Miracle-dz/UniFAR-FTUs huggingface dataset:
Native Plasmid-Encoded Mercury Resistance Genes Are Functional and Demonstrate Natural Transformation in Environmental Bacterial Isolates

Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments. ABSTRACT Plasmid-mediated horizontal gene transfer (HGT) is a major driver of genetic diversity in bacteria. We experimentally validated the function of a putative mercury resistance operon present on an abundant 8-kbp native plasmid found in groundwater samples without detectable levels of mercury. Phylogenetic analyses of the plasmid-encoded mercury reductases from the studied groundwater site show them to be distinct from those reported in proximal metal-contaminated sites. We synthesized the entire native plasmid and demonstrated that the plasmid was sufficient to confer functional mercury resistance in Escherichia coli. Given the possibility that natural transformation is a prevalent HGT mechanism in the low-cell-density environments of groundwaters, we also assayed bacterial strains from this environment for competence. We used the native plasmid-encoded metal resistance to design a screen and identified 17 strains positive for natural transformation. We selected 2 of the positive strains along with a model bacterium to fully confirm HGT via natural transformation. From an ecological perspective, the role of the native plasmid population in providing advantageous traits combined with the microbiome’s capacity to take up environmental DNA enables rapid adaptation to environmental stresses. IMPORTANCE Horizontal transfer of mobile genetic elements via natural transformation has been poorly understood in environmental microbes. Here, we confirm the functionality of a native plasmid-encoded mercury resistance operon in a model microbe and then query for the dissemination of this resistance trait via natural transformation into environmental bacterial isolates. We identified 17 strains including Gram-positive and Gram-negative bacteria to be naturally competent. These strains were able to successfully take up the plasmid DNA and obtain a clear growth advantage in the presence of mercury. Our study provides important insights into gene dissemination via natural transformation enabling rapid adaptation to dynamic stresses in groundwater environments.
How neurons move during action potentials

Neurons undergo nanometer-scale deformations during action potentials, and the underlying mechanism has been actively debated for decades. Previous observations were limited to a single spot or the cell boundary, while movement across the entire neuron during the action potential remained unclear. We report full-field imaging of cellular deformations accompanying the action potential in mammalian neuron somas (−1.8nm~1.3nm) and neurites (−0.7nm~0.9nm), using fast quantitative phase imaging with a temporal resolution of 0.1ms and an optical pathlength sensitivity of <4pm per pixel. Spike-triggered average, synchronized to electrical recording, demonstrates that the time course of the optical phase changes matches the dynamics of the electrical signal, with the optical signal revealing the intracellular potential rather than its time derivative detected via extracellular electrodes. Using 3D cellular morphology extracted via confocal microscopy, we demonstrate that the voltage-dependent changes in the membrane tension induced by ionic repulsion can explain the magnitude, time course and spatial features of the phase imaging. Our full-field observations of the spike-induced deformations in mammalian neurons opens the door to non-invasive label-free imaging of neural signaling.
Communities at the extreme: Aquatic food webs in desert landscapes

Abstract Studying food webs across contrasting abiotic conditions is an important tool in understanding how environmental variability impacts community structure and ecosystem dynamics. The study of extreme environments provides insight into community‐wide level responses to environmental pressures with relevance to the future management of aquatic ecosystems. In the western Lake Eyre Basin of arid Australia, there are two characteristic and contrasting aquatic habitats: springs and rivers. Permanent isolated Great Artesian Basin springs represent hydrologically persistent environments in an arid desert landscape. In contrast, hydrologically variable river waterholes are ephemeral in space and time. We comprehensively sampled aquatic assemblages in contrasting ecosystem types to assess patterns in community composition and to quantify food web attributes with stable isotopes. Springs and rivers were found to have markedly different invertebrate communities, with rivers dominated by more dispersive species and springs associated with species that show high local endemism. Qualitative assessment of basal resources shows autochthonous carbon appears to be a key basal resource in both types of habitat, although the particular sources differed between habitats. Food‐web variables such as trophic length, trophic breadth, and community isotopic niche size were relatively similar in the two habitat types. The basis for the similarity in food‐web structure despite differences in community composition appears to be broader isotopic niches for predatory invertebrates and fish in springs as compared with rivers. In contrast to published theory, our findings suggest that the food webs of the hydrologically variable river sites may show less dietary generalization and more compact food‐web modules than in springs.
Let-7f-5p regulates TGFBR1 in glucocorticoid-inhibited osteoblast differentiation and ameliorates glucocorticoid-induced bone loss

Previous studies indicated that let-7 enhances osteogenesis and bone formation of human adipose-derived mesenchymal stem cells (MSCs). We also have confirmed that let-7f-5p expression was upregulated during osteoblast differentiation in rat bone marrow-derived MSCs (BMSCs) and was downregulated in the vertebrae of patients with glucocorticoid (GC)-induced osteoporosis (GIOP). The study was performed to determine the role of let-7f-5p in GC-inhibited osteogenic differentiation of murine BMSCs in vitro and in GIOP in vivo. Here, we report that dexamethasone (Dex) inhibited osteogenic differentiation of BMSCs and let-7f-5p expression, while increasing the expression of transforming growth factor beta receptor 1 (TGFBR1), a direct target of let-7f-5p during osteoblast differentiation under Dex conditions. In addition, let-7f-5p promoted osteogenic differentiation of BMSCs, as indicated by the promotion of alkaline phosphatase (ALP) staining and activity, Von Kossa staining, and osteogenic marker expression (Runx2,Osx, Alp, and Ocn), but decreased TGFBR1 expression in the presence of Dex. However, overexpression of TGFBR1 reversed the upregulation of let-7f-5p during Dex-treated osteoblast differentiation. Knockdown of TGFBR1 reversed the effect of let-7f-5p downregulation during Dex-treated osteogenic differentiation of BMSCs. We also found that glucocorticoid receptor (GR) mediated transcriptional silencing of let-7f-5p and its knockdown enhanced Dex-inhibited osteogenic differentiation. Further, when injected in vivo, agomiR-let-7f-5p significantly reversed bone loss induced by Dex, as well as increased osteogenic marker expression (Runx2, Osx, Alp, and Ocn) and decreased TGFBR1 expression in bone extracts. These findings indicated that the regulatory axis of GR/let-7f-5p/TGFBR1 may be important for Dex-inhibited osteoblast differentiation and that let-7f-5p may be a useful therapeutic target for GIOP.
Prediction of best features in heterogeneous Lung adenocarcinoma samples using Least Absolute Shrinking and Selection Operator

This study aims to create a tumor heterogeneity-based model for predicting the best features of lung adenocarcinoma (LUAD) in multiple cancer subtypes using the Least Absolute Shrinking and Selection Operator (LASSO). The RNA-Seq raw count data of 533 LUAD samples and 59 normal samples were downloaded from the TCGA data portal. Based on consensus clustering method samples was divided into two subtypes, and clusters were validated using silhouette width. Furthermore, we estimated subtypes for the abundance of immune and non-immune stromal cell populations which infiltrated cancer tissue. We established the LASSO model for predicting each subtype’s best features. Enrichment pathway analysis was then carried out. Finally, the validity of the LASSO model for identifying features was established by the survival analysis. Our study suggests that the unsupervised clustering and Machine learning methods such as LASSO model-based feature selection can be effectively used to predict relevant genes which might play an essential role in cancer diagnosis.
Vermiculated sailfin catfish, Pterygoplichthys disjunctivus (Actinopterygii: Siluriformes: Loricariidae): Invasion, biology, and initial impacts in East Kolkata Wetlands, India

Background. The East Kolkata Wetlands in India (a Ramsar site) are sewage-fed, nutrient-rich water bodies successfully used for fish production. The vermiculated sailfin catfish, Pterygoplichthys disjunctivus (Weber, 1991), exotic to India, has invaded these wetlands. The management and control of this catfish has been hindered, because of the lack of information on its abundance, population structure, biological traits, level of establishment, and competition with native fish species. Materials and methods. Within 2013–2015 studies were carried out on the population structure of P. disjunctivus, its food habits, reproductive biology, and initial impacts in the wetlands through monthly and seasonal collection of samples, examination of food items, reproductive parameters, catch data, and gathering fishers experience. Results. The length (TL) and weight of the specimens ranged from 10 to 55 cm and from 120 to 1250 g, respectively. Major food items of the catfish were detrital matter (%IRI 56), unidentified plant matter (%IRI 11), fish eggs (%IRI 11), polychaete worms (%IRI 5), and other minor items (%IRI 0.3 to 4). At 50% similarity, the food items of P. disjunctivus overlapped with that of Macrognathus pancalus, Channa punctata, Nandus nandus, Anabas testudineus, Clarias batrachus, Oreochromis niloticus, Cirrhinus mrigala, and Cyprinus carpio while at 80% it overlapped with that of C. mrigala and C. carpio. The fecundity of P. disjunctivus, in the wetlands, was the highest recorded for the species. Females attained the first maturity at 24 cm TL and reproduced multiple times within July–November. The breeding period of the species overlapped with 13 native fish species, of which it seriously overlapped with that of Gudusia chapra, Amblypharyngodon mola, Pethia conchonius, P. ticto, N. nandus, C. punctata, and A. testudineus. The sailfin catfish has established reproducing populations in the wetlands and reached ‘invasive’ proportions constituting 4.83% (300.04 t · year–1) of the mean annual fish catch (6203.85 t · year–1) from the wetlands. The invasive risk assessment showed a high risk of the species in the current scenario and probable climate change scenarios in future in the region. Conclusions. Pterygoplichthys disjunctivus has successfully colonized the sensitive East Kolkata Wetlands, which might easily spread to neighbouring water bodies including the sensitive Ganga River and Sundarban mangroves and cause ecological and economic disturbance unless preventive measures are taken as the species has high invasive risk in the region.
Chlorophyll α Fluorescence Parameters as an Indicator to Identify Drought Susceptibility in Common Bush Bean

The common bean is susceptible to drought conditions and the evaluation of plant responses to low water availability can be difficult. The quantification of chlorophyll fluorescence as a sensitive trait to environmental stresses is an important alternative in the characterization of drought-susceptible genotypes. The objective of this study was to evaluate mainly the use of chlorophyll α fluorescence (maximum efficiency of PSII (Fv/Fm), photochemical quenching (qP), non-photochemical quenching (NPQ)) and rapid light-response curves (RLCs) (initial slope of the curve (α), minimum saturation irradiance (Ik) and maximum relative electron transport rate (ETRmax)) parameters as tools for the identification of susceptible or tolerant bush bean cultivars to water deficit stress conditions in two different phenological stages. Using a randomized block design in a factorial arrangement, five bush bean cultivars (Cerinza, Bachue, NUA35, Bacata and Bianca) were evaluated under water deficit conditions by the suspension of irrigation for 15 days from 40 to 55 Days after Emergence (DAE) (vegetative stage) or 50 to 65 DAE (reproductive stage). The results showed that Fv/Fm and NPQ recorded the highest variation due to water deficit conditions, especially in the vegetative stage. The greatest reductions in Fv/Fm (0.67) and NPQ (0.71) were evidenced in cultivar NUA35 compared to its control plants (0.78 and 1.07, respectively). The parameters obtained from RLCs showed that cultivar Bacata registered the lowest α (0.17) and Ik (838.19 μmol∙m−2∙s−1) values compared to its control plants (α 0.23; Ik 769.99 μmol∙m−2∙s−1). Differences were only obtained in ETRmax in the reproductive stage (50–65 DAE) in which cultivar NUA35 reached values of 158.5 in stressed plants compared to control plants (251.22). In conclusion, the parameters derived from RLCs such as α and Ik can be used as tools to identify drought susceptibility in the vegetative stage, whereas ETRmax can be used in the reproductive stage. In addition, PSII photochemistry (Fv/Fm and NPQ) can also help to understand the agronomic responses of common bush bean cultivars to drought conditions.
Monitoring public awareness about the endangered northern bald ibis: a case study involving primary school children as citizen scientists

Background Citizen science has evolved over the past decades by motivating members of the public to interact with scientists and actively participate in scientific research and monitoring. For this purpose, a proficient communication is mandatory in order to efficiently convey messages and reduce the gap of knowledge between scientists and lay people. In the present study, we aimed at evaluating the multiplying effect of children, who were trained to communicate their knowledge on an endangered bird species in order to engage the local community in the long-term ornithological monitoring of the free flying and individually marked colony of northern bald ibis (NBI, Geronticus eremita), which was established at the research station in 1997. Methods Pupils of the local primary schools were in regular contact with researchers, enjoyed outdoor encounters with the birds, and were invited to talk about their experience with as many people as possible. Later on, they acted as surveyors to assess the knowledge of the public on (i) the general knowledge about the species, (ii) specific knowledge about the local colony, and (iii) attitudes towards science. In two different years of evaluation (2012 and 2016) a total number of 387 persons were surveyed. The questions were generated together with the pupils and their teachers and the questionnaires were similar for both years of evaluation. All queries were in a closed format. Results Our results show an increase in the proportion of correct answers provided by the surveyed persons between the two years of evaluation. Education-based activities may encourage children to effectively act as multipliers of information and attitudes. This has the potential to induce sustainable changes with respect to attitude towards science, at least among local communities. Furthermore, the study suggests caution with the quality of some information reported by citizen scientists, which might be solved by more careful training actions and more specific information about local particularities. Even though the study would have gained more informative power with some additional precautions than in its current form, our findings recommend the empowerment of pupils as multipliers of scientific knowledge.
Nutrient Profile and In vitro Degradability of New Promising Mutant Lines Sorghum as Forage in Indonesia

| G5 and G8 are two sorghum mutant lines projected as special sorghum varieties for forage in Indonesia. The objective of this research was to investigate the nutrient profile and in vitro gas production characteristics from two sorghum mutant lines as forage for ruminants. The two mutant lines were compared with Numbu and Pahat variety. Nutients and in vitro digestibility studies were also investigated at different generative phase. This research was arranged into a randomized block design with two factors. The first factor was the variety/mutant lines of sorghum. The second factor was the generative phase (flowering, soft dough and hard dough). Variables measured were nutrients profile, in vitro gas production and rumen fermentation products. Results showed that G5 at hard dough phase produced the highest stem sugar content (P<0.01). The highest potential in vitro gas production (a+b) was found at G5 mutant lines at hard dough stage (P<0.01). Pahat and G5 at hard dough phase had the highest in vitro true digestibility (IVTD) with 54.48 and 54.61% repectively. The highest total volatile fatty acids (TVFA) was found at G5 and G8 mutant lines at hard dough stage (P<0.01). Meanwhile, the best CO2:CH4 ratio was produced by Pahat, G5 and G8 (P<0.01). Based on those findings, it can be concluded that G5 mutant lines had higher quality of nutrients profile, potential in vitro gas production and IVTD. Increasing generative phase also could increase in vitro digestibility for all varieties/ mutant lines.
Biopreservation of meat using the essential oil from Hyptis suaveolens Poit. (Lamiaceae) in Burkina Faso

Essential oils are natural substances which can be used as natural conservators for foods. The present work aimed to evaluate biological properties of essential oil of Hyptis suaveolens and its effect on shelf-life of beef. The extraction was carried out by hydro-distillation. Antioxidant activity was determined by method of DPPH and FRAP. Antimicrobial activity was determined by the microdilution and agar diffusion methods. The sensitivity of eleven pathogen microbial strains was tested. The conservation test of ground meat using essential oil was carried out by monitoring the evolution of the microbial groups. Result showed that extraction yield of essential oil was 0.21% (m/v). The DPPH assay gave IC50 of 16.367 ± 0.0739 µL and was confirmed by the FRAP assay. The essential oil from H. suaveolens showed inhibitory activity on microbial strains. Biopreservation assay revealed a significant decrease of microbial charge during conservation time. Thus essential oil was successful in vitro and its activity on prolonging shelf-life of beef was found to be 7 days. The results of the present study demonstrated the possibility of essential oil from H. suaveolens to be used as natural conservator for food industry. Key words: Hyptis suaveolens, essential oil, biopreservation, biological properties, meat.
Short-Term Efficacy and Safety of IL-17, IL-12/23, and IL-23 Inhibitors Brodalumab, Secukinumab, Ixekizumab, Ustekinumab, Guselkumab, Tildrakizumab, and Risankizumab for the Treatment of Moderate to Severe Plaque Psoriasis: A Systematic Review and Network Meta-Analysis of Randomized Controlled Trial

Background The role of interleukin-12 (IL-12), interleukin-23 (IL-23), and interleukin-17 (IL-17) has been recognized in psoriasis pathogenesis, and new drugs targeting this axis have already been developed which may provide a new therapeutic approach for patients with moderate to severe psoriasis. Objective To compare the direct and indirect evidences of the efficacy and safety of brodalumab, secukinumab, ixekizumab, ustekinumab, guselkumab, tildrakizumab, and risankizumab in the short-term treatment of moderate to severe plaque psoriasis using network meta-analysis (NMA). Methods A comprehensive literature search was performed in PubMed, EMBASE, and Cochrane Central Register of Controlled Trials for the available relevant studies. NMA was conducted by Stata 15.0 software using relative risks (RR) with 95% confidence interval to assess the clinical effectiveness and safety. Ranked the efficacy and safety for each drug accordance with the surface under the cumulative ranking curve (SUCRA). Results This meta-analysis included 28 studies. All the interventions performed better than placebo in short-term achievement. Based on the result of SUCRA, ixekizumab 80 mg every 2 weeks ranked the highest in short-term achievement of PASI 75 (SUCRA = 93.0%). Brodalumab 210 mg ranked the highest in short-term achievement of PASI 100 (SUCRA = 85.0%). Secukinumab 300 mg ranked the highest in short-term achievement of sPGA 0/1 or IGA 0/1 or PGA 0/1 (SUCRA = 98.1%). In terms of having a risk of adverse events, the rates were higher in brodalumab, secukinumab, ixekizumab, and ustekinumab 45 mg compared with placebo. Ixekizumab 80 mg every 4 weeks ranked the highest in the risk of adverse events during short-term treatment (SUCRA = 4.5%). Guselkumab 50 mg ranked the highest in the risk of serious adverse events during short-term treatment (SUCRA = 25.9%). Ixekizumab 80 mg every 4 weeks ranked the highest in the risk of discontinuations due to adverse events during short-ter treatment (SUCRA = 10.7%). Conclusions IL-17, IL-12/23, and IL-23 inhibitors had high efficacy in the achievement of PASI 75, PASI 100, and sPGA 0/1 or IGA 0/1 or PGA 0/1 in moderate to severe plaque psoriasis after 12 or 16 weeks of treatment. IL-17 inhibitors showed superior efficacy. However, its clinical safety was poor. Risankizumab appeared to have relatively high efficacy and low risk. The clinical tolerance of other biological agents needs to be further observed.
The complete chloroplast genome of agarwood producing species, Aquilaria sinensis (Lour.) Gilg: a species on IUCN red list

Abstract The entire chloroplast genome of Aquilaria sinensis (Lour.) Gilg was identified as a circular molecule of 174,885 bp length with a typical tetrad structure, including a pair of inverted repeats (42,103 bp each), a large single copy (87,331 bp) and a small single copy (3,348 bp) regions. The A. sinensis cp genome encoded 8 rRNAs, 39 tRNAs, and 90 proteins. A phylogenetic tree was reconstructed using the 43 protein-coding genes of eight Thymelaeaceae. Two other Malvales, Abelmoschus esculentus and Durio zibethinus, were selected as the outgroup. Our phylogenetic analysis suggests that the five examined species of Aquilaria appeared a monophyletic group with robust support.
Comparison of the cuticular profiles of several dung beetles used as host carriers by the phoretic mite Macrocheles saceri (Acari: Mesostigmata)

Macrochelid mites have developed phoretic interactions with coprophilous arthropods in order to disperse and colonize new substrate. Macrocheles saceri (Acari: Mesostigmata) is a mite phoretically specialized on the dung beetles of the Scarabaeus genus. A previous study has demonstrated that M. saceri can discriminate among available hosts and showed host preferences using the host cuticular material. In this present study, we have compared the cuticular chemicals including the volatiles present among several species of Scarabaeus and Bubas genera. By comparing the host chemical profiles to the host preferences, several hypotheses regarding the role of some of these volatile chemicals in host discrimination based on attractiveness and repellency, are proposed.