Miracle-dz/UniFAR-FTUs huggingface dataset:
Divergent assembly trajectories: a comparison of the plant and soil microbiome with plant communities in a glacier forefield

Community assembly is a result of dispersal, abiotic and biotic characteristics of the habitat as well as stochasticity. A direct comparison between the assembly of microbial and ‘macrobial’ organisms is hampered by the sampling of these communities in different studies, at different sites, or on different scales. In a glacier forefield in the Austrian Alps, we recorded the soil and plant microbiome (bacteria and fungi) and plants that occurred in the same landscape and in close proximity in the same plots. We tested five predictions deduced from assembly processes and revealed deviating patterns of assembly in these community types. In short, microbes appeared to be less dispersal limited than plants, soil microbes and plants strongly responded to abiotic factors whereas the leaf microbiome was plant species-specific and well buffered from environmental conditions. The observed differences in community assembly processes may be attributed to the organisms’ dispersal abilities, the exposure of the habitats to airborne propagules, and habitat characteristics. The finding that assembly is conditional to the characteristics of the organisms, the habitat, and the spatial scale under consideration is thus central for our understanding about the establishment and the maintenance of biodiversity.
Temporal regulation of Pten is essential for retina regeneration in zebrafish

Unlike mammals, zebrafish possess a remarkable ability to regenerate damaged retina after an acute injury. Retina regeneration in zebrafish involves the induction of Müller glia-derived progenitor cells (MGPCs) exhibiting stem cell-like characteristics, which are capable of restoring all retinal cell-types. Here, we explored the importance of Phosphatase and tensin homolog (Pten), a dual-specificity phosphatase and tumor suppressor during retina regeneration. The Pten undergo rapid downregulation in the Müller glia and is absent in MGPCs, which is essential to trigger Akt-mediated cell proliferation to cause retina regeneration. We found that the forced downregulation of Pten accelerates MGPCs formation, while its overexpression restricts the regenerative response. We observed that Pten regulates the proliferation of MGPCs not only through Akt pathway but also by Mmp9/Notch signaling. Mmp9-activity is essential to induce the proliferation of MGPCs in the absence of Pten. Lastly, we show that Pten expression is fine-tuned through Mycb/histone deacetylase1 and Tgf-β signaling. The present study emphasizes on the stringent regulation of Pten and its crucial involvement during the zebrafish retina regeneration.
Homology Modelling, In Silico Prediction And Characterization Of Cytochrome c oxidase In Cyprinus carpio And Tubifex tubifex And Molecular Docking Studies Between The Modelled Protein And Three Commonly Used Surfactants Sodium Dodecyl Sulphate, Cetylpyridinium Chloride And Sodium Laureth Sulphate

The purpose of this work is to evaluate the homology modeling, in silico prediction, and characterisation of Cytochrome c oxidase from Cyprinus carpio and Tubifex tubifex, as well as molecular docking experiments between the modelled protein and three frequently used surfactants. Using the template crystal structure of bovine heart Cytochrome c oxidase, homology modeling of Cytochrome c oxidase (Subunit 2) of Cyprinus carpio (Accession # P24985) and Cytochrome c oxidase (Subunit 1) of Tubifex tubifex (Accession # Q7YAA6) was conducted. The model structure was improved further with 3Drefine, and the final 3D structure was verified with PROCHEK and ERRATA. The physiochemical, as well as the stereochemical parameters of the modelled protein, were evaluated using various tools like ExPASy’s ProtParam, Hydropathy Analysis and EMBOSS pepwheel. The projected model was then docked with toxic ligands, Sodium dodecyl sulfate (SDS), Cetylpyridinium chloride (CPC), and Sodium laureth sulfate (SLES), whose 3D structures were obtained from the Uniprot database. CPC interacted best with Cytochrome c oxidase subunit 2 of Cyprinus carpio and Cytochrome c oxidase subunit 1 of Tubifex tubifex, according to our findings. Furthermore, in the case of all surfactants, hydrophobic interactions with the active site amino acid residues of the modelled protein were observed to be more common than hydrogen bonds and salt bridges. Molecular simulation studies exhibited that the surfactants alter the structural flexibility of the predicted proteins. Hence it may be inferred that the surfactants might alter the structure and dynamics of Cytochrome c oxidase of both worm and fish.
Borgs are giant extrachromosomal elements with the potential to augment methane oxidation

Anaerobic methane oxidation exerts a key control on greenhouse gas emissions 1, yet factors that modulate the activity of microorganisms performing this function remain little explored. In studying groundwater, sediments, and wetland soil where methane production and oxidation occur, we discovered extraordinarily large, diverse DNA sequences that primarily encode hypothetical proteins. Four curated, complete genomes are linear, up to ~1 Mbp in length and share genome organization, including replicore structure, long inverted terminal repeats, and genome-wide unique perfect tandem direct repeats that are intergenic or generate amino acid repeats. We infer that these are a new type of archaeal extrachromosomal element with a distinct evolutionary origin. Gene sequence similarity, phylogeny, and local divergence of sequence composition indicate that many of their genes were assimilated from methane-oxidizing Methanoperedens archaea. We refer to these elements as “Borgs”. We identified at least 19 different Borg types coexisting with Methanoperedens in four distinct ecosystems. Borg genes expand redox and respiratory capacity (e.g., clusters of multiheme cytochromes), ability to respond to changing environmental conditions, and likely augment Methanoperedens capacity for methane oxidation (e.g., methyl coenzyme M reductase). By this process, Borgs could play a previously unrecognized role in controlling greenhouse gas emissions.
Two-Stream Dense Feature Fusion Network Based on RGB-D Data for the Real-Time Prediction of Weed Aboveground Fresh Weight in a Field Environment

The aboveground fresh weight of weeds is an important indicator that reflects their biomass and physiological activity and directly affects the criteria for determining the amount of herbicides to apply. In precision agriculture, the development of models that can accurately locate weeds and predict their fresh weight can provide visual support for accurate, variable herbicide application in real time. In this work, we develop a two-stream dense feature fusion convolutional network model based on RGB-D data for the real-time prediction of the fresh weight of weeds. A data collection method is developed for the compilation and production of RGB-D data sets. The acquired images undergo data enhancement, and a depth transformation data enhancement method suitable for depth data is proposed. The main idea behind the approach in this study is to use the YOLO-V4 model to locate weeds and use the two-stream dense feature fusion network to predict their aboveground fresh weight. In the two-stream dense feature fusion network, DenseNet and NiN methods are used to construct a Dense-NiN-Block structure for deep feature extraction and fusion. The Dense-NiN-Block module was embedded in five convolutional neural networks for comparison, and the best results were achieved with DenseNet201. The test results show that the predictive ability of the convolutional network using RGB-D as the input is better than that of the network using RGB as the input without the Dense-NiN-Block module. The mAP of the proposed network is 75.34% (IoU value of 0.5), the IoU is 86.36%, the detection speed of the fastest model with a RTX2080Ti NVIDIA graphics card is 17.8 fps, and the average relative error is approximately 4%. The model proposed in this paper can provide visual technical support for precise, variable herbicide application. The model can also provide a reference method for the non-destructive prediction of crop fresh weight in the field and can contribute to crop breeding and genetic improvement.
Mapping Croplands in the Granary of the Tibetan Plateau Using All Available Landsat Imagery, A Phenology-Based Approach, and Google Earth Engine

The Tibetan Plateau (TP), known as “The Roof of World”, has expansive alpine grasslands and is a hotspot for climate change studies. However, cropland expansion and increasing anthropogenic activities have been poorly documented, let alone the effects of agricultural activities on food security and environmental change in the TP. The existing cropland mapping products do not depict the spatiotemporal characteristics of the TP due to low accuracies and inconsistent cropland distribution, which is affected by complicated topography and impedes our understanding of cropland expansion and its associated environmental impacts. One of the biggest challenges of cropland mapping in the TP is the diverse crop phenology across a wide range of elevations. To decrease the classification errors due to elevational differences in crop phenology, we developed two pixel- and phenology-based algorithms to map croplands using Landsat imagery and the Google Earth Engine platform along the Brahmaputra River and its two tributaries (BRTT) in the Tibet Autonomous Region, also known as the granary of TP, in 2015–2019. Our first phenology-based cropland mapping algorithm (PCM1) used different thresholds of land surface water index (LSWI) by considering varied crop phenology along different elevations. The second algorithm (PCM2) further offsets the phenological discrepancy along elevational gradients by considering the length and peak of the growing season. We found that PCM2 had a higher accuracy with fewer images compared with PCM1. The number of images for PCM2 was 279 less than PCM1, and the Matthews correlation coefficient for PCM2 was 0.036 higher than PCM1. We also found that the cropland area in BRTT was estimated to be 1979 ± 52 km2 in the late 2010s. Croplands were mainly distributed in the BRTT basins with elevations of 3800–4000 m asl. Our phenology-based methods were effective for mapping croplands in mountainous areas. The spatially explicit information on cropland area and distribution in the TP aid future research into the effects of cropland expansion on food security and environmental change in the TP.
Deep Learning Based Approach for Secure Web of Things (WoT)

Internet of Things (IoT) includes smart devices that are connected through a common network, in order to increase the potential of these smart devices, the concept of the Web of things (WoT) has been introduced. The main aim of WoT is to connect all the smart devices through the internet so that they can share the services and resources globally. But this increase in connectivity makes the devices vulnerable to different types of cyber-attacks. Different types of cyber-attacks like DDoS attacks, DoS attacks, etc., affect the normal operation of smart devices and leak private information, so detection and prevention of cyber-attacks in the WoT is an important research issue. In this paper, we proposed a Deep-learning-based approach for the detection of different cyber attacks like DoS, U2R, R2L in the WoTs. We used the KDDCUP99 dataset for training and testing purposes and achieved an accuracy of 99.73%. We also compared our proposed approach with other machine learning approaches and check its effectiveness.
Factors Associated With Uptake of Iron Supplement During Pregnancy Among Women of Reproductive Age in Tanzania: an Analysis of Data From the 2015 to 2016 Tanzania Demographic and Health Survey and Malaria Indicators Survey

Background: Pregnant women are vulnerable to iron deficiency due to the fact that more iron is needed primarily to supply the growing fetus and placenta and to increase the maternal red cell mass. Little is known on the factors associated with uptake of iron supplement during pregnancy. Methods: The study used data from the 2015 to 2016 Tanzania Demographic and Health Survey and Malaria Indicators Survey. A total of 6,924 women of active reproductive age from 15 to 49 were included in the analysis. Both univariate and multiple regression analyses were used to determine factors associated with uptake of iron supplement during pregnancy. Results: Majority of the interviewed women 5,648 (81.6%) always took iron supplement during pregnancy, while a total of 1,276 (18.4%) women never took iron supplement during pregnancy. After controlling for confounders, the predictors for uptake of iron supplement during pregnancy were early antenatal booking (adjusted odds ratio, AOR = 1.603 at 95% CI = 1.362–1.887, p < 0.001); rural residence (AOR = 0.711 at 95% CI = 0.159–0.526, p = 0.007); wealth index [rich (AOR = 1.188 at 95% CI = 0.986–1.432, p = 0.07)]—poor was the reference population; level of education [primary education (AOR = 1.187 at 95% CI = 1.013–1.391, p = 0.034)]—no formal education was the reference population; parity [para 2 to 4 (AOR = 0.807 at 95% CI = 0.668–0.974, p = 0.026), para 5 and above (AOR = 0.75 at 95% CI = 0.592–0.95, p = 0.017)], para 1 was the reference population; zones [mainland rural (AOR = 0.593 at 95% CI = 0.389–0.905, p = 0.015) and Unguja Island AOR = 0.63 at 95% CI = 0.431–0.92, p = 0.017]—mainland urban was the reference population; and current working status [working (AOR = 0.807 at 95% CI = 0.687–0.949, p = 0.009)]. Conclusion: The study revealed that, despite free access to iron supplement during pregnancy, there are women who fail to access the supplement at least once throughout the pregnancy. The likelihood to fail to access iron supplement during pregnancy was common among pregnant women who initiated antenatal visits late, were from poor families, had no formal education, reside in rural settings, had high parity, were from mainland rural, and were in working status. Interventional studies are recommended in order to come up with effective strategies to increase the uptake of iron supplement during pregnancy.
Enhanced Placental Mitochondrial Respiration in Tibetan Women at High Altitude

Living at high altitudes is extremely challenging as it entails exposure to hypoxia, low temperatures, and high levels of UV radiation. However, the Tibetan population has adapted to such conditions on both a physiological and genetic level over 30,000–40,000 years. It has long been speculated that fetal growth restriction is caused by abnormal placental development. We previously demonstrated that placentas from high-altitude Tibetans were protected from oxidative stress induced by labor compared to those of European descent. However, little is known about how placental mitochondria change during high-altitude adaptation. In this study, we aimed to uncover the mechanism of such adaptation by studying the respiratory function of the placental mitochondria of high-altitude Tibetans, lower-altitude Tibetans, and lower-altitude Chinese Han. We discovered that mitochondrial respiration was greater in high-altitude than in lower-altitude Tibetans in terms of OXPHOS via complexes I and I+II, ETSmax capacity, and non-phosphorylating respiration, whereas non-ETS respiration, LEAK/ETS, and OXPHOS via complex IV did not differ. Respiration in lower-altitude Tibetans and Han was similar for all tested respiratory states. Placentas from high-altitude Tibetan women were protected from acute ischemic/hypoxic insult induced by labor, and increased mitochondrial respiration may represent an acute response that induces mitochondrial adaptations.
Editorial: Somatosensory Integration in Human Movement: Perspectives for Neuromechanics, Modelling and Rehabilitation

1 Institute for Modelling and Simulation of Biomechanical Systems, Chair for Continuum Biomechanics and Mechanobiology, University of Stuttgart, Stuttgart, Germany, 2 SimTech Cluster of Excellence “Data Integrated Simulation Science” EXT 2075, University of Stuttgart, Stuttgart, Germany, Department of Electrical Engineering and Automation, Aalto University, Espoo, Finland, Department of Biomechanical Engineering, University of Twente, AE Enschede, Netherlands, 5 School of Electrical
Australian Fires 2019–2020: Tropospheric and Stratospheric Pollution Throughout the Whole Fire Season

The historically large and severe wildfires in Australia from September 2019 to March 2020 are known to have injected a smoke plume into the stratosphere around New Year, due to pyro-cumulonimbus (pyro-Cb) activity, that was subsequently distributed throughout the Southern Hemisphere (SH). We show with satellite, ground based remote sensing, and in situ observations that the fires before New Year, had already a substantial impact on the SH atmosphere, starting as early as September 2019, with subsequent long-range transport of trace gas plumes in the upper-troposphere. Airborne in situ measurements above Southern Argentina in November 2019 show elevated CO mixing ratios at an altitude of 11 km and can be traced back using FLEXPART trajectories to the Australian fires in mid-November 2019. Ground based solar-FTS (Fourier Transform Spectroscopy) observations of biomass burning tracers CO, HCN and C2H6 at Lauder, South Island, New Zealand show enhanced tropospheric columns already starting in September 2019. In MLS observations averaged over 30°–60°S, enhanced CO mixing ratios compared to previous years become visible in late October 2019 only at and below the 147 hPa pressure level. Peak differences are found with satellite and ground-based observations for all altitude levels in the Southern Hemisphere in January. With still increased aerosol values following the Ulawun eruption in 2019, averaged satellite observations show no clear stratospheric and upper-tropospheric aerosol enhancements from the Australian fires, before the pyro-Cb events at the end of December 2019. However, with the clear enhancement of fire tracers, we suggest the period September to December 2019 (prior to the major pyro-Cb events) should be taken into account in terms of fire pollutant emissions when studying the impact of the Australian fires on the SH atmosphere.
Carbohydrate-Binding Module and Linker Allow Cold Adaptation and Salt Tolerance of Maltopentaose-Forming Amylase From Marine Bacterium Saccharophagus degradans 2-40T

Marine extremophiles produce cold-adapted and/or salt-tolerant enzymes to survive in harsh conditions. These enzymes are naturally evolved with unique structural features that confer a high level of flexibility, solubility and substrate-binding ability compared to mesophilic and thermostable homologs. Here, we identified and characterized an amylase, SdG5A, from the marine bacterium Saccharophagus degradans 2-40T. We expressed the protein in Bacillus subtilis and found that the purified SdG5A enabled highly specific production of maltopentaose, an important health-promoting food and nutrition component. Notably, SdG5A exhibited outstanding cold adaptation and salt tolerance, retaining approximately 30 and 70% of its maximum activity at 4°C and in 3 M NaCl, respectively. It converted 68 and 83% of starch into maltooligosaccharides at 4 and 25°C, respectively, within 24 h, with 79% of the yield being the maltopentaose. By analyzing the structure of SdG5A, we found that the C-terminal carbohydrate-binding module (CBM) coupled with an extended linker, displayed a relatively high negative charge density and superior conformational flexibility compared to the whole protein and the catalytic domain. Consistent with our bioinformatics analysis, truncation of the linker-CBM region resulted in a significant loss in activities at low temperature and high salt concentration. This highlights the linker-CBM acting as the critical component for the protein to carry out its activity in biologically unfavorable condition. Together, our study indicated that these unique properties of SdG5A have great potential for both basic research and industrial applications in food, biology, and medical and pharmaceutical fields.
Evidence for Persistent Heteroplasmy and Ancient Recombination in the Mitochondrial Genomes of the Edible Yellow Chanterelles From Southwestern China and Europe

Mitochondrial genes and genomes have patterns of inheritance that are distinctly different from those of nuclear genes and genomes. In nature, the mitochondrial genomes in eukaryotes are generally considered non-recombining and homoplasmic. If heteroplasmy and recombination exist, they are typically very limited in both space and time. Here we show that mitochondrial heteroplasmy and recombination may not be limited to a specific population nor exit only transiently in the basidiomycete Cantharellus cibarius and related species. These edible yellow chanterelles are an ecologically very important group of fungi and among the most prominent wild edible mushrooms in the Northern Hemisphere. At present, very little is known about the genetics and population biology of these fungia cross large geographical distances. Our study here analyzed a total of 363 specimens of edible yellow chanterelles from 24 geographic locations in Yunnan in southwestern China and six geographic locations in five countries in Europe. For each mushroom sample, we obtained the DNA sequences at two genes, one in the nuclear genome and one in the mitochondrial genome. Our analyses of the nuclear gene, translation elongation factor 1-alpha (tef-1) and the DNA barcode of C. cibarius and related species, suggested these samples belong to four known species and five potential new species. Interestingly, analyses of the mitochondrial ATP synthase subunit 6 (atp6) gene fragment revealed evidence of heteroplasmy in two geographic samples in Yunnan and recombination within the two new putative species in Yunnan. Specifically, all four possible haplotypes at two polymorphic nucleotide sites within the mitochondrial atp6 gene were found distributed across several geographic locations in Yunnan. Furthermore, these four haplotypes were broadly distributed across multiple phylogenetic clades constructed based on nuclear tef-1 sequences. Our results suggest that heteroplasmy and mitochondrial recombination might have happened repeatedly during the evolution of the yellow chanterelles. Together, our results suggest that the edible yellow chanterelles represent an excellent system from which to study the evolution of mitochondrial-nuclear genome relationships.
Revisiting the Antigen-Presenting Function of β Cells in T1D Pathogenesis

Type 1 diabetes (T1D) is characterized by the unresolved autoimmune inflammation and islet β cell destruction. The islet resident antigen-presenting cells (APCs) including dendritic cells and macrophages uptake and process the β cell-derived antigens to prime the autoreactive diabetogenic T cells. Upon activation, those autoreactive T cells produce copious amount of IFN-γ, TNF-α and IL-1β to induce β cell stress and death. Autoimmune attack and β cell damage intertwine together to push forward this self-destructive program, leading to T1D onset. However, β cells are far beyond a passive participant during the course of T1D development. Herein in this review, we summarized how β cells are actively involved in the initiation of autoimmune responses in T1D setting. Specifically, β cells produce modified neoantigens under stressed condition, which is coupled with upregulated expression of MHC I/II and co-stimulatory molecules as well as other immune modules, that are essential properties normally exhibited by the professional APCs. At the cellular level, this subset of APC-like β cells dynamically interacts with plasmacytoid dendritic cells (pDCs) and manifests potency to activate autoreactive CD4 and CD8 T cells, by which β cells initiate early autoimmune responses predisposing to T1D development. Overall, the antigen-presenting function of β cells helps to explain the tissue specificity of T1D and highlights the active roles of structural cells played in the pathogenesis of various immune related disorders.