Miracle-dz/UniFAR-FTUs huggingface dataset:
LC3B phosphorylation regulates FYCO1 binding and directional transport of autophagosomes

Macroautophagy (hereafter referred to as autophagy) is a conserved process that promotes cellular homeostasis through the degradation of cytosolic components, also known as cargo. During autophagy, cargo is sequestered into double-membrane vesicles called autophagosomes, which are predominantly transported in the retrograde direction to the perinuclear region to fuse with lysosomes, thus ensuring cargo degradation [1]. The mechanisms regulating directional autophagosomal transport remain unclear. The ATG8 family of proteins associate with autophagosome membranes [2] and play key roles in autophagy, such as the movement of autophagosomes. This is achieved via the interaction of ATG8 with adaptor proteins, including FYCO1, a protein involved in the anterograde transport of autophagosomes toward the cell periphery [1,3–5]. We previously reported that phosphorylation of LC3B/ATG8 on threonine 50 (LC3B-T50) by the Hippo kinase STK4 is required for autophagy through unknown mechanisms [6]. Here, we show that LC3B-T50 phosphorylation decreases the interaction between LC3B and FYCO1, which in turn regulates the starvation-induced perinuclear positioning of autophagosomes. Moreover, non-phosphorylatable LC3B-T50A aberrantly switches the predominant retrograde movement of autophagosomes to anterograde movement towards the cell periphery in multiple cell types, including in mouse primary hippocampal neurons. Our data support a role of a nutrient-sensitive STK4–LC3B–FYCO1 axis in the regulation of the directional transport of autophagosomes via the post-translational regulation of LC3B. Given that autophagy is impaired in many human conditions, including neurodegenerative diseases, our findings may highlight new principles of vesicle transport regulation critical for disease etiology. Graphical abstract
Mutations in Tomato 1-Aminocyclopropane Carboxylic Acid Synthase2 Uncover Its Role in Development beside System II Responses

The role of ethylene in plant development is mostly inferred from its exogenous application. The usage of the mutants affecting ethylene biosynthesis proffers a better alternative to decipher its role. In tomato, 1-aminocyclopropane carboxylic acid synthase2 (ACS2) is a key enzyme regulating ripening-specific ethylene biosynthesis. We characterized two contrasting acs2 mutants; acs2-1 overproduces ethylene, has higher ACS activity, and increased protein levels, while acs2-2 is an ethylene under-producer, displays lower ACS activity, and protein levels than wild type. Consistent with high/low ethylene emission, the mutants show opposite phenotypes, physiological responses, and metabolomic profiles than the wild type. The acs2-1 showed early seed germination, faster leaf senescence, and accelerated fruit ripening. Conversely, acs2-2 had delayed seed germination, slower leaf senescence, and prolonged fruit ripening. The phytohormone profiles of mutants were mostly opposite in the leaves and fruits. The faster/slower senescence of acs2-1/acs2-2 leaves correlated with the endogenous ethylene/zeatin ratio. The genetic analysis showed that the metabolite profiles of respective mutants co-segregated with the homozygous mutant progeny. Our results uncover that besides ripening, ACS2 participates in vegetative and reproductive development of tomato. The distinct influence of ethylene on phytohormone profiles indicates intertwining of ethylene action with other phytohormones in regulating plant development. One sentence summary Genetic and functional analysis of ACS2 mutants reveal high/low ethylene emission oppositely modulates developmental processes and metabolite profiles in tomato.
Photosynthetic activity of natural microphytobenthos populations measured by fluorescence (PAM) and 14C-tracer methods: a comparison

PAM (pulse-amplitude-modulated) fluorescence measurements of motile microphytobenthic algae were carried out in June 1996 at Sylt, Germany. Compansons between "C-based and fluorescence-based production rates were made. A very high correlation between 14Cand fluorescence-based production rates was found for maximal production rates (P,, values). I4C-based maximal production rates var~ed uring the study penod between 0.65 and 1.7 mg C mg chl a-' h-', comparable to variations of P,,, measured with the fluorescence-based method. For other photosynthetic parameters [a (maximum light utilization coefficient). Ek (light saturation index), E,,, (light intensity at which P, is reached)], differences between the 2 methods were much larger. Highest carbon quantum yields (@,) (m01 C m01 quanta-' absorbed) were obtained at low irradiances. Considering the whole range of investigated carbon quantum yields, we found that initially these values decreased at low to moderate irradiances without a concomitant decline of the actual photochemical efficiency (F,' F)/F,,' (Fand F,'. m~nimal and maximai iiuoresce~lct' signals in :he ! igh! ) Therefcre, e high ! ine~rit)r between the actual photochemical efficiency and the carbon quantum yield could only be observed up to values of 0.018 m01 C m01 quanta-' This is different to higher plants, for which linearity can be observed up to carbon quantum yields of 0.042 m01 C m01 quanta-' It was shown that, for the calculation of the overall production rates based on the fluorescence method, it is necessary to carefully measure the mean specific absorption coefficient (a ' ) of the algae. Unless this is achieved. PAM measurements cannot be used to calculate absolute production rates.
Delayed effect of drought on the xylem vulnerability to cavitation in Fagus sylvatica L

Knowledge on variations of drought resistance traits is needed to predict the potential of trees to adapt to severe drought events expected to be more intense and frequent. Xylem vulnerability to cavitation is among the most important traits related to drought-induced mortality and exhibits a large variability between species. Acclimation of this trait to environmental conditions implies changes in the xylem structure and organization, leading previous studies to investigate its variations under conditions preserving growth. In European beech saplings, we assessed the effect of droughts of on the vulnerability to cavitation in branches that develop during recovery. The newly formed branches displayed lower vulnerability to cavitation in the plants that underwent the severest droughts leading to native embolism; the pressure that induces 50% loss of conductance being of −3.98 MPa in severely droughted plants whereas it was of −3.1 MPa in control plants, respectively. Although unexpected, these results argue for an acclimation, and not a weakening, of this trait to drought events. Key message severe water stress make the future developed shoots less vulnerable to xylem cavitation.
Streptomyces endophytes promote the growth of Arabidopsis thaliana

Streptomyces bacteria are ubiquitous in soils and are well-known for producing secondary metabolites, including antimicrobials. Increasingly, they are being isolated from plant roots and several studies have shown they are specifically recruited to the rhizosphere and the endosphere of the model plant Arabidopsis thaliana. Here we test the hypothesis that Streptomyces bacteria have a beneficial effect on A. thaliana growth and could potentially be used as plant probiotics. To do this, we selectively isolated streptomycetes from surface washed A. thaliana roots and generated high quality genome sequences for five strains which we named L2, M2, M3, N1 and N2. Re-infection of A. thaliana plants with L2, M2 and M3 significantly increased plant biomass individually and in combination whereas N1 and N2 had a negative effect on plant growth, likely due to their production of polyene natural products which can bind to phytosterols and reduce plant growth. N2 exhibits broad spectrum antimicrobial activity and makes filipin-like polyenes, including 14-hydroxyisochainin which inhibits the Take-all fungus, Gaeumannomyces graminis var. tritici. N2 antifungal activity as a whole was upregulated ~2-fold in response to indole-3-acetic acid (IAA) suggesting a possible role during competition in the rhizosphere. Furthermore, coating wheat seeds with N2 spores protected wheat seedlings against Take-all disease. We conclude that at least some soil dwelling streptomycetes confer growth promoting benefits on A. thaliana while others might be exploited to protect crops against disease. Importance It is vital that we reduce our reliance on agrochemicals and there is increasing interest in using bacterial strains to promote plant growth and protect against disease. Our study follows up reports that Arabidopsis thaliana specifically recruits Streptomyces bacteria to its roots. In particular, we test the hypothesis that these bacteria can offer benefits to their A. thaliana hosts and that strains isolated from these plants might be used as probiotics. We isolated Streptomyces strains from surface washed A. thaliana roots and genome sequenced five phylogenetically distinct strains. Genome mining and bioassays indicated that all five strains have plant growth promoting properties, including production of IAA, siderophores and ACC deaminase activity. Three strains significantly increased A. thaliana growth in vitro and when applied in combination in soil. Another produces potent filipin-like antifungal metabolites and we used it as a seed coating to protect germinating wheat seeds against the fungal pathogen Gaeumannomyces graminis var. tritici (wheat Take-all fungus). We conclude that introducing an optimal combination of Streptomyces strains into the root microbiome can provide significant benefits to plants.
Reappraisal of methods of application of nitrogen and phosphorus at sowing on the yield, grain protein content and nitrogen economy of malting barley in Sweden

Abstract To compare the relative efficiency of different fertilisation strategies, malting barley was fertilised with calcium ammonium nitrate (CAN) or compound ammonium nitrate with phosphorus (NP) applied in two ways: broadcast and harrowed into the seedbed before seeding or banded using the Scandinavian combi-drill design, with the fertiliser between every second seed row, and 40 mm below. A fixed nitrogen level (120 kg N ha−1) was used, giving four fertiliser treatments. Eleven experiments were carried out the years 1992–1994, with latitudes 55° 55′ N as southern and 59° 36′ N as northern limit. Fertiliser-use efficiency, defined as grain yield, or grain nitrogen yield, per unit of applied N, was strongly affected by the treatments: values for combi-drilled were higher than for broadcast fertiliser and higher for NP than for CAN, with the effects being additive. The best treatment, using both banding and NP, resulted, as a mean of all trials, in a grain yield increase of 939 kg ha−1 at 15% moisture content, or a nitrogen yield increase of 18 kg nitrogen ha−1 compared with the poorest, using broadcast CAN. The N combi-drill effect was expected to be dependent on water availability, but this could not be confirmed when accumulated rainfall during crop establishment was used as test variable. The combi-drill effect was strongest in places where major extractable cations were abundant, possible explanations for this are discussed. Application of P to the crop and the use of combi-drill are recommended for malting barley fertilisation in Sweden.
Summer browsing by moose on Scots pine

Abstract Moose (Alces alces L.) browse Scots pine (Pinus sylvestris L.) mainly during the winter. There is a growing concern also regarding summer browsing by moose on Scots pine. We studied summer browsing on Scots pine during two consecutive years. In a survey of 47 stands in 2003, current summer browsing was found for 20.4% of the Scots pine main stems, and on almost half of them (9.8%) the top shoot was browsed. This indicates that the pine damage causing reduced wood quality was as serious during summer as during the preceding winter. There was significantly more summer browsing on previously browsed pines, compared to a random use, both at tree and stand level, and summer browsing was also spatially clumped within stands. Browsing on top shoots occurred up to a height of 2.8 m, whereas side shoot browsing was recorded for pines with a height up to 4.8 m. In 2004, 11 of the 47 stands were randomly selected for a more detailed study of pines browsed during that summer. The summer browsed trees contained, on average, 114 current shoots tree−1, and 10.5 shoots tree−1 (9.2%) were browsed. In this area, summer browsing may explain a considerable part of the moose-related forest damage recorded. The proportion of pines subjected to summer browsing did not change with availability of pines. Hence, increasing the number of Scots pine trees in young stands may be a way to increase the number of unbrowsed pine trees at a given moose population density.
Gas chromatography-mass spectrometry elucidation and antipsoriatic activity on developed herbal formulations from Carissa congesta, Catharanthus roseus, Annona squamosa, and Polyalthia longifolia Plant Extracts

Background: Annonaceae and Apocynaceae families are known for their plethora of pharmacotherapeutic potential. Objectives: To evaluate antipsoriatic potential (ultraviolet [UV]-induced photodermatitis and tail model) and gas chromatography-mass spectrometry (GC-MS) studies on developed formulations from the plant extracts. Materials and Methods: Formulations of ethanolic extracts of Carissa congesta and Catharanthus roseus and petroleum ether extracts of Annona squamosa and Polyalthia longifolia were evaluated for antipsoriatic activity (UV-induced photodermatitis and tail model) at 250 and 500 mg/kg. GC-MS studies were done subsequently after 6 months. Formulation batches were tested by different tests, viz., pH, viscosity, spreadability, washability, homogeneity, grittiness, drug content, Sudan red, bleeding, and sensitivity tests. Results: Histopathology studies indicated the absence of Munro's microabscess, regular elongation of rete ridges, capillary loop dilatation, granular cell layer, and prominent parakeratosis at 500 mg/kg. Formulations of the plant extracts did not reveal toxic components by GC-MS interpretation. No greasiness was observed during washing. Uniform homogeneity was observed with neither clumps nor large aggregates. The dispersed globules appeared red against colorless water background. Bleeding time was found to be stable during the experimentation.Conclusion: Developed topical plant formulations showed antipsoriatic potential on selected models. The GC-MS studies confirmed the presence of no drastic changes in the quantity of active constituents assuring its stability.
SEASONAL CHANGES IN THE STANDARD RATE OF OXYGEN CONSUMPTION OF FISHES

The standard rate of oxygen consumption for brook and brown trout acclimated to 10 °C and exposed to natural daylight varied seasonally. For male brook trout, standard oxygen consumption increased from a low of 30 mg/kg hour during March and April to a maximum of 63 mg/kg hour during the late fall spawning period. The standard rates of the females approximated those for males. For male brown trout, standard oxygen uptake increased from a value of approximately 20 mg/kg hour during the winter and spring months to a high of roughly 30 mg/kg hour during the fall spawning period. Little change was observed in the standard oxygen consumption of female brown trout.
Functional network analysis of the sub-regions of the primary motor cortex during rest

The cytoarchitectonic properties of the primary motor cortex have shown two distinct sub-regions: Anterior Broadmann area 4 (BA4a) and Posterior Broadmann area 4 (BA4p). Some previous studies have suggested that these two sub-regions are functionally different and showed that in few fMRI experiments, these sub-regions may have different roles in brain functions. Resting-state fMRI (rsfMRI) is advanced technique that allows investigating in detail the functional connectivity and provides a greater understanding of the physiological behavior of different brain regions. In this study, 198 healthy subjects were examined using a region-based rsfMRI analysis to investigate whether BA4a and BA4p have similar or different connections to other brain networks. The finding shows that indeed these two sub-regions have distinct connectivity to different brain networks. BA4a has a greater connection to motor-related areas while BA4p has connections to nonmotor-related areas (such as sensory, attentional, and higher order regions), suggesting that these two sub-regions should be considered as two separate regions of interests.
High-performance thin-layer chromatography analysis of gallic acid and other phytoconstituents of methanolic extracts of Myrica nagi fruit

Background: Myrica nagi Thunb. (family: Myricaceae) is effective against gastric, metabolic, and hepatic disorders. The therapeutic effect of its fruit, which is consumed in North India, has not been confirmed, and detailed chemical profiling of the fruit is thus required. Objectives: The study objective was to develop and optimize a high-performance thin-layer chromatography (HPTLC) method for the characterization of gallic acid, quercetin, myricetin, and caffeic acid in the methanolic extract of M. nagi fruit and the quantification of gallic acid. Materials and Methods: Analyses were performed using HPTLC, and liquid chromatography-mass spectrometry. HPTLC experiments were carried out using an optimized solvent mixture, which enabled the separation and detection (at 254 and 366 nm) of four flavonoid compounds in the dried M. nagi extract. Gallic acid was quantified using calibration curves. Results: The proposed method enabled the detection of gallic acid, quercetin, myricetin, and caffeic acid. Validation took into account the estimation of linearity, limit of detection, limit of quantification, accuracy, and recovery of gallic acid. Gallic acid was quantified at 12.93 μg/mg of dry plant concentrate. Conclusion: This study describes the development of an HPTLC method for the analysis and characterization of phytoconstitutents in the methanolic solution of a dried M. nagi fruit extract. The method was successfully validated for the analysis of gallic acid.
A Study on Intrusion Detection System in Wireless Sensor Networks

The technology of Wireless Sensor Networks (WSNs) has become most significant in present day. WSNs are extensively used in applications like military, industry, health, smart homes and smart cities. All the applications of WSN require secure communication between the sensor nodes and the base station. Adversary compromises at the sensor nodes to introduce different attacks into WSN. Hence, suitable Intrusion Detection System (IDS) is essential in WSN to defend against the security attack. IDS approaches for WSN are classified based on the mechanism used to detect the attacks. In this paper, we present the taxonomy of security attacks, different IDS mechanisms for detecting attacks and performance metrics used to assess the IDS algorithm for WSNs. Future research directions on IDS in WSN are also discussed.
The Impact of SMOS Soil Moisture Data Assimilation within the Operational Global Flood Awareness System (GloFAS)

In this study the impacts of Soil Moisture and Ocean Salinity (SMOS) soil moisture data assimilation upon the streamflow prediction of the operational Global Flood Awareness System (GloFAS) were investigated. Two GloFAS experiments were performed, one which used hydro-meteorological forcings produced with the assimilation of the SMOS data, the other using forcings which excluded the assimilation of the SMOS data. Both sets of experiment results were verified against streamflow observations in the United States and Australia. Skill scores were computed for each experiment against the observation datasets, the differences in the skill scores were used to identify where GloFAS skill may be affected by the assimilation of SMOS soil moisture data. In addition, a global assessment was made of the impact upon the 5th and 95th GloFAS flow percentiles to see how SMOS data assimilation affected low and high flows respectively. Results against in-situ observations found that GloFAS skill score was only affected by a small amount. At a global scale, the results showed a large impact on high flows in areas such as the Hudson Bay, central United States, the Sahel and Australia. There was no clear spatial trend to these differences as opposing signs occurred within close proximity to each other. Investigating the differences between the simulations at individual gauging stations showed that they often only occurred during a single flood event; for the remainder of the simulation period the experiments were almost identical. This suggests that SMOS data assimilation may affect the generation of surface runoff during high flow events, but may have less impact on baseflow generation during the remainder of the hydrograph. To further understand this, future work could assess the impact of SMOS data assimilation upon specific hydrological components such as surface and subsurface runoff.
Integration of TanDEM-X and SRTM DEMs and Spectral Imagery to Improve the Large-Scale Detection of Opencast Mining Areas

Land use and land cover (LULC) is a key variable of the Earth’s system and has become an important indicator to evaluate the impact of human activities on the Earth’s ecosystems. With the increasing demand of mine resources, widespread opencast mining has led to significant changes in LULC and caused substantial damage to the environment. An efficient approach of detecting mining activities at large scales is of critical importance in mitigating their potential impacts on downstream settlements and in assessing LULC characteristics. In this study, we present a novel approach for enabling large-scale automatic detection of opencast mining areas by integrating multitemporal digital elevation models (DEMs, including the SRTM DEM and the recently released TanDEM-X DEM) and multispectral imagery in object-based image analysis and random forest (RF) algorithms. A sequence of data preparation, image segmentation, threshold analysis, calculation of metrics, and influence factor regulation was developed and tested on the Landsat 8 sample dataset in Inner Mongolia in China, which is a mineral-rich area. Aside from spectral metrics, such as brightness and reflectance value, introduced topographical features enhanced the modeling and classification significantly, and the overall performance is greatly influenced by feature selection (the out-of-bag error rate in the RF algorithm is 7.54% for the integrated DEM method in comparison with 12.70% for the only-optical images method). The integrated use of spectral imagery and multitemporal DEMs reveals that the identified mining area is about 1100 km2 in the study area and period, and the topographic changes of opencast mining in terms of elevation difference is between −258 and 162 m. The results show that the method can map the locations and extents of mining areas automatically from spectral and DEM data and can potentially be applied to larger areas.