Miracle-dz/UniFAR-FTUs huggingface dataset:
Differences in the regulatory strategies of marine oligotrophs and copiotrophs reflect differences in motility

Aquatic bacteria frequently are divided into lifestyle categories oligotroph or copiotroph. Oligotrophs have proportionately fewer transcriptional regulatory genes than copiotrophs and are generally non-motile/chemotactic. We hypothesized that the absence of chemotaxis/motility in oligotrophs prevents them from occupying nutrient patches long enough to benefit from transcriptional regulation. We first confirmed that marine oligotrophs are generally reduced in genes for transcriptional regulation and motility/chemotaxis. Next, using a non-motile oligotroph (Ca. Pelagibacter st. HTCC7211), a motile copiotroph (Alteromonas macleodii st. HOT1A3), and [14C]L-alanine, we confirmed that L-alanine catabolism is not transcriptionally regulated in HTCC7211 but is in HOT1A3. We then found that HOT1A3 took 2.5-4 min to initiate L-alanine oxidation at patch L-alanine concentrations, compared to <30s for HTCC7211. By modeling cell trajectories, we predicted that, in most scenarios, non-motile cells spend <2 min in patches, compared to >4 mins for chemotactic/motile cells. Thus, the time necessary for transcriptional regulation to initiate prevents transcriptional regulation from being beneficial for non-motile oligotrophs. This is supported by a mechanistic model we developed, which predicted that HTCC7211 cells with transcriptional regulation of L-alanine metabolism would produce 12% of their standing ATP stock upon encountering an L-alanine patch, compared to 880% in HTCC7211 cells without transcriptional regulation.
Emergence of Small Colony Variants (SCVs) is an adaptive strategy used by Pseudomonas aeruginosa to palliate O2 limitations

The ability to generate a subpopulation of Small Colony Variants (SCVs) is a conserved feature of Pseudomonas aeruginosa and could represent a key adaptive strategy to colonize and persist in multiple niches. However, very little is known about the role of the SCV phenotype, the conditions that promote its emergence and its possible involvement in an adaptive strategy. In the present work, we investigated the in vitro selective conditions promoting the emergence of SCVs from the prototypical strain PA14, which readily forms SCVs in non-agitated standing cultures. We found that O2 limitations, which cause a redox imbalance, is the main factor selecting for the SCV phenotype, which promotes survival of the population via formation of a biofilm at the air-liquid interface to access the electron acceptor. When this selective pressure is relieved by aeration or supplementation of an alternative electron acceptor, SCVs are barely detectable. We also observed that SCV emergence contributes to redox rebalancing, suggesting that it is involved in an adaptive strategy. We conclude that selection for the SCV phenotype is an adaptive solution adopted by P. aeruginosa to access poorly available O2. IMPORTANCE The bacterium P. aeruginosa is an opportunistic pathogen that thrives in many environments. It poses a significant health concern, notably because it is a causative agent of nosocomial infections and the most prevalent pathogen found in the lungs of people with cystic fibrosis. In infected hosts, its persistence is often related to the emergence of an alternative phenotype known as Small Colony Variant (SCV). Identification of conditions selecting for the SCV phenotype contributes to knowledge regarding adaptive mechanisms exploited by P. aeruginosa to survive in multiple niches and persist during infections. Hindering this adaptation strategy could help control P. aeruginosa persistent infections.
Transcriptomic Insights Into Root Development and Overwintering Transcriptional Memory of Brassica rapa L. Grown in the Field

As the only overwintering oil crop in the north area of China, living through winter is the primary feature of winter rapeseed. Roots are the only survival organ during prolonged cold exposure during winter to guarantee flowering in spring. However, little is known about its root development and overwintering memory mechanism. In this study, root collar tissues (including the shoot apical meristem) of three winter rapeseed varieties with different cold resistance, i.e., Longyou-7 (strong cold tolerance), Tianyou-4 (middle cold tolerance), and Lenox (cold-sensitive), were sampled in the pre-winter period (S1), overwintering periods (S2–S5), and re-greening stage (S6), and were used to identify the root development and overwintering memory mechanisms and seek candidate overwintering memory genes by measuring root collar diameter and RNA sequencing. The results showed that the S1–S2 stages were the significant developmental stages of the roots as root collar diameter increased slowly in the S3–S5 stages, and the roots developed fast in the strong cold resistance variety than in the weak cold resistance variety. Subsequently, the RNA-seq analysis revealed that a total of 37,905, 45,102, and 39,276 differentially expressed genes (DEGs), compared to the S1 stage, were identified in Longyou-7, Tianyou-4, and Lenox, respectively. The function enrichment analysis showed that most of the DEGs are significantly involved in phenylpropanoid biosynthesis, plant hormone signal transduction, MAPK signaling pathway, starch and sucrose metabolism, photosynthesis, amino sugar and nucleotide sugar metabolism, and spliceosome, ribosome, proteasome, and protein processing in endoplasmic reticulum pathways. Furthermore, the phenylpropanoid biosynthesis and plant hormone signal transduction pathways were related to the difference in root development of the three varieties, DEGs involved in photosynthesis and carbohydrate metabolism processes may participate in overwintering memory of Longyou-7 and Tianyou-4, and the spliceosome pathway may contribute to the super winter resistance of Longyou-7. The transcription factor enrichment analysis showed that the WRKY family made up the majority in different stages and may play an important regulatory role in root development and overwintering memory. These results provide a comprehensive insight into winter rapeseed's complex overwintering memory mechanisms. The identified candidate overwintering memory genes may also serve as important genetic resources for breeding to further improve the cold resistance of winter rapeseed.
Transcriptional response to VZV infection is modulated by RNA polymerase III in lung epithelial cell lines

Ancestral RNA polymerase III (Pol III) is a multi-subunit polymerase responsible for transcription of short non-coding RNA, such as double-stranded short interspersed nuclear elements (SINEs). Although SINE ncRNAs are generally transcriptionally repressed, they can be induced in response to viral infections and can stimulate immune signaling pathways. Indeed, mutations in RNA Pol III have been associated with poor antiviral interferon response following infection with varicella zoster virus (VZV). In this study, we probed the role of Pol III transcripts in the detection and initial immune response to VZV by characterizing the transcriptional response following VZV infection of wild type A549 lung epithelial cells as well as A549 cells lacking specific RNA sensors MAVS and TLR3, or interferon-stimulated genes RNase L and PKR in presence or absence of functional RNA Pol III. Multiple components of the antiviral sensing and interferon signaling pathways were involved in restricting VZV replication in lung epithelial cells thus suggesting an innate defense system with built-in redundancy. In addition, RNA Pol III silencing altered the antiviral transcriptional program indicating that it plays an essential role in the sensing of VZV infection.
The effects of lactic acid bacteria and molasses on microbial community and fermentation performance of mixed silage of king grass and cassava foliage

In the present study, we aim to investigate the effects of lactic acid bacteria (LAB) and molasses (M) on the microbial community and fermentation performance of mixed silage of king grass (KG) and cassava foliage (CF). A completely randomized design was used for the experiment. Mixed material was ensiled with no additive added (CK) for 60 days. Alternatively, mixed silage was supplemented with M, LAB (L), or M + LAB (ML) and then subjected to fermentation. Compared with the CK group, the contents of lactic acid and propionic acid in the L group were enhanced, whereas the content of acetic acid was reduced. Moreover, the levels of pH, butyric acid, and ammonia-N were not significantly changed. In contrast, the lower contents of pH, acetic acid, propionic acid, and butyric acid, as well as ammonia-N in the M and ML groups were observed, whereas the content of lactic acid was elevated. Additives could change the silage quality of mixed silage to different extents. The effect of the L treatment was not ideal, and the ML group had a better fermentation quality compared with the M group. In terms of microbial community, the relative abundance of desirable Lactobacillus was increased in the M, L, and ML groups. The relative abundance of Pseudomonas was decreased in the M and L groups. Compared with the CK group, the relative abundance of Stenotrophomonas was decreased, especially in the M (0.18%) and ML (0.19%) groups. For Paenibacillus, its relative abundance was increased in the ML group and more significantly increased in the M group. In summary, the combination of LAB and M at an equal ratio had a more positive effect on the fermentation quality and microbial community of mixed silage than LAB and M alone.
Innovating workplace learning: Training methodology analysis based on content, instructional design, programmed learning, and recommendation framework

The quality of sales processes is crucial in automotive and directly related to the firm’s competitive advantage and financial success. Sales training is the most prevalent intervention to guarantee quality and productivity. Extant literature has attempted to measure training effectiveness adequately, and the Context, Input, Process, and Product evaluation (CIPP) model has been a popular approach. This study endeavored to advance current literature and suggest a novel effectiveness framework, Content, Instructional design, Programmed learning, and Recommendation (CIP-R). The framework was applied to examine three different methodologies—traditional, pure digital, and hybrid training—collecting 583 instances from the automotive sales training conducted from 2019 to 2020 in South Korea. The findings advocate the importance of human elements, the role of efficacy, and self-determination in generating learning transferability, leading to performance in the digital age.
Porcine epidemic diarrhea virus strain FJzz1 infection induces type I/III IFNs production through RLRs and TLRs-mediated signaling

Interferons (IFNs) including type I/III IFNs are the major components of the host innate immune response against porcine epidemic diarrhea virus (PEDV) infection, and several viral proteins have been identified to antagonize type I/III IFNs productions through diverse strategies. However, the modulation of PEDV infection upon the activation of the host’s innate immune response has not been fully characterized. In this study, we observed that various IFN-stimulated genes (ISGs) were upregulated significantly in a time- and dose-dependent manner in LLC-PK1 cells infected with the PEDV G2 strain FJzz1. The transcriptions of IRF9 and STAT1 were increased markedly in the late stage of FJzz1 infection and the promotion of the phosphorylation and nuclear translocation of STAT1, implicating the activation of the JAK-STAT signaling pathway during FJzz1 infection. In addition, abundant type I/III IFNs were produced after FJzz1 infection. However, type I/III IFNs and ISGs decreased greatly in FJzz1-infected LLC-PK1 cells following the silencing of the RIG-I-like receptors (RLRs), including RIG-I and MDA5, and the Toll-like receptors (TLRs) adaptors, MyD88 and TRIF. Altogether, FJzz1 infection induces the production of type-I/III IFNs in LLC-PK1 cells, in which RLRs and TLRs signaling pathways are involved, followed by the activation of the JAK-STAT signaling cascade, triggering the production of numerous ISGs to exert antiviral effects of innate immunity.
Integrated management of charcoal rot disease in susceptible genotypes of mungbean with soil application of micronutrient zinc and green manure (prickly sesban)

Charcoal rot disease is incited by the soil-borne fungus Macrophomina phaseolina (Tassi). Goid is a challenging disease due to long-term persistence of fungus sclerotia in the soil. This study assessed the potential of zinc (Zn: 1.25, 2.44, and 5 mg/kg) and green manure (GM: 1 and 2%) in solitary and bilateral combinations to alleviate infection stress incited by M. phaseolina on disease, growth, physiology, and yield attributes in mungbean. A completely randomized design experiment was conducted in potted soil, artificially inoculated with the pathogen, and sown with surface-sterilized seeds of mungbean genotypes (susceptible: MNUYT-107 and highly susceptible: MNUYT-105). Concealment of plant resistance by M. phaseolina in both genotypes resulted in 53–55% disease incidence and 40–50% plant mortality, which contributed in causing a significant reduction of 30–90% in attributes of growth, biomass, yield, photosynthetic pigment, and total protein content with an imbalance of production of antioxidant enzymes (polyphenol oxidase, superoxide dismutase, catalase, and peroxidase). Soil application with Zn-based fertilizer (ZnSO4: 33%) in combination with GM significantly managed up to 80% of the charcoal rot disease, hence improving growth (50–100%) and physiochemical (30–100%) attributes and sustainably enhancing grain average yield (300–600%), biological yield (100–200%), and harvest index (100–200%) in mungbean plants. The heat map and principal component analyses based on 19 measured attributes with 16 treatments separated Zn (2.44 or 5 mg/kg) combined with 2% GM as the best treatments for alleviating charcoal rot disease stress by improving growth, yield, and biological attributes to an extent to profitable farming in terms of harvest index (HI) and benefit-cost ratio (BCR).
Identification of circulating immune landscape in ischemic stroke based on bioinformatics methods

Ischemic stroke (IS) is a high-incidence disease that seriously threatens human life and health. Neuroinflammation and immune responses are key players in the pathophysiological processes of IS. However, the underlying immune mechanisms are not fully understood. In this study, we attempted to identify several immune biomarkers associated with IS. We first retrospectively collected validated human IS immune-related genes (IS-IRGs) as seed genes. Afterward, potential IS-IRGs were discovered by applying random walk with restart on the PPI network and the permutation test as a screening strategy. Doing so, the validated and potential sets of IS-IRGs were merged together as an IS-IRG catalog. Two microarray profiles were subsequently used to explore the expression patterns of the IS-IRG catalog, and only IS-IRGs that were differentially expressed between IS patients and controls in both profiles were retained for biomarker selection by the Random Forest rankings. CLEC4D and CD163 were finally identified as immune biomarkers of IS, and a classification model was constructed and verified based on the weights of two biomarkers obtained from the Neural Network algorithm. Furthermore, the CIBERSORT algorithm helped us determine the proportions of circulating immune cells. Correlation analyses between IS immune biomarkers and immune cell proportions demonstrated that CLEC4D was strongly correlated with the proportion of neutrophils (r = 0.72). These results may provide potential targets for further studies on immuno-neuroprotection therapies against reperfusion injury.
The association between different hypoglycemic regimens and postoperative diabetic macular edema after vitrectomy in the Japanese patients with proliferative diabetic retinopathy

Purpose To study the association between different hypoglycemic regimens and postoperative diabetic macular edema (DME). Methods A secondary analysis based on a retrospective cohort study. Results In this secondary analysis, 124 eyes from patients with proliferative diabetic retinopathy (PDR) who underwent pars plana vitrectomy (PPV) between January 2008 and September 2012 were included. We found that compared with oral hypoglycemic medication, oral hypoglycemic medication plus insulin treatment revealed an insignificant relationship with postoperative DME (odds ratio [OR]=0.8, 95% confidence interval [CI]: 0.12-5.21, P=0.8167), only insulin treatment revealed a significant association with postoperative DME (OR=0.10, 95% CI: 0.01-0.84, P=0.0337) after adjusted age, sex. After adjusted age, sex, diabetes mellitus (DM) duration, glycosylated hemoglobin (HbA1c), the results did not have obvious changes (OR=0.61, 95% CI: 0.09-4.26, P=0.6187; OR=0.07, 95% CI: 0.01-0.65, P=0.0197). Furthermore, after adjusted age, sex, DM duration, HbA1c, hypertension, intraoperative retinal photocoagulation, vitreous hemorrhage, macular detachment, fibrovascular membrane, intraocular lens implantation and microincision vitrectomy surgery, the results were consistent (OR=0.66, 95% CI: 0.05-9.49, P=0.7621; OR=0.06, 95% CI: 0.00-0.81, P=0.0342). The same trend was observed in these adjusted models as well (p for trend was 0.0254, 0.0141, and 0.0311, respectively). Conclusion In conclusion, our results of the secondary analysis should be interpreted as a significant association between insulin treatment and reduced risks of postoperative DME in Japanese PDR patients with PPV surgery, compared with oral medications. Well glycemic control with longstanding insulin therapy may be beneficial to reduce the risks of postoperative DME in PDR patients. Our investigation calls for large-scale and long-term prospective clinical studies for a full evaluation of the exact role of insulin in the progression of postoperative DME.
On the investigation of an economic value for forest ecosystem services in the past 30 years: Lessons learnt and future insights from a North–South perspective

Since the publication of the Millennium Ecosystem Assessment, the research of ecosystem services valuation has seen an exponential growth with a consequent development, improvement, and spread of different qualitative and quantitative methods. The interest is due to the benefits that ecosystem services provide for human wellbeing. A large part of ecosystem services is provided by the so-called forest ecosystem services (FES) in both protected and non-protected areas. The aim of the present study is to investigate key variables driving the FES value at the global level. These include, other than socio-economic information, the ecosystem services' quality condition and the location of the study. The research uses a meta-regression of 478 observations from 57 studies in the time span 1992–2021 retrieved from the online Ecosystem Service Valuation Database (ESVD). The main results show that both the ES quality condition and spatial aspect are relevant factors in determining the estimated value of FES, suggesting the existence of a difference in the forest value from a North-South perspective. The investigation of an economic assessment of FES is advised as a key research trend in the immediate future. This allows to close the gap between the global North and South and favors the implementation of adequate socio-economic and environmental governance for an efficient forest management.
Mild reinfection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant: First case report from Indonesia

Background Reinfection with SARS-CoV-2 has been well documented, yet little is known about the degree of protection a previous infection provides against reinfection, especially against Variants of Concern (VOC). Case presentation Here we describe a case of an unvaccinated 49-year-old man who experienced two sequential SARS-CoV-2 infections with two different variants, as evidenced by genomic sequencing. The first episode was caused by the Pango lineage B.1. 466.2 and resulted in severe COVID-19 with 5 days in an intensive care unit (ICU). The second episode occurred approximately 6 months later, during the Delta surge in Indonesia. Genomic analysis showed that the second infection was caused by the Delta variant (Pango lineage B.1.617.2) and resulted in mild disease that did not require hospitalization. No SARS-CoV-2 nucleic acid was detected between the two episodes, but both binding and neutralizing antibodies to SARS-CoV-2 were detected prior to the reinfection, with the second infection leading to an increase in the levels of antibody. Conclusion We confirmed that the patient experienced a reinfection instead of persistent viral shedding from the first infection based on epidemiological, clinical, serological, and genomic analyses. Our case supports the hypothesis that SARS-CoV-2 reinfection may occur once antibody titers decrease or following the emergence of a new variant. The milder presentation in the patient’s second infection deserves further investigation to provide a clear picture of the role of post-infection immunity in altering the course of subsequent disease.
Contribution of Submicron Particles to the Unpolarized and Linearly Polarized Angular Scattering

The scattering by suspended particles is being measured with increasing frequency in the global oceans. Yet, little is known of size fractioned contribution, particularly from submicron particles and to the polarized scattering. In this study, three Mueller scattering matrix elements, P11, P12, and P22, for the bulk particles and for size fractions <0.2 μm and <0.7/0.8 μm were measured using a commercial instrument LISST-VSF in the North Pacific Ocean in 2018 (NPO-18) and in the North Atlantic Ocean in 2021 (NAO-21). We found that P11 and P12 by particles <0.2 μm each had median value that was very similar between the two sites, even though the variability was greater in the NAO-21 than in the NPO-18. Relatively, particles <0.2 µm accounted for the same fraction of total particle scattering in P11 and P12, approximately 20% at near surface water and 40–60% at deeper depths. In contrast, P11 and P12 by particles <0.7/0.8 μm differed between the two sites, which we found was because particles of sizes 0.25–1.0 µm had greater concentration in the NAO-21 than in the NPO-18. P22 normalized to P11 indicated that the sphericity of particles was the same between submicron and bulk particles in the NPO-18 site, but bulk particles deviated more from sphericity than submicron particles in the NAO-21 site where the experiment took place during a phytoplankton spring bloom. Simulations were conducted using three particle models including homogenous spheres, mix of homogenous/coated spheres, and homogenous asymmetric hexahedra to account for the effects of particle shapes or internal structures on the polarized scattering. Using the size distribution that was measured, each of the models can reproduce some of the scattering features measured in this study, but neither of them can reproduce all. Our results suggest that accurate simulation of the polarized scattering by oceanic particles needs to account for both their nonsphericity and heterogeneity, in addition to the concentration and size distribution of the particles.