Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural insights into the PrpTA toxin–antitoxin system in Pseudoalteromonas rubra

Bacteria could survive stresses by a poorly understood mechanism that contributes to the emergence of bacterial persisters exhibiting multidrug tolerance (MDT). Recently, Pseudoalteromonas rubra prpAT module was found to encode a toxin PrpT and corresponding cognate antidote PrpA. In this study, we first reported multiple individual and complex structures of PrpA and PrpT, which uncovered the high-resolution three-dimensional structure of the PrpT:PrpA2:PrpT heterotetramer with the aid of size exclusion chromatography-multi-angle light scattering experiments (SEC-MALS). PrpT:PrpA2:PrpT is composed of a PrpA homodimer and two PrpT monomers which are relatively isolated from each other and from ParE family. The superposition of antitoxin monomer structures from these structures highlighted the flexible C-terminal domain (CTD). A striking conformational change in the CTDs of PrpA homodimer depolymerized from homotetramer was provoked upon PrpT binding, which accounts for the unique PrpT-PrpARHH mutual interactions and further neutralizes the toxin PrpT. PrpA2–54-form I and II crystal structures both contain a doughnut-shaped hexadecamer formed by eight homodimers organized in a cogwheel-like form via inter-dimer interface dominated by salt bridges and hydrogen bonds. Moreover, PrpA tends to exist in solution as a homodimer other than a homotetramer (SEC-MALS) in the absence of flexible CTD. Multiple multi-dimers, tetramer and hexamer included, of PrpA2–54 mediated by the symmetric homodimer interface and the complicated inter-dimer interface could be observed in the solution. SEC-MALS assays highlighted that phosphate buffer (PB) and the increase in the concentration appear to be favorable for the PrpA2–54 oligomerization in the solution. Taken together with previous research, a model of PrpA2–54 homotetramer in complex with prpAT promoter and the improved mechanism underlying how PrpTA controls the plasmid replication were proposed here.
The Coronavirus pandemic and closed fitness clubs negatively affected members exercise habits

Introduction Due to the Coronavirus pandemic, politicians enacted directions to reduce social interactions, including lockdown of fitness clubs. We aimed to investigate how this changed exercise habits of Norwegian gym members. Method Based on survey data, men and women (≥18 years, n = 233, data collection from Aug. 2020 to Jan. 2021) were recruited to this study by an email-invitation from their fitness club chain or by Facebook advertisement. The participants reported on background variables (e.g., age, gender, total household income, occupation, and education), and exercise habits pre- and during social lockdown. Data were analyzed using independent or student t-test, chi-squared test, or McNemar's test, as appropriate. Results Home-based exercise (18.0 vs. 72.5%, p = <0.001), walking (49.8 vs. 65.2%, p = <0.001), and cycling (16.7 vs. 24.5%, p = 0.004) was more common during than pre-lockdown. Also, men (4.33 to 3.68 days/week, p =0.013) and women (4.20 to 3.79 days/week, p = 0.001) reported a lower exercise frequency, and a shorter duration. Exercise frequency was lower in those with a BMI ≥25 than in those with BMI <25 (3.95 vs. 4.48 days/week, p = <0.007) pre-lockdown. High exercise attendees (≥3 sessions/week, 66.5%) reported a smaller decrease in exercise frequency (mean change: 0.06 vs. 1.24 days/week, p = <0.001) and duration (>60 min. per session: 33.0 vs. 3.8%, p = <0.001) than low exercise attendees during lockdown. Discussion Home-based exercise, walking, and cycling were most frequently reported during lockdown. Participants reported a small decrease in exercise duration and frequency compared with pre-lockdown. Closure of fitness clubs impacted low attendees more than high attendees.
Evaluation of the effect of jasmonic acid elicitation on composition of pigments and biological activities in green callus of neem (Azadirachta indica)

This study was carried out with the aim of determining the effects of jasmonic acid (JA) elicitation on the bioactive pigments' biosynthesis and the antioxidant activities in green callus of Azadirachta indica of two different ages (4- and 8-week-old). Plant tissue culture technique was employed to induce the formation of green callus from leaf explants of A. indica on Murashige and Skoog (MS) medium supplemented with 0.6 mg/L thidiazuron (CM) and three different concentrations of JA (2, 4, and 6 mg/L). The methanolic extracts from the green callus were used for determination of total chlorophyll content (TCh), total carotenoid content (TC), total anthocyanin content (TAC), total phenolic content (TPC), and total flavonoid content (TFC) through colorimetric and HPLC analyses. The highest amount of yield was obtained from CM and 2 mg/L JA (2JA) extracts for 4- and 8-week-old samples, respectively. Phytochemical screening revealed the presence of alkaloids, flavonoids, phenols, tannins, and terpenoids in all 4- and 8-week-old samples elicited with 2, 4 and 6 mg/L JA. The highest value for TAC, TCh, TC, TPC, and TFC of 4- and 8-week-old samples were from callus cultured on media supplemented with 6 mg/L JA (6JA) and 4 mg/L JA (4JA), respectively. The lowest IC50 values were found to be 8.29 ± 0.10 mg/mL (6JA) for 4-week-old and 7.73 ± 0.03 mg/mL (4JA) for 8-week-old samples. The highest Ferric Reducing Antioxidant Power (FRAP) values obtained in this study were 90.60 ± 1.55 g/g (6JA), and 74.59 ± 3.91 g/g (4JA), respectively, for 4- and 8-week-old samples. Moreover, Pearson's correlation analysis revealed a significant correlation between TAC, TCh, TC, TPC, and TFC with ABTS and FRAP assays. In addition, PCA analysis revealed that 83.5% of the information (variances) contained in the data were retained by the first two principal components. Overall, these findings suggested that JA supplementation into the culture media significantly increase the chlorophyll, carotenoid, anthocyanin, phenolic and flavonoid contents and JA concentrations at 6 mg/L JA and 4 mg/L JA yielded the highest pigments content in 4- and 8-weeks-old callus, respectively.
Exposure to endosulfan can cause long term effects on general biology, including the reproductive system of mice

Increased infertility in humans is attributed to the increased use of environmental chemicals in the last several decades. Various studies have identified pesticides as one of the causes of reproductive toxicity. In a previous study, infertility was observed in male mice due to testicular atrophy and decreased sperm count when a sublethal dose of endosulfan (3 mg/kg) with a serum concentration of 23 μg/L was used. However, the serum concentration of endosulfan was much higher (up to 500 μg/L) in people living in endosulfan-exposed areas compared to the one used in the investigation. To mimic the situation in an experimental setup, mice were exposed to 5 mg/kg body weight of endosulfan, and reproductive toxicity and long-term impact on the general biology of animals were examined. HPLC analysis revealed a serum concentration of ∼50 μg/L of endosulfan after 24 h endosulfan exposure affected the normal physiology of mice. Histopathological studies suggest a persistent, severe effect on reproductive organs where vacuole degeneration of basal germinal epithelial cells and degradation of the interstitial matrix were observed in testes. Ovaries showed a reduction in the number of mature Graafian follicles. At the same time, mild vacuolation in liver hepatocytes and changes in the architecture of the lungs were observed. Endosulfan exposure induced DNA damage and mutations in germ cells at the molecular level. Interestingly, even after 8 months of endosulfan exposure, we observed increased DNA breaks in reproductive tissues. An increased DNA Ligase III expression was also observed, consistent with reported elevated levels of MMEJ-mediated repair. Further, we observed the generation of tumors in a few of the treated mice with time. Thus, the study not only explores the changes in the general biology of the mice upon exposure to endosulfan but also describes the molecular mechanism of its long-term effects.
The impact of multi-enzyme fortification on growth performance, intestinal morphology, nutrient digestibility, and meat quality of broiler chickens fed a standard or low-density diet

This research aimed to study the impact of supplementation of three multi-enzyme levels (0, 0.1, and 0.2% of feed) and two levels of dietary treatments [standard diet (SD) and low-density diet (LDD)] on growth performance, carcass traits, digestibility, and meat quality of broilers from 1 to 38 days of age. A total of 216 1-day-old Arbor Acres broiler chicks were randomly assigned to a factorial experiment (2 × 3) comprising six dietary treatments, each with six replicates and each replicate with six chickens. The results showed that the LDD significantly reduced body weight gain by 5.0%, compared with the SD. Multi-enzymes significantly improved body weight gain and the production index (PI) relative to the SD. The feed conversion ratio was significantly enhanced with increased multi-enzymes from 1 to 21 days. A significant relation between the multi-enzyme concentration and type of dietary treatment was observed in body weight gain and feed conversion ratio from 1 to 21 days of age. Nitrogen-free extract digestibility was significantly increased by using the SD diet compared with using the LDD. Multi-enzyme supplementation improved the digestibility of dry matter, crude protein, crude fiber, and nitrogen-free extract in the LDD. A significant relationship was found between the multi-enzyme concentration and type of dietary treatment on the pancreas, liver, and intestinal length percentages. The meat dry matter concentration was significantly higher in the LDD group than in the SD group. The low-density diet significantly reduced the total revenue compared with the SD, whereas broilers fed the SD recorded significantly higher total revenue and economic efficiency than those fed the LDD. The low-density diet significantly increased economic efficiency compared with the SD. Multi-enzymes significantly increased the total revenue, net revenue, and economic efficiency than the standard set. In conclusion, using multi-enzymes in broiler diets improved body weight gain. The LDD with multi-enzymes showed enhanced body weight gain compared with the SD without multi-enzymes.
Mild and moderate cardioembolic stroke patients may benefit more from direct mechanical thrombectomy than bridging therapy: A subgroup analysis of a randomized clinical trial (DIRECT-MT)

Background The benefit of intravenous alteplase before endovascular thrombectomy is unclear in patients with acute cardioembolic stroke. Methods We collected cardioembolic (CE) stroke patient data from the multicentre randomized clinical trial of Direct Intra-arterial Thrombectomy to Revascularize Acute Ischaemic Stroke Patients with Large Vessel Occlusion Efficiently in Chinese Tertiary Hospitals (DIRECT-MT). The primary outcome was the 90-day modified Rankin Scale (mRS) score. Five subgroups of cardioembolic stroke patients were analyzed. A multivariable ordinal logistic regression analysis analyzed the difference in the primary outcome between the direct mechanical thrombectomy (MT) and bridging therapy groups. An interaction term was entered into the model to test for subgroup interaction. The DIRECT-MT trial is registered with clinicaltrials.gov Identifier: NCT03469206. Results A total of 290 CE stroke patients from the DIRECT-MT trial were enrolled in this study: 146 patients in the direct MT group and 144 patients in the bridging therapy group. No difference between the two treatment groups in the primary outcome was found (adjusted common odds ratio, 1.218; 95% confidence interval, 0.806 to 1.841; P = 0.34). In the subgroup analysis, CE stroke patients with an NIHSS ≤ 15 in the direct MT group were associated with better outcomes (47 vs. 53, acOR, 3.14 [1.497, 6.585]) and lower mortality (47 vs. 53, aOR, 0.16 [0.026, 0.986]) than those in the bridging therapy group, while there were no significant differences between the two treatment groups in the outcome and mortality of CE stroke patients with an NIHSS >15. Conclusion Mild and moderate cardioembolic stroke patients may benefit more from direct mechanical thrombectomy than bridging therapy. This need to be confirmed by further prospective studies in a larger number of patients.
Chemical elicitation as an avenue for discovery of bioactive compounds from fungal endophytes

The present study investigated the molecular phylogeny, antimicrobial and cytotoxic activities of fungal endophytes obtained from the A*STAR Natural Organism Library (NOL) and previously isolated from Sungei Buloh Wetland Reserve, Singapore. Phylogenetic analysis based on ITS2 gene suggests that these isolates belong to 46 morphotypes and are affiliated to 23 different taxa in 17 genera of the Ascomycota phylum. Colletotrichum was the most dominant fungal genus accounting for 37% of all the isolates, followed by Diaporthe (13%), Phyllosticta (10.9%) and Diplodia (8.7%). Chemical elicitation using 5-azacytidine, a DNA methyltransferase inhibitor and suberoylanilide hydroxamic acid, a histone deacetylase inhibitor resulted in an increase in the number of active strains. Bioassay-guided isolation and structural elucidation yielded pestahivin and two new analogues from Bartalinia sp. F9447. Pestahivin and its related analogues did not exhibit antibacterial activity against Staphylococcus aureus but displayed strong antifungal activities against Candida albicans and Aspergillus brasiliensis, with IC50 values ranging from 0.46 ± 0.06 to 144 ± 18 µM. Pestahivin and its two analogues furthermore exhibited cytotoxic activity against A549 and MIA PACA-2 cancer cell lines with IC50 values in the range of 0.65 ± 0.12 to 42 ± 5.2 µM. The finding from this study reinforces that chemical epigenetic induction is a promising approach for the discovery of bioactive fungal secondary metabolites encoded by cryptic gene clusters.
Partial cutting in a dry temperate forest ecosystem alleviates growth loss under drought

The increasing frequency of severe drought and heat events under climate change is a major cause for concern for forest productivity and survival. One potential solution to improve forest resilience to drought may involve tree removal to reduce competition. To quantify potential benefits of partial cutting systems under drought, we use tree-ring data from a long-term partial cutting experiment in a dry ecosystem in western Canada, composed primarily of mature interior Douglas-fir (Pseudotsuga menziesii var. glauca). We ask: (1) How does tree removal change growth responses to drought and (2) how persistent are effects across multiple drought events? We compare growth responses in 83 trees up to 400 years in age from eight treatment units in a randomized experimental design representing a logging treatment with 25% basal area retention and a control (100% basal area retention). Retention harvesting was conducted in winter of 2002/2003 after a moderate drought in the summer of 2002. The site experienced a more severe drought in 2009 and a drought-heat event in 2015. In 2020, we obtained tree height and diameter data as well as tree increment cores from canopy dominant Douglas-fir, which were used to derive basal area increments. Based on these growth increments, we calculated four indices of resilience to drought. Growth increments of remaining individuals substantially increased after tree removal. Relative to the control, the low retention treatment expressed significantly higher post-drought growth increments compared to growth increments after the drought years of 2002 and 2009, i.e., higher drought recovery. Growth increments in the low retention treatment also had a significantly higher ability to regain pre-drought growth levels after the 2002 and 2009 droughts, i.e., higher drought resilience. However, the treatment did not show higher resilience under a heat-drought event in 2015. Although the treatment effects on drought response indices diminished over time, the absolute growth increments of residual trees remained higher than the control 17 years after harvest, despite repeated droughts. These results suggest that partial cutting on moisture-limited sites provides immediate and medium term benefits for remaining trees in terms of drought resilience, which may help forests adapt to climate change.
Intrinsic properties and dopability effects on the thermoelectric performance of binary Sn chalcogenides from first principles

High-performance thermoelectric (TE) materials rely on semiconductors with suitable intrinsic properties for which carrier concentrations can be controlled and optimized. To demonstrate the insights that can be gained in computational analysis when both intrinsic properties and dopability are considered in tandem, we combine the prediction of TE quality factor (intrinsic properties) with first-principles simulations of native defects and carrier concentrations for the binary Sn chalcogenides SnS, SnSe, and SnTe. The computational predictions are compared to a comprehensive data set of previously reported TE figures-of-merit for each material, for both p-type and n-type carriers. The combined analysis reveals that dopability limits constrain the TE performance of each Sn chalcogenide in a distinct way. In SnS, TE performance for both p-type and n-type carriers is hindered by low carrier concentrations, and improved performance is possible only if higher carrier concentrations can be achieved by suitable extrinsic dopants. For SnSe, the p-type performance of the Cmcm phase appears to have reached its theoretical potential, while improvements in n-type performance may be possible through tuning of electron carrier concentrations in the Pnma phase. Meanwhile, assessment of the defect chemistry of SnTe reveals that p-type TE performance is limited by, and n-type performance is not possible due to, the material’s degenerate p-type nature. This analysis highlights the benefits of accounting for both intrinsic and extrinsic properties in a computation-guided search, an approach that can be applied across diverse sets of semiconductor materials for TE applications.
Enhancing the electrochemical performance of TiO2 based material using microwave air plasma treatment with an ECR cavity

The microwave-based plasma treatment facility at the Central University of Punjab Bathinda (CUPB) based on 2.45 GHz has been used to investigate the impact on the electrochemical performance of TiO2. This was accomplished by treating a number of pellets of TiO2 sample material with microwave plasma at an input power of 80 W. The palette is subjected to microwave plasma treatment at 30-, 60-, 80-, and 100-s intervals. Many such characterization methods, including UV-visible spectroscopy, FTIR, XRD, and FESEM, have been applied to the study of the impact of plasma treatment on other physical and chemical properties in the context of untreated pellets. In the 80-s plasma treatment, the FTIR study showed that the (O-Ti-O) vibration band at 500–900 cm−1 was wider than other bands. The UV results showed that an 80-s plasma treatment decreased the sample’s band gap by 37% and increased the amount of disordered, amorphous material in the sample that had not been treated. XRD studies show that a sample that was treated with plasma for 80 s has low crystallinity and a high disorder (amorphous) factor. The Nyquist plot showed that the electrochemical charge transfer resistance drops from 7 (not treated) to 4 after 80 s of plasma treatment. In a study of electrochemical performance, a sample that was treated with plasma for 80 s has a capacitance that is 35% higher than a sample that was not treated.
Potential global distribution area projections of the aphid Lipaphis erysimi and its predator Eupeodes corollae in the context of climate change

Climate change affects the population distribution of pests and their natural enemies, and predicting these effects is necessary for pest monitoring and green control. Lipaphis erysimi is an important vegetable pest, and its natural enemy, the Eupeodes corollae Fabricius has a strong predatory effect on the L. erysimi. To assess the spread trends of L. erysimi and its natural enemy, the hoverfly, E. corollae under current (1970-2000) and future climates (2041-2060), based on the MaxEnt model, this paper uses data on the geographical distribution of the historical occurrence of L. erysimi and E. corollae to speculate on their potential distribution areas worldwide and analyze the key environmental factors affecting the survival and spread of both. The results showed that the Representative Concentration Pathway (RCP) 2.6 and RCP4.5 climatic conditions are favorable for the spread of L. erysimi, the RCP8.5 climatic conditions are unfavorable for the spread of L. erysimi, and all three future climatic conditions are unfavorable for the spread of E. corollae. The highest fitness of L. erysimi was found at the annual average temperature of 18 °C and the annual average precipitation of 900 mm, while the highest fitness of E. corollae was found at the annual average temperature of 10 °C and the lowest temperature in the coldest month of 0 °C. This study can provide a reference basis for monitoring and early warning and biological control of L. erysimi.
The role of exercise-and high fat diet-induced bone marrow extracellular vesicles in stress hematopoiesis

Exercise and obesity regulate hematopoiesis, in part through alterations in cellular and soluble components of the bone marrow niche. Extracellular vesicles (EVs) are components of the bone marrow niche that regulate hematopoiesis; however, the role of exercise training or obesity induced EVs in regulating hematopoiesis remains unknown. To address this gap, donor EVs were isolated from control diet-fed, sedentary mice (CON-SED), control diet-fed exercise trained mice (CON-EX), high fat diet-fed, sedentary mice (HFD-SED), and high fat diet-fed, exercise trained mice (HFD-EX) and injected into recipient mice undergoing stress hematopoiesis. Hematopoietic and niche cell populations were quantified, and EV miRNA cargo was evaluated. EV content did not differ between the four groups. Mice receiving HFD-EX EVs had fewer hematopoietic stem cells (HSCs) (p < 0.01), long-term HSC (p < 0.05), multipotent progenitors (p < 0.01), common myeloid progenitors (p<0.01), common lymphoid progenitors (p < 0.01), and granulocyte-macrophage progenitors (p < 0.05), compared to mice receiving HFD-SED EVs. Similarly, mice receiving EX EVs had fewer osteoprogenitor cells compared to SED (p < 0.05) but enhanced mesenchymal stromal cell (MSC) osteogenic differentiation in vitro (p < 0.05) compared to SED EVs. HFD EVs enhanced mesenchymal stromal cell (MSC) adipogenesis in vitro (p < 0.01) compared to CON EVs. HFD-EX EVs had lower microRNA-193 and microRNA-331-5p content, microRNAs implicated in inhibiting osteogenesis and leukemic cell expansion respectively, compared to HFD-SED EVs. The results identify alterations in EV cargo as a novel mechanism by which exercise training alters stress hematopoiesis and the bone marrow niche.