Miracle-dz/UniFAR-FTUs huggingface dataset:
Legacy Metal Contaminants and Excess Nutrients in Low Flow Estuarine Embayments Alter Composition and Function of Benthic Bacterial Communities

Coastal systems such as estuaries are threatened by multiple anthropogenic stressors worldwide. However, how these stressors and estuarine hydrology shape benthic bacterial communities and their functions remains poorly known. Here, we surveyed sediment bacterial communities in poorly flushed embayments and well flushed channels in Sydney Harbour, Australia, using 16S rRNA gene sequencing. Sediment samples were collected monthly during the Austral summer-autumn 2014 at increasing distance from a large storm drain in each channel and embayment. Bacterial communities differed significantly between sites that varied in proximity to storm drains, with a gradient of change apparent for sites within embayments. We explored this pattern for embayment sites with analysis of RNA-Seq gene expression patterns and found higher expression of multiple genes involved in bacterial stress response far from storm drains, suggesting that bacterial communities close to storm drains may be more tolerant of localised anthropogenic stressors. Several bacterial groups also differed close to and far from storm drains, suggesting their potential utility as bioindicators to monitor contaminants in estuarine sediments. Overall, our study provides useful insights into changes in the composition and functioning of benthic bacterial communities as a result of multiple anthropogenic stressors in differing hydrological conditions.
Feasibility of Droplet Digital PCR Analysis of Plasma Cell-Free DNA From Kidney Transplant Patients

Increasing research demonstrates the potential of donor-derived cell-free DNA (dd-cfDNA) as a biomarker for monitoring the health of various solid organ transplants. Several methods have been proposed for cfDNA analysis, including real-time PCR, digital PCR, and next generation sequencing-based approaches. We sought to revise the droplet digital PCR (ddPCR)-based approach to quantify relative dd-cfDNA in plasma from kidney transplant (KTx) patients using a novel pilot set of assays targeting single nucleotide polymorphisms that have a very high potential to distinguish cfDNA from two individuals. The assays are capable of accurate quantification of down to 0.1% minor allele content when analyzing 165 ng of human DNA. We found no significant differences in the yield of extracted cfDNA using the three different commercial kits tested. More cfDNA was extracted from the plasma of KTx patients than from healthy volunteers, especially early after transplantation. The median level of donor-derived minor alleles in KTx samples was 0.35%. We found that ddPCR using the evaluated assays within specific range is suitable for analysis of KTx patients' plasma but recommend prior genotyping of donor DNA and performing reliable preamplification of cfDNA.
Rapid Mining of Candidate Genes for Verticillium Wilt Resistance in Cotton Based on BSA-Seq Analysis

Cotton is a globally important cash crop. Verticillium wilt (VW) is commonly known as “cancer” of cotton and causes serious loss of yield and fiber quality in cotton production around the world. Here, we performed a BSA-seq analysis using an F2:3 segregation population to identify the candidate loci involved in VW resistance. Two QTLs (qvw-D05-1 and qvw-D05-2) related to VW resistance in cotton were identified using two resistant/susceptible bulks from the F2 segregation population constructed by crossing the resistant cultivar ZZM2 with the susceptible cultivar J11. A total of 30stop-lost SNPs and 42 stop-gained SNPs, which included 17 genes, were screened in the qvw-D05-2 region by SnpEff analysis. Further analysis of the transcriptome data and qRT-PCR revealed that the expression level of Ghir_D05G037630 (designated as GhDRP) varied significantly at certain time points after infection with V. dahliae. The virus-induced gene silencing of GhDRP resulted in higher susceptibility of the plants to V. dahliae than the control, suggesting that GhDRP is involved in the resistance to V. dahlia infection. This study provides a method for rapid mining of quantitative trait loci and screening of candidate genes, as well as enriches the genomic information and gene resources for the molecular breeding of disease resistance in cotton.
Using Machine Learning to Predict the Fuel Peak Cladding Temperature for a Large Break Loss of Coolant Accident

In this paper the use of machine learning (ML) is explored as an efficient tool for uncertainty quantification. A machine learning algorithm is developed to predict the peak cladding temperature (PCT) under the conditions of a large break loss of coolant accident given the various underlying uncertainties. The best estimate approach is used to simulate the thermal-hydraulic system of APR1400 large break loss of coolant accident (LBLOCA) scenario using the multidimensional reactor safety analysis code (MARS-KS) lumped parameter system code developed by Korea Atomic Energy Research Institute (KAERI). To generate the database necessary to train the ML model, a set of uncertainty parameters derived from the phenomena identification and ranking table (PIRT) is propagated through the thermal hydraulic model using the Dakota-MARS uncertainty quantification framework. The developed ML model uses the database created by the uncertainty quantification framework along with Keras library and Talos optimization to construct the artificial neural network (ANN). After learning and validation, the ML model can predict the peak cladding temperature (PCT) reasonably well with a mean squared error (MSE) of ∼0.002 and R2 of ∼0.9 with 9 to 11 key uncertain parameters. As a bounding accident scenario analysis of the LBLOCA case paves the way to using machine learning as a decision making tool for design extension conditions as well as severe accidents.
Distribution of Peptidyl-Prolyl Isomerase (PPIase) in the Archaea

Cis-trans isomerization of the peptide bond prior to proline is an intrinsically slow process but plays an essential role in protein folding. In vivo cis-trans isomerization reaction is catalyzed by Peptidyl-prolyl isomerase (PPIases), a category of proteins widely distributed among all the three domains of life. The present study is majorly focused on the distribution of different types of PPIases in the archaeal domain. All the three hitherto known families of PPIases (namely FKBP, Cyclophilin and parvulin) were studied to identify the evolutionary conservation across the phylum archaea. The basic function of cyclophilin, FKBP and parvulin has been conserved whereas the sequence alignment suggested variations in each clade. The conserved residues within the predicted motif of each family are unique. The available protein structures of different PPIase across various domains were aligned to ascertain the structural variation in the catalytic site. The structural alignment of native PPIase proteins among various groups suggested that the apo-protein may have variable conformations but when bound to their specific inhibitors, they attain similar active site configuration. This is the first study of its kind which explores the distribution of archaeal PPIases, along with detailed structural and functional analysis of each type of PPIase found in archaea.
Growth Patterns in Seedling Roots of the Pincushion Cactus Mammillaria Reveal Trends of Intra- and Inter-Specific Variation

Genetic mechanisms controlling root development are well-understood in plant model species, and emerging frontier research is currently dissecting how some of these mechanisms control root development in cacti. Here we show the patterns of root architecture development in a gradient of divergent lineages, from populations to species in Mammillaria. First, we show the patterns of variation in natural variants of the species Mammillaria haageana. Then we compare this variation to closely related species within the Series Supertexta in Mammillaria (diverging for the last 2.1 million years) in which M. haageana is inserted. Finally, we compared these patterns of variation to what is found in a set of Mammillaria species belonging to different Series (diverging for the last 8 million years). When plants were grown in controlled environments, we found that the variation in root architecture observed at the intra-specific level, partially recapitulates the variation observed at the inter-specific level. These phenotypic outcomes at different evolutionary time-scales can be interpreted as macroevolution being the cumulative outcome of microevolutionary phenotypic divergence, such as the one observed in Mammillaria accessions and species.
Weighted Gene Co-expression Network Analysis Identifies a Cancer-Associated Fibroblast Signature for Predicting Prognosis and Therapeutic Responses in Gastric Cancer

Background: Cancer-associated fibroblasts (CAFs) are the most prominent cellular components in gastric cancer (GC) stroma that contribute to GC progression, treatment resistance, and immunosuppression. This study aimed at exploring stromal CAF-related factors and developing a CAF-related classifier for predicting prognosis and therapeutic effects in GC. Methods: We downloaded mRNA expression and clinical information of 431 GC samples from Gene Expression Omnibus (GEO) and 330 GC samples from The Cancer Genome Atlas (TCGA) databases. CAF infiltrations were quantified by the estimate the proportion of immune and cancer cells (EPIC) method, and stromal scores were calculated via the Estimation of STromal and Immune cells in MAlignant Tumors using Expression data (ESTIMATE) algorithm. Stromal CAF-related genes were identified by weighted gene co-expression network analysis (WGCNA). A CAF risk signature was then developed using the univariate and least absolute shrinkage and selection operator method (LASSO) Cox regression model. We applied the Spearman test to determine the correlation among CAF risk score, CAF markers, and CAF infiltrations (estimated via EPIC, xCell, microenvironment cell populations-counter (MCP-counter), and Tumor Immune Dysfunction and Exclusion (TIDE) algorithms). The TIDE algorithm was further used to assess immunotherapy response. Gene set enrichment analysis (GSEA) was applied to clarify the molecular mechanisms. Results: The 4-gene (COL8A1, SPOCK1, AEBP1, and TIMP2) prognostic CAF model was constructed. GC patients were classified into high– and low–CAF-risk groups in accordance with their median CAF risk score, and patients in the high–CAF-risk group had significant worse prognosis. Spearman correlation analyses revealed the CAF risk score was strongly and positively correlated with stromal and CAF infiltrations, and the four model genes also exhibited positive correlations with CAF markers. Furthermore, TIDE analysis revealed high–CAF-risk patients were less likely to respond to immunotherapy. GSEA revealed that epithelial–mesenchymal transition (EMT), TGF-β signaling, hypoxia, and angiogenesis gene sets were significantly enriched in high–CAF-risk group patients. Conclusion: The present four-gene prognostic CAF signature was not only reliable for predicting prognosis but also competent to estimate clinical immunotherapy response for GC patients, which might provide significant clinical implications for guiding tailored anti-CAF therapy in combination with immunotherapy for GC patients.
Plasma EVs Display Antigen-Presenting Characteristics in Patients With Allergic Rhinitis and Promote Differentiation of Th2 Cells

Background Allergic rhinitis (AR) is characterized by IgE-mediated mucosa response after exposure to allergens. Extracellular vesicles (EVs) are nano-size vesicles containing biological cargos for intercellular communications. However, the role of plasma EVs in pathogenesis of AR remains largely unknown. Methods Plasma EVs from patients with AR were isolated, quantified, and characterized. The expression of Der p 1 and antigen-presenting molecules on EVs was determined by Western blot, flow cytometry, or ELISA. PKH26- and CFSE (carboxyfluorescein succinimidyl ester)-stained AR-EVs were used to determine the uptake of EVs by CD4+T cells and their effects on CD4+T cell proliferation, respectively. Results Plasma EVs in healthy control (HC) and AR patients were similar in the concentration of particles, expression for specific EV markers, and both had structural lipid bilayer. However, the levels of Der p 1 on plasma EVs from both mild and moderate-severe AR patients were significantly higher than that on HC. The levels of antigen-presenting molecules on plasma EVs were similar from three subjects. Moreover, levels of Der p 1 on EVs in plasma, but not nasal secretion, were significantly associated with the symptom score of AR patients and level of plasma IL-13. Additionally, plasma EVs from patients with AR promoted the development of Th2 cells, while no effect was found on CD4+ T-cell proliferation. Conclusions Plasma EVs derived from patients with AR exhibited antigen-presenting characteristics and promoted differentiation of Th2 cells, thus providing novel understanding of the pathogenesis of AR.
Carboxymethylchitin Nanocarrier (CMCNC): A Novel Therapeutic Formulation for Drug Release

ABSTRACT In the present work, chitin based derivatives carboxymethylchitin, CMC were synthesised for nanocarriers (NCs). Cu and Fu loaded NCs had also been prepared and characterized by various physiochemical & biological techniques. Here, drug release profiles and drug kinetics were also studied. In vitro cytotoxicity test (Cell Viability-A549 cells) result found most effected. CMCNC also fitted best in Higuchi model which proved that this prepared nanocarriers followed the mechanism of diffusion rather than dissolution and degradation. The overall analysis leads to the conclusion that CMCNC found to be a suitable nanocarrier for targeted drug delivery. Graphical Abstract
Dynamics and structure of an apolar active suspension in an annulus

We study the complex dynamics of a two-dimensional suspension comprising non-motile active particles confined in an annulus. A coarse-grained liquid crystal model is employed to describe the nematic structure evolution, and is hydrodynamically coupled with the Stokes equation to solve for the induced active flows in the annulus. For dilute suspensions, coherent structures are captured by varying the particle activity and gap width, including unidirectional circulations, travelling waves and chaotic flows. For concentrated suspensions, the internal collective dynamics features motile disclination defects and flows at finite gap widths. In particular, we observe an intriguing quasi-steady-state at certain gap widths during which $+1/2$ -order defects oscillate around equilibrium positions accompanying travelling-wave flows that switch circulating directions periodically. We perform linear stability analyses to reveal the underlying physical mechanisms of pattern formation during a concatenation of instabilities.
Effect of Monoclonal Antibody Blockade of Long Fragment Neurotensin on Weight Loss, Behavior, and Metabolic Traits After High-Fat Diet Induced Obesity

Background Obesity is a major public health problem of our time as a risk factor for cardiometabolic disease and the available pharmacological tools needed to tackle the obesity pandemic are insufficient. Neurotensin (NTS) is a 13 amino acid peptide, which is derived from a larger precursor hormone called proneurotensin or Long Form NTS (LF NTS). NTS modulates neuro-transmitter release in the central system nervous, and facilitates intestinal fat absorption in the gastrointestinal tract. Mice lacking LF NTS are protected from high fat diet (HFD) induced obesity, hepatic steatosis and glucose intolerance. In humans, increased levels of LF NTS strongly and independently predict the development of obesity, diabetes mellitus, cardiovascular disease and mortality. With the perspective to develop therapeutic tools to neutralize LF NTS, we developed a monoclonal antibody, specifically inhibiting the function of the LF NTS (LF NTS mAb). This antibody was tested for the effects on body weight, metabolic parameters and behavior in mice made obese by high-fat diet. Methods C57bl/6j mice were subjected to high-fat diet (HFD) until they reached an obesity state, then food was switched to chow. Mice were treated with either PBS (control therapy) or LF NTS mAb at the dose of 5 mg/kg once a week (i.v.). Mice weight, plasma biochemical analysis, fat and muscle size and distribution and behavioral tests were performed during the losing weight period and the stabilization period. Results Obese mice treated with the LF NTS mAb lost weight significantly faster than the control treated group. LF NTS mAb treatment also resulted in smaller fat depots, increased fecal cholesterol excretion, reduced liver fat and larger muscle fiber size. Moreover, mice on active therapy were also less stressed, more curious and more active, providing a possible explanation to their weight loss. Conclusion Our results demonstrate that in mice subjected to HFD-induced obesity, a blockade of LF NTS with a monoclonal antibody results in reduced body weight, adipocyte volume and increased muscle fiber size, possibly explained by beneficial effects on behavior. The underlying mechanisms as well as any future role of LF NTS mAb as an anti-obesity agent warrants further studies.
Isolation and Identification of Talaromyces sp. Strain Q2 and Its Biocontrol Mechanisms Involved in the Control of Fusarium Wilt

Fusarium wilt is an important disease of many food crops and often causes serious damages to yield and food quality. Consequently, numerous studies mainly focused on exploring the control strategy for Fusarium oxysporum as well as the mechanism of interaction between the F. oxysporum and other beneficial soil microorganisms. In this study, we have screened and identified an efficient biocontrol strain from the soil with infection of F. oxysporum f. sp. momordica (referred to as Fom), Talaromyces purpurogenus Q2 (referred to as TpQ2), which could be effective to reduce relative abundance of the rhizospheric Fom, leading to a significant decrease of Fusarium wilt disease incidence in bitter gourd during the greenhouse and field trails. TpQ2 can reduce the relative abundance of rhizospheric Fom through inhibition of growth and development of Fom. During the co-cultivation of TpQ2 and Fom, we confirmed that TpQ2 could significantly suppress the growth and development of Fom through disturbing the normal hyphae shape and function of the cell walls of Fom via secreting cell wall–degrading enzymes and suppression of the expression of cell wall biosynthesis genes, such as FomCFEM. In the meantime, TpQ2 showed a strong negative correlation with F. oxysporum in soil and positive correlation with beneficial indigenous microorganisms that had significant negative correlation with Fusarium populations, such as Streptomycetes, Lysobacter, and Sphingobium. To summarize, TpQ2 has a good biocontrol efficacy on Fusarium wilt of bitter gourd. The biocontrol mechanisms of TpQ2 on Fusarium wilt are complex and diverse.
Metabolic Engineering of Enterobacter aerogenes for Improved 2,3-Butanediol Production by Manipulating NADH Levels and Overexpressing the Small RNA RyhB

Biotechnological production of 2,3-butanediol (2,3-BD), a versatile platform bio-chemical and a potential biofuel, is limited due to by-product toxicity. In this study, we aimed to redirect the metabolic flux toward 2,3-BD in Enterobacter aerogenes (E. aerogenes) by increasing the intracellular NADH pool. Increasing the NADH/NAD+ ratio by knocking out the NADH dehydrogenase genes (nuoC/nuoD) enhanced 2,3-BD production by up to 67% compared with wild-type E. aerogenes. When lactate dehydrogenase (ldh) was knocked out, the yield of 2,3-BD was increased by 71.2% compared to the wild type. Metabolic flux analysis revealed that upregulated expression of the sRNA RyhB led to a noteworthy shift in metabolism. The 2,3-BD titer of the best mutant Ea-2 was almost seven times higher than that of the parent strain in a 5-L fermenter. In this study, an effective metabolic engineering strategy for improved 2,3-BD production was implemented by increasing the NADH/NAD+ ratio and blocking competing pathways.
A Simple Approach to Isolate Slow and Fast Cycling Organic Carbon Fractions in Central European Soils—Importance of Dispersion Method

Numerous approaches have been developed to isolate fast and slow cycling soil organic carbon (SOC) pools using physical and chemical fractionation. Most of these methods are complex, expensive, and time consuming and unsuited for high-throughput application, such as for regional scale assessments. For simpler and faster fractionation via particle size the key issue is the dispersion of soil. It is unclear how the initial dispersion of soil affects the turnover rates of isolated fractions. We investigated five commonly used dispersion methods using different intensities: shaking in water, shaking in water with glass beads, ultrasonication at 100 and 450 J ml−1 and sodium hexametaphosphate (Na-HMP). We used soils from long-term field experiments that included a change from C3 to C4 vegetation and adjacent control sites using δ13C isotope ratio mass spectrometry. We evaluated the degree of C3/C4 moieties of the fractions, mass and carbon recovery and reproducibility as well as the time expenditures of the dispersions, sieving and drying techniques to develop an efficient and cheap fractionation method. Our results indicate that ultrasonication as well as H2O treatment with and without glass beads resulted in fractions with different turnover. Moreover, isolation performances depended on soil texture. While the isolation of the fractions using water with and without glass beads was equivalent to ultrasonication in soils with low clay contents, these methods had limited potential for soils with high clay contents. Furthermore, treatment with water alone had less reproducible results than other tested methods. The SOC recovery was comparable and satisfactory amongst non-chemical dispersion methods and reached over 95% for each of these methods. The use of Na-HMP was unsuccessful due to high time expenditures and strong SOC leaching. We propose particle size fractionation combined with ultrasonic dispersion as a fast and highly reliable method to quantify slow and fast cycling SOC pools for a wide range of soil types and textures from agricultural sites in central Europe.
Flight Altitudes of Raptors in Southern Africa Highlight Vulnerability of Threatened Species to Wind Turbines

Energy infrastructure, particularly for wind power, is rapidly expanding in Africa, creating the potential for conflict with at-risk wildlife populations. Raptor populations are especially susceptible to negative impacts of fatalities from wind energy because individuals tend to be long-lived and reproduce slowly. A major determinant of risk of collision between flying birds and wind turbines is the altitude above ground at which a bird flies. We examine 18,710 observations of flying raptors recorded in southern Africa and we evaluate, for 49 species, the frequency with which they were observed to fly at the general height of a wind turbine rotor-swept zone (50–150 m). Threatened species, especially vultures, were more likely to be observed at turbine height than were other species, suggesting that these raptors are most likely to be affected by wind power development across southern Africa. Our results highlight that threatened raptor species, particularly vultures, might be especially impacted by expanded wind energy infrastructure across southern Africa.