their adaptation to salts and for potential biotechnological applications.
Effect of maize-soybean relay cropping shade on nitrogen metabolism of soybean seedlings

The effects of shading on nitrogen metabolism of soybean seedlings were studied under maize-soybean relay cropping and monoculture.Results showed that under relay cropping condition,the plants had higher total nitrogen and relatively lower total carbon with decreased C/N value.The C/N of leaf was lower than that of the stem.At the same time,the NO3-content increased and the activities of nitrate reductase(NR) and glufamine synthetase(GS) in functional leaves increased significantly.The low light of relay cropping condition led to low expression of leaf soluble protein but slightly high synthesis of amino acid in leaf.These effects were significantly different among varieties with various shade tolerance.There were lower C/N,less decrease of soluble protein content,but higher NO3-and amino acid contents in plants of tolerant cultivars Gongxuan 1 and Nandou 12.
Role of Innate Immune Cells in Psoriasis

Psoriasis is a chronic inflammatory skin condition caused by a combination of hereditary and environmental factors. Its development is closely related to the adaptive immune response. T helper 17 cells are major IL-17-producing cells, a function that plays an important role in the pathogenesis of psoriasis. However, recent findings have demonstrated that innate immune cells also contribute to the development of psoriasis. Innate lymphoid cells, γδ T cells, natural killer T cells, and natural killer cells are activated in psoriasis, contributing to disease pathology through IL-17-dependent and -independent mechanisms. The present review provides an overview of recent findings, demonstrating a role for innate immunity in psoriasis.
Sirt6 is required for spermatogenesis in mice

SIRT6, a nuclear protein, has been implicated in a number of essential cellular processes, such as the DNA damage response, metabolic homeostasis, inflammation, tumorigenesis and aging. However, the role of Sirt6 in the regulation of spermatogenesis is yet unknown. In the present study, we successfully generated Sirt6-/- mice on a C57BL6/ICR mixed background and found that some Sirt6-/- mice survived beyond eight weeks. We further revealed that spermatogenesis in Sirt6-/- mice was arrested at the elongated spermatid stage. Sirt6-/- male mice were completely infertile and had an increased number of apoptotic spermatids. To our surprise, deacetylation activities of SIRT6 on H3K9ac, H3K18ac and H3K56c were not required for spermatogenesis. Therefore, our findings establish a novel link between Sirt6 and male fertility, suggesting an essential role of Sirt6 in spermatogenesis.
Carrot Pomace Polysaccharide (CPP) Improves Influenza Vaccine Efficacy in Immunosuppressed Mice via Dendritic Cell Activation

Despite the advancements in vaccination research and practices, influenza viruses remain a global health concern. Inducing a robust immune response by vaccination is especially challenging in the elderly, the immunocompromised, and persons with chronic illnesses. Polysaccharides derived from food may act as a safe and readily accessible means to boost the immune system during vaccination. In this study, we investigated whether crude polysaccharides derived from carrot pomace (CPP) could stimulate innate immune cell function and promote influenza vaccine immunogenicity. In bone marrow-derived dendritic cells (BMDCs), CPP increased the fraction of CD11c+MHCII+ cells and the expression of co-stimulatory molecules CD40 and CD80, indicative of enhanced maturation and activation. Functionally, CPP-treated BMDCs promoted inflammatory cytokine production in splenic lymphocytes. In a mouse model of immunosuppression induced by cyclophosphamide, animals given CPP before and after an influenza vaccine challenge showed increased frequencies of dendritic cells and natural killer cells in the spleen, in addition to the recovery of vaccine-specific antibody titers. Moreover, innate myeloid cells in CPP-fed mice showed evidence of phenotypic modification via markedly enhanced interleukin(IL)-12 and interferon(IFN)-γ production in response to lipopolysaccharide(LPS) stimulation ex vivo. Our findings suggest that the administration of carrot pomace polysaccharides can significantly enhance the efficacy of influenza vaccination.
Stable integration of an optimized inducible promoter system enables spatiotemporal control of gene expression throughout avian development

ABSTRACT Precisely altering gene expression is critical for understanding molecular processes of embryogenesis. Although some tools exist for transgene misexpression in developing chick embryos, we have refined and advanced them by simplifying and optimizing constructs for spatiotemporal control. To maintain expression over the entire course of embryonic development we use an enhanced piggyBac transposon system that efficiently integrates sequences into the host genome. We also incorporate a DNA targeting sequence to direct plasmid translocation into the nucleus and a D4Z4 insulator sequence to prevent epigenetic silencing. We designed these constructs to minimize their size and maximize cellular uptake, and to simplify usage by placing all of the integrating sequences on a single plasmid. Following electroporation of stage HH8.5 embryos, our tetracycline-inducible promoter construct produces robust transgene expression in the presence of doxycycline at any point during embryonic development in ovo or in culture. Moreover, expression levels can be modulated by titrating doxycycline concentrations and spatial control can be achieved using beads or gels. Thus, we have generated a novel, sensitive, tunable, and stable inducible-promoter system for high-resolution gene manipulation in vivo. Summary: We have designed an optimized and integrating inducible-promoter system to control the timing, spatial domains, and levels of gene misexpression throughout avian development.
Electrochemiluminescence Biosensors Using Screen-Printed Electrodes

Electrogenerated chemiluminescence (also called electrochemiluminescence (ECL)) has become a great focus of attention in different fields of analysis, mainly as a consequence of the potential remarkably high sensitivity and wide dynamic range. In the particular case of sensing applications, ECL biosensor unites the benefits of the high selectivity of biological recognition elements and the high sensitivity of ECL analysis methods. Hence, it is a powerful analytical device for sensitive detection of different analytes of interest in medical prognosis and diagnosis, food control and environment. These wide range of applications are increased by the introduction of screen-printed electrodes (SPEs). Disposable SPE-based biosensors cover the need to perform in-situ measurements with portable devices quickly and accurately. In this review, we sum up the latest biosensing applications and current progress on ECL bioanalysis combined with disposable SPEs in the field of bio affinity ECL sensors including immunosensors, DNA analysis and catalytic ECL sensors. Furthermore, the integration of nanomaterials with particular physical and chemical properties in the ECL biosensing systems has improved tremendously their sensitivity and overall performance, being one of the most appropriates research fields for the development of highly sensitive ECL biosensor devices.
Morfo-anatomia foliar comparativa de espécies conhecidas como espinheira-santa: Maytenus ilicifolia (Celastraceae), Sorocea bonplandii (Moraceae) e Zollernia ilicifolia (Leguminosae)

Maytenus ilieifolia (Celastraceae) e a verdadeira espinheira-santa. Entretanto, Sorocea bonplandii (Moraceae) e Zollernia ilicifolia (Leguminosae) sao frequentemente confundidas, devido a semelhanca morfologica das folhas. Foi usado material fresco e fixado em glutaraldeido 2,5%, em tampao fosfato de sodio 0,1M, pH 7,2. Para microscopia eletronica de varredura as amostras foram desidratadas e depois imersas em HMDS. A folha de M. ilieifolia e oblonga estreita, de S.bonplandii e obovada oblongolanceolada e a de Z. ilicifolia e eliptica estreita. As folhas das tres especies sao dorsiventrais e hipoestomaticas. So Z. ilicifolia apresenta estrato subepiderrnico ac1orofilado, na face adaxial. Os estomatos sao do tipo paracitico em M. ilicifolia e Z. ilicifolia e do tipo anomocitico emS. bonplandii. Tricomas ocorrem em Z.ilicifolia e em S.bonplandii, nao tendo sido encontrados em M. ilicifolia. Apenas S. bonplandii apresenta vasos laticiferos. A forma e disposicao dos tecidos na nervura central, no bordo e no peciolo apresentam diferencas nas tres especies. Os resultados revelaram que algumas caracteristicas morfoanatomicas da folha podem ser utilizadas na distincao entre as tres especies.
In Search of Evidence for Using Noninvasive Ventilation for Severe Acute Asthma

* Abbreviations: IMV — : invasive mechanical ventilation NIV — : noninvasive ventilation Noninvasive ventilation (NIV) is appealing for the treatment of severe asthma because it likely avoids the potential airway and lung trauma of intubation and invasive mechanical ventilation (IMV). In this issue of Pediatrics , Smith et al1 illustrate the compelling appeal of NIV in clinical use, showing that centers with high use of NIV in 2014 doubled their use of NIV in the next 4 years and that NIV is more common as a mode of respiratory support than IMV. … Address correspondence to Michael D. Johnson, MD, MS, Primary Children’s Hospital, 100 N Mario Capecchi Dr, Salt Lake City, UT 84108. E-mail: mike.johnson{at}hsc.utah. edu