Miracle-dz/UniFAR-FTUs huggingface dataset:
Genome Sequencing of Thermoplasma acidophilum and Characterization of the Translation-Associated ATPase of 43 kDa (TAA43), a member of the AAA+ Family

Thermoplasma acidophilum (T. acidophilum), an obligatory acidophilic and thermophilic organism contains one of the smallest genomes (1.5 Mbp). Due to its simplicity, it is an excellent model for studying its proteins and for the comparison with corresponding proteins of higher organisms. The sequencing of its entire genome has provided an enormous amount of information: 55% of its chromosomal coding sequences have similarity to known proteins from all domains of life (archaea, bacteria, and eukarya), 29% have similarity to proteins of unknown function, and the remaining 16% contain no assignable information. Within the 29% of coding sequences without a known function, a set of proteins from the superfamily of ATPases associated with various activities (AAA+ family) was found. AAA+ proteins are a family of enzymatic machines involved in diverse cellular functions ranging from DNA repair and replication to organelle biogenesis, membrane trafficking, transcriptional regulation, and protein quality control. The T. acidophilum genome is lacking the presence of the AAA-regulatory particle of the 26S proteasome of eukaryotes, or the archaeal PAN in Methanococcus jannaschii, which are needed to unfold and disaggregate protein substrates and to facilitate their entry into the chamber which harbors the proteolytic active sites in proteasomes. Therefore, it was of particular interest to find out if one of the AAA+ proteins (VAT, Lon-2, and/or TAA43) found in T. acidophilum could participate directly or indirectly in the ATP- and proteasome-dependent protein degradation pathway. The T. acidophilum ORF 1175 (namely TAA43) was selected for such investigation. In vitro and in vivo interaction analyses provide a hint of AAA+ TAA43 protein as associated with proteins found in two major molecular machineries of the cell, the transcription and the translation apparatus, thus discarding the hypothesis proposed above. Analysis of the gene organization of T. acidophilum indicates the taa43 ORF to be in close proximity to genetic elements resembling a superoperon (a cluster of genes composed by ribosomal proteins, a DNA-directed RNA polymerase subunit, and transfer RNAs, among others).
Stereological Analysis of Oligodendrocyte Progenitor Cells In the Adult Mouse Brain

Oligodendrocyte precursor cells (OPC) are glial cells that metamorphose into myelinating oligodendrocytes during embryogenesis and early stages of post-natal life. OPCs continue to divide throughout adulthood and some eventually differentiate into oligodendrocytes in response to demyelinating lesions. There is growing evidence that OPCs are also involved in activitydriven de novo myelination of previously unmyelinated axons and myelin remodelling in adulthood. In this review, we summarize the interwoven factors and cascades that promote the activation, recruitment and differentiation of OPCs into myelinating oligodendrocytes in the adult brain based mostly on results found in the study of demyelinating diseases. The goal of the review was to draw a complete picture of the transformation of OPCs into mature oligodendrocytes to facilitate the study of this transformation in both the normal and diseased adult brain.
Assessment of Keratinase and Other Hydrolytic Enzymes in Thermophilic Bacteria Isolated from Geothermal Areas in Patagonia Argentina

ABSTRACT Thermophilic aerobic bacteria were isolated from two geothermal areas in Neuquén province using two different enrichment methods and a total of 30 isolates were obtained. From chicken feather enrichment cultures, strains affiliated to Bacillus cytotoxicus and Bacillus licheniformis were isolated and all of them demonstrated the capability to degrade completely chicken feather. A preliminary research on biotechnological enzymes' potential demonstrated that all the isolates displayed at least one of the extracellular hydrolytic enzymes tested. Most of the isolates showed protease, inulinase and/or pectinase activities, while cellulase and xylanase activities were less common. In light of these findings, geothermal areas of Argentina may be considered as a potential source of thermophilic bacteria able to produce many industrially relevant enzymes.
Effect of feeding Thymolina® powder on the gene expression IGF-1 in Ross 308 broiler chickens.

In the present experiment, 320 one day old Ross 308 broiler chickens were used based on a completely randomized design with 4 treatments, 4 replicates, and each replicate contained 20 broiler chickens. Experimental treatments include control, 0.5, 1, and 2% of Thymolina powder in chickens’ diet. Thymolina ® is an anti-bacterial powder drug which is made by composing 4 medicinal plants. In addition, to the gene expression of IGFI, the same birds were selected and at the end of the period, the amount of 1-2 ml blood were taken under the wing of venous vessel, and then the investigation of the amount of the gene expression of IGF-1 was conducted using specific primers ® GEN, and Real Time PCR Reaction. The gene expression of IGF-1 increased and significant differences among different treatments were observed (P<0.05). In general, results indicated that using Thymolina ® in the diet of broiler chickens causes improvements in the immune system by increasing the gene expression of IGF-1. Therefore, it can be effective on the immune responses of broiler chickens and cause the improvement creation of the favorable and effective immune system in broiler chickens.
Alanine minimises hepatocyte injury aft er ischemia-reperfusion in an ex vivo rat liver model

Ischemia-reperfusion injury is a determinant in liver injury occurring during surgery, ischemic states and multiple organ failure. The pre-existing nutritional status of the liver, i.e., fasting, might contribute to the extent of tissue injury. This study investigated whether alanine, an amino acid precursor of glucose, could protect ex vivo perfused livers of fasting rats from reperfusion injury. The portal vein was cannulated, the liver removed and perfused in a closed ex vivo system. Isolated livers were perfused either with glucose 1 g/L and 10 g/L, or with equal concentrations of alanine (n = 10 in each group). The experiment consisted of perfusion for 15 min, ischemia for 60 min, and reoxygenation during 60 min. Enzymes, glucose, lactate and bilirubin were analysed in perfusate samples. The proportion of glycogen as well as activation of caspase 3 was determined in biopsies. Alanine at a concentration of 10 g/L attenuated enzymes release in the perfusate during reoxygenation when compared to glucose-treated groups. Lactate level in the perfusate was lowest in alanine groups. Ischemia-reperfusion and mainly alanine activated apoptosis, specifically in Kupffer and endothelial cells. Alanine presents a protective effect on normothermic ischemia-reperfusion injury of the fasting rat liver when compared to glucose.
Dynamical Laser Beams Steering with Phase-Only Spatial Light Modulator

A non-mechanical beam steering system is proposed and designed to resolve the problem of approaching the far-field diffractive pattern with laser beams.A beam steering method based on the phase only modulation with a liquid crystal spatial light modulator(LCSLM) is studied and described to control the light! beams programmably.The Fourier iterative optimal algorithm is adopted to design the optimal phases approaching the expected far-field diffractive pattern.The schematic diagram and the experimental set-up are given.Results show that the method can generate 2-D spots arrays with the intensity error rate less than 8%. The response time of generating the dynamical diffractive pattern is less than 100 ms.With the merits of lightness,precision and quick response,this scanning system is of value in the fields of multi-object tracing,laser guiding and multi-object defense.
Nearly-diffraction-limited laser focal spot obtained using an optically addressed light valve in an adaptive optics loop

Ultra-intense laser systems with peak power in the 10 TW-1 PW range are difficult to focus close to the diffraction limit because of phase-front aberrations. In this paper, we describe a new technique we have implemented, which significantly improves the focal spot quality by correcting the wave front from a highly distorted laser beam. In this experiment, detection is achieved through an achromatic three-wave lateral shearing interferometer.
Methods to enhance embryo quality and recovery rates in superovulated beef cows

Methods to enhance embryo quality and recovery rates in superovulated beef cows were investigated. In the first study, uteri from superovulated heifers on day of recovery were harvested immediately following exsanguination and sectioned into 3 segments per horn plus the oviduct (8 sections per total uterus). Each section was thoroughly flushed through individual filters, searched and evaluated. Sectioning of the uterine horns impacted location of embryos with the majority of embryos located in the tip and middle third of each horn. In comparing these two sections, a greater percentage of the embryos were in the tip than in the middle third. Interestingly, embryos were recovered in both the oviduct and the base of the uterine horns. Based on these data, at time of embryo recovery, an embryo transfer (ET) practitioner should focus their recovery efforts towards the tip and middle third of the horns and potentially incorporating the body of the uterus to be include all potential embryo locations. In the second study, effects of endogenous progesterone (P4) concentrations on embryo production were evaluated. Beef cows were superovulated following a CIDR-based presynchronization coupled with ultrasound-guided dominant follicle ablation (DFA). Comparison of high progesterone (HP) concentrations to low progesterone (LP) concentrations was achieved by administration of prostaglandin F2α (PGF) at DFA to the LP group while HP maintained their CL during superstimulation. Superovulation protocol included decreasing dosages of follicle stimulating hormone twice daily over 4 days and timed artificial insemination performed twice (12 hours apart). A greater proportion of
The Role of Planktonic Organisms in Urea Metabolism in Lakes of Temperate Zone - Case Study

ABSTRACT Although urea is the simplest N-containing organic compound ubiquitous in all aquatic environments, its role in N-nutrition of planktonic biota and relevance for eutrophication of freshwater ecosystems is still insufficiently defined and often bypassed. The dynamics of production of autochthonous urea as well as maximal potential net ureolytic activity (net URA Vmax) of phyto- and bacterioplakton were studied in mesocosm experiment and verified during the field studies conducted in the Great Mazurian Lake system (GMLS). Analysis of the obtained results revealed that the proteins were the main autochthonous urea precursors. Urea concentration in the studied mesocosms and in GMLS surface waters was positively correlated with flagellate, ciliate and crustacean biomass and, less evidently, with bacterial biomass (BB). In surface waters of GMLS net URA Vmax, similarly as urea concentrations, increased with their trophic status. Analysis of correlation of potential ureolytic activity with chlorophylla, (Chla) BB and L-leucine aminopeptidase activity (AMP) in lakes of different trophic status suggests that although both groups of planktonic microorganisms participated in urea decomposition processes, in eutrophic ones bacterial decomposition of urea is more evident. In highly eutrophic lakes excess of phosphorus induced higher nitrogen requirement resulting in the increase in protein decomposition rate. Intensified protein degradation resulted faster urea production, which finally induced higher ureolytic activity of planktonic microorganisms. In profundal waters of GMLS potential ureolytic activity was distinctly lower than in surface waters. This was caused by low temperature of hypolymnetic waters, inhibitory effect of hydrogen sulphide and lack of phytoplankton, which is known as a primary urea consumer.
Using the CSM–CERES–Maize model to assess the gap between actual and potential yields of grain maize

SUMMARY Maize in Canada is grown mainly in the south-eastern part of the country. No comprehensive studies on Canadian maize yield levels have been done so far to analyse the barriers of obtaining optimal yields associated with cultivar, environmental stress and agronomic management practices. The objective of the current study was to use a modelling approach to analyse the gaps between actual and potential (determined by cultivar, solar radiation and temperature without any other stresses) maize yields in Eastern Canada. The CSM–CERES–Maize model in DSSAT v4·6 was calibrated and evaluated with measured data of seven cultivars under different nitrogen (N) rates across four sites. The model was then used to simulate grain yield levels defined as: yield potential (YP), water-limited (YW, rainfed), and water- and N-limited yields with N rates 80 kg/ha (YW, N-80N) and 160 kg/ha (YW, N-160N). The options were assessed to further increase grain yield by analysing the yield gaps related to water and N deficiencies. The CSM–CERES–Maize model simulated the grain yields in the experiments well with normalized root-mean-squared errors <0·20. The model was able to capture yield variations associated with varying N rates, cultivar, soil type and inter-annual climate variability. The seven calibrated cultivars used in the experiments were divided into three grades according to their simulated YP: low, medium and high. The simulation results for the 30-year period from 1981 to 2010 showed that the average YP was 15 000 kg/ha for cultivars with high yield potential. The YP is generally about 6000 kg/ha greater than the actual yield (YA) at each experimental site in Eastern Canada. Two-thirds of this gap between YP and YA is probably associated with water stress, as a gap of approximately 4000 kg/ha between the YW and the YP was simulated. This gap may be reduced through crop management, such as introducing irrigation to improve the distribution of available water during the growing season. The simulated yields indicated a gap of about 3000 and 1000 kg/ha between YW and YW,N-80N for cultivars with high YP and low YP, respectively. The gap between YW and YW,N-160N decreased to <2000 kg/ha for high Yp cultivars with little difference for the low Yp cultivars. The different yield gaps among cultivars suggest that cultivars with high YP require high N rates but cultivars with low YP may need only low N rates.
Analyzing spatio-temporal characteristics of urban LULC and LST over Shanghai during 2009-2019

The expansion of urban areas is always accompanied by land use/land cover (LULC) changes and associated with the distribution of urban heat islands (UHI) simultaneously. In particular, in the metropolis such as Shanghai, the land cover transitions between the impervious surface (IS) and vegetation areas highly influence the ecological quality. This study focused on the monitoring and analysis on the LULC and land surface temperature (LST) spatio-temporal changes in Shanghai during the period between 2009 and 2019. We evaluated LULC and LST changes based on the multitemporal Landsat images acquired over five individual years (i.e., 2009, 2012, 2015, 2017 and 2019). In particular, the Fully Constrained Least Squares (FCLS) spectral unmixing and several derived spectral indices are used for generating the LULC maps, and Radiative Transfer Equation (RTE) temperature inversion method is utilized for estimating the LST. In order to compare the dominance of different land classes, then we analyzed the classification maps from different landscape levels. Experimental results demonstrate that during the past ten years the IS of Shanghai continually expanded from the city center mainly towards the Pudong, Songjiang and Jiading three districts directions. Vegetation especially the cropland in the urban fringe areas were replaced by the newly appeared IS, which lead to the rising temperature in the corresponding areas. This may further accelerate the urban heat island phenomenon.
Expression of Heat Shock Proteins by Heat Stress in Soybean

Heat stress is one of the factors disturb productivity and growth of plants. Many genes including heat shock protein (HSP), heat shock transcription factors (HSF) and chaperones, were identified and characterized in many plants to play role in increased tolerance to abiotic stress. To reveal responsive gene to heat stress, we performed RNA-seq using two Korean soybean varieties under heat stress and normal conditions. The transcripts were analyzed, and we obtained 2,458 genes including 46 co-up regulation and 55 co-down regulated genes in both soybean varieties. We also revealed HSPs, HSFs and chaperones in the differentially expressed genes using BLAST and Pfam analyzation and verified expression changes under heat stress. Finally, we find 68 genes involved in HSP, HSF, chaperones in heat responsive genes associated increasing heat tolerance. As a result, relatively small HSP families were up regulated and continuously expressed in long period heat stress. On the other hand, large molecule HSPs, HSFs and chaperonin did not response to long heat stress. The expression profiling and characterization provide invaluable information to understand heat tolerance of soybean.
Fc-erythropoietin fusion protein with improved pharmacokinetics

The present invention provides novel highly sialylated Fc-EPO fusion proteins preferably comprising a couple of modifications in the Fc- portion as well as in the EPO portion and having improved pharmacokinetics. Specifically, the Fc-EPO proteins have a prolonged serum half-life and increased in vivo potency. The Fc-EPO fusion proteins synthesized in BHK cells have dramatically prolonged serum half-lives and increased in vivo potency when compared to corresponding Fc-EPO fusion proteins produced in other cell lines, such as, for example, NS/O cells.
Study of waves at different fetches using WAVEWATCH III modeling and precipitation radar data

WAVEWATCH III wave model is used to simulate wave parameters in Persian Gulf at different wind fetches. The default packages of the wind input source terms and the authors adaptation of WAVEWATCH III model are tested in several points with various fetches and compared with the Dual-frequency Precipitation Radar (DPR) data. The proposed new technique may be used for the verification of the modeled data.
Regional native seed cooperatives: working toward available, affordable, and appropriate native seed

ABSTRACT:Regional native seed cooperatives are emerging as a tool to vastly improve the availability of genetically appropriate native seed. Within a cooperative, practical and ecological requirements for native seed are balanced by bringing users and producers together to jointly develop genetic protocols. Regional native seed cooperatives promote a novel agricultural niche that requires the development of new farms, infrastructure, and techniques. The South Sound Prairies partnership has a successful cooperative that is used here as a case study to explore this model of seed production.
The Rumen Metatranscriptome Landscape Reflects Dietary Adaptation and Methanogenesis in Lactating Dairy Cows

Methane eructed by ruminant animals is a main contributor to greenhouse gas emissions and is solely produced by members of the phylum Euryarchaeota within the domain Archaea. Methanogenesis depends on the availability of hydrogen, carbon dioxide, methanol and acetate produced, which are metabolic products of anaerobic microbial degradation of feed-derived fibers. Changing the feed composition of the ruminants has been proposed as a strategy to mitigate methanogenesis of the rumen microbiota. We investigated the impact of corn silage enhanced diets on the rumen microbiota of rumen-fistulated dairy cows, with a special focus on carbohydrate breakdown and methanogenesis. Metatranscriptome analysis of rumen samples taken from animals fed corn silage enhanced diets revealed that genes involved in starch metabolism were significantly more expressed while archaeal genes involved in methanogenesis showed lower expression values. The nutritional intervention also influenced the cross-feeding between Archaea and Bacteria. The results indicate that the ruminant diet is important in methanogenesis. The diet-induced changes resulted in a reduced methane emission. The metatranscriptomic analysis provided insights into key underlying mechanisms and opens the way for new rational methods to further reduce methane output of ruminant animals.
Discovery of novel bioactive compounds: Molecular awakening of silent clusters in Streptomyces natalensis

The healthcare system is facing a serious problem: the emergence of antimicrobial drug resistance. However, antimicrobial drug discovery and development has decelerated considerably throughout the past decades, creating an urgent need for the development of new strategies for antibiotic discovery. Streptomyces are the native producers of approximately 75% of the antibacterial drugs in clinical use and it is believed that we are only taking advantage of a small part of their production potential. In this work, we performed an in silico genome mining approach combined with genetic engineering, for the development of novel hit compounds that will ultimately feed the drug discovery pipeline. Genome mining analysis of S. natalensis ATCC 27448 unveiled 29 biosynthetic gene clusters coding for unknown specialized products. Six of these were submitted for an in silico and transcription analysis. Three predicted positive cluster situated regulators (CSRs), located within three different clusters and that showed no expression under laboratory conditions were selected for overexpression. RT-PCR analysis of S. natalensis strains overexpressing the CSR encoding genes SNA01173, SNA01239 and SNA06246 did not show up-regulation of structural genes at the analysed time point. Comparative metabolic profiling assays by bioassays and HPLC revealed different production patterns which suggest that novel biologically active compounds might being produced. Such products may further feed the drug discovery pipeline. Finally, overexpression of SNA01239 and SNA01173 also significantly altered pimaricin yield. Supervisor: Marta Vaz Mendes, PhD Co-supervisor: Tiago Beites, PhD Affiliation: IBMC – Institute for Molecular and Cell Biology