Miracle-dz/UniFAR-FTUs huggingface dataset:
NEUROCHEMICAL MECHANISMS OF THE NUCLEUS ACCUMBENS REALIZING THE REINFORCING EFFECTS OF SELF-STIMULATION OF THE LATERAL HYPOTHALAMUS

The purpose of the investigation was to clear the significance of GABA, dopamine and corticoliberin (CRF) systems of the nucleus accumbens for the reinforcing effects of a number of psychotropic drugs (opiates, opioids, psychostimulants) on self-stimulation of the lateral hypothalamus in rats. The Wistar male rats were implanted bipolar electrodes in the lateral hypothalamus to study self-stimulation reaction in the Skinner box. Simultaneously, the microcannules were implanted into the nucleus accumbens to inject the drugs studied (1 |! g in 1 |ll in volume for each injection). Some drugs, lidocain, a blocker of sodium influx ionic currents, antagonists of GABAa receptors bicuculline, D 1 dopamine receptors SCH23390, D 2 dopamine receptors sulpiride and CRF receptors astessin, which were administered intrastructurally into the nucleus accumbens, were used for pharmacological analysis. Bicuculline > astressin > sulpiride > SCH23390 (the drugs are located in the range of descending inhibition activity), administered into the nucleus accumbens, inhibited, but lidocain, a blocker of sodium influx ionic currents, enhanced self-stimulation of the lateral hypothalamus. The reinforcing properties of all psychoactive drugs (amphetamine, fentanyl, sodium ethaminal and leu-enkephaline) were changed on the background of their action. After administration of sulpiride amphetamine had no effect, and after bicuculline, lidocaine and SCH23390 the amphetamine effect, clear reproducible from the lateral hypothalamus, was decreased. Ch the other hand, both bicuculline and sulpiride did not pre- vent of psychoactivating effect of opioid analgetic fentanyl. In all other cases the positive effect of fentanyl inverted into negative one (lidocain, SCH23390, astressin). The blockade of dopamine receptors (SCH23390, sulpiride) and CRF receptors (CRF) did not change sodium ethaminal effect whereas bicuculline and lidocaine declined them. None blocker instead of astressin changed the inhibitory effects of leu-enkephaline on hypothalamic self-stimulation significantly. In the latter case, astressin strengthened the negative action of leuenkephaline on self-stimulation. It is concluded that the nucleus accumbens controls the hypothalamic self-stimulation via GABA- and CRF-ergic mechanisms preferably, which are able to limit the positive effects of narcogenic drugs.
Electrochemical dithiothreitol assay for large-scale particulate matter studies

Abstract Particulate matter (PM) air pollution is associated with human morbidity and mortality. Measuring PM oxidative potential has been shown to provide a predictive measurement between PM exposure and adverse health impacts. The dithiothreitol (DTT) assay is commonly used to measure the oxidative potential of PM2.5 (PM less than 2.5 µm aerodynamic diameter). In the common, kinetic form of this assay, the decay of DTT is quantified over time (indirectly) using 5,5′-dithiobis(2-nitrobenzoic acid) (DTNB, Ellman’s reagent) via UV/vis absorbance spectroscopy. The loss of DTT can also be quantified directly using electrochemical detection. The objectives of this work were (1) to evaluate the electrochemical assay, using commercially available equipment, relative to the UV/vis absorbance assay and (2) to apply the electrochemical method to a large (>100) number of PM2.5 filter samples. Also presented here is the comparison of an endpoint assay to the kinetic assay, in an attempt to reduce the time, labor, and materials necessary to quantify PM oxidative potential. The endpoint, electrochemical assay gave comparable results to the UV/vis absorbance assay for PM2.5 filter sample analysis. Finally, high filter mass loadings (higher than about 0.5 µg PM per mm2 filter) lead to suboptimal DTT assay performance, which suggests future studies should limit particle mass loadings on filters. Copyright © 2019 American Association for Aerosol Research
Breaking Molecular Nitrogen under Mild Conditions with an Atomically Clean Lanthanide Surface

A route to break molecular nitrogen (N2) under mild conditions is demonstrated by N2 gas cracking on, and incorporation into, lanthanide films. Successful growth of lanthanide nitride thin films, made by evaporation of lanthanides in a partial N2 atmosphere at room temperature and pressure as low as 10–4 Torr, is confirmed using X-ray diffraction. In situ conductance measurements of pure lanthanide thin films exposed to N2 gas show an immediate surface reaction and a slower bulk reaction. Finally, we report partial reversal of the nitrogen incorporation in a lanthanide nitride by cycling vacuum and nitrogen conditions in the sample chamber.
Caracterização biogeoquímica da matéria orgânica em um estuário de macromaré localizado na interface Amazônia-semiárido no nordeste do Brasil

Os estuarios sao ambientes costeiros de transicao, que atuam como um filtro natural e sitio de troca de agua e materia, principalmente materia orgânica, onde grande parte do carbono pode ser importado e/ou exportado. O objetivo deste estudo e compreender a composicao da materia orgânica na coluna de agua do Complexo Estuarino da Baia de Sao Marcos, um ambiente sob a influencia de macromare semi-diurna. Para tracar a distribuicao da materia orgânica com mais precisao, a composicao elementar e usada juntamente com a composicao isotopica do carbono e do nitrogenio. A amostragem foi realizada em agosto de 2016, em tres transectos, totalizando 14 estacoes. A agua foi amostrada em duas profundidades diferentes, subsuperficie e fundo. Os seguintes parâmetros foram medidos: material particulado em suspensao, carbono orgânico dissolvido, carbono orgânico particulado, isotopos estaveis de carbono e nitrogenio, razao atomica (C/N)a. Os parâmetros condutividade eletrica, oxigenio dissolvido e temperatura foram medidos in situ . O material particulado em suspensao teve media de 360,6 mg L -1 ) no meio com uma pequena diminuicao (media de 344,6 mg L -1 ) para a parte mais interna da baia. O carbono orgânico apresentou maiores concentracoes sob a forma dissolvida (media 10,97 mg L -1 ), variando entre as profundidades e os pontos amostrais. As concentracoes de nitrogenio total foram baixas (media 0,38 mg L -1 ), estando relacionadas a pouca influencia de compostos nitrogenados. A razao isotopica e C/N indicam que o manguezal representa uma importante fonte de carbono orgânico particulado e dissolvido nesse estuario.
Intermolecular reorganisation of single-component condensates during ageing promotes multiphase architectures

Intracellular proteins can undergo phase separation to form liquid-like biomolecular condensates with a multitude of functional roles. Liquid condensates can, however, further age and progressively rigidify. In addition to single-phase systems, multiphase condensates are increasingly identified commonly within multi-component systems, where the different molecular components present sufficient physicochemical diversity to sustain separate phases. Here, we develop a multiscale modelling approach that predicts conditions under which multiphase architectures can arise also within single-component protein condensates. Such single-component condensates are initially homogeneous but become heterogeneous over time due to the gradual enhancement of interprotein interactions. We find that such enhancement could originate, for instance, from intermolecular disorder-to-order transitions within low-complexity aromatic-rich kinked segments in the prion-like domain of FUS. Our model reveals that as increasing numbers of molecules undergo a disorder-to-order transition over time, single-component protein condensates convert into either gel-core/liquid-shell or liquid-core/gel-shell multiphase structures, depending on the relative surface tension of the liquid and gel phases. Despite being formed by proteins that are chemically-identical, the different liquid and gel phases present diverse surface tensions due to their fundamentally different molecular organization. Our study highlights the regulatory role of prion-like domains in tuning condensate behavior and, more generally, suggests a new route by which multilayered compartments or hierarchically organized condensate structures can emerge.
Development of a Highly Sensitive Luciferase-Based Reporter System To Study Two-Step Protein Secretion in Cyanobacteria

Protein secretion allows bacteria to interact and communicate with the external environment. Secretion is also biotechnologically relevant, where it is often beneficial to target proteins to the extracellular space. ABSTRACT Cyanobacteria, ubiquitous oxygenic photosynthetic bacteria, interact with the environment and their surrounding microbiome through the secretion of a variety of small molecules and proteins. The release of these compounds is mediated by sophisticated multiprotein complexes, also known as secretion systems. Genomic analyses indicate that protein and metabolite secretion systems are widely found in cyanobacteria; however, little is known regarding their function, regulation, and secreted effectors. One such system, the type IVa pilus system (T4aPS), is responsible for the assembly of dynamic cell surface appendages, type IVa pili (T4aP), that mediate ecologically relevant processes such as phototactic motility, natural competence, and adhesion. Several studies have suggested that the T4aPS can also act as a two-step protein secretion system in cyanobacteria akin to the homologous type II secretion system in heterotrophic bacteria. To determine whether the T4aP are involved in two-step secretion of nonpilin proteins, we developed a NanoLuc (NLuc)-based quantitative secretion reporter for the model cyanobacterium Synechocystis sp. strain PCC 6803. The NLuc reporter presented a wide dynamic range with at least 1 order of magnitude more sensitivity than traditional immunoblotting. Application of the reporter to a collection of Synechocystis T4aPS mutants demonstrated that the two-step secretion of NLuc is independent of T4aP. In addition, our data suggest that secretion differences typically observed in T4aPS mutants are likely due to a disruption of cell envelope homeostasis. This study opens the door to exploring protein secretion in cyanobacteria further. IMPORTANCE Protein secretion allows bacteria to interact and communicate with the external environment. Secretion is also biotechnologically relevant, where it is often beneficial to target proteins to the extracellular space. Due to a shortage of quantitative assays, many aspects of protein secretion are not understood. Here, we introduce an NLuc-based secretion reporter in cyanobacteria. NLuc is highly sensitive and can be assayed rapidly and in small volumes. The NLuc reporter allowed us to clarify the role of type IVa pili in protein secretion and identify mutations that increase secretion yield. This study expands our knowledge of cyanobacterial secretion and offers a valuable tool for future studies of protein secretion systems in cyanobacteria.
Predicting selection-response gradients of heat tolerance in a wide-ranging reef-building coral

Ocean temperatures continue to rise due to climate change but it is unclear if heat tolerance of marine organisms will keep pace. Understanding how tolerance scales from individuals to species and quantifying adaptive potentials is essential to forecasting responses to warming. We reproductively crossed corals from a globally distributed species (Acropora tenuis) on the Great Barrier Reef (Australia) from three thermally distinct reefs to create 85 novel offspring lineages. Individuals were experimentally exposed to temperatures (27.5, 31, and 35.5 - 36 °C) in adult and two critical early life-history stages (larval development and settlement) to assess acquired heat tolerance via introgression on offspring phenotypes by comparing multiple physiological responses (photosynthetic yields, bleaching, necrosis, settlement, and survival). Adaptive potentials and physiological reaction norms were calculated across multiple life-stages to integrate heat tolerance at different biological scales. Selective breeding improved larval survival to heat by 1.5-2.5x but settlement success showed limited improvement. Adult responses to selection at heat were similar but were greater in larvae from warmer reefs compared to the cooler reef. There was also a divergence between adults and offspring mean population responses, likely underpinned by heat stress imposing strong divergent selection on adult colonies. These results have implications for downstream selection during reproduction, as evidenced by variability in a conserved heat tolerance response across offspring lineages. These results inform our ability to forecast the impacts of climate change on wild populations of corals and will aid in developing novel conservation tools like the assisted evolution of at-risk species. SUMMARY STATEMENT Heat stress exerts disruptive selection on adult corals. This likely underpins variability in offspring survival and results in differences in offspring responses to selection.
Tuning the Sensitivity of Genetically Encoded Fluorescent Potassium Indicators through Structure-Guided and Genome Mining Strategies

Genetically encoded potassium indicators lack optimal binding affinity for monitoring intracellular dynamics in mammalian cells. Through structure-guided design and genome mining of potassium binding proteins, we developed green fluorescent potassium indicators with a broad range of binding affinities. KRaION1, based on the insertion of a potassium binding protein (Ec-Kbp) into the fluorescent protein mNeonGreen, exhibits an isotonically measured Kd of 69±10 (mM; mean ± standard deviation used throughout). We identified Ec-Kbp’s binding site using NMR spectroscopy to detect protein-thallium scalar couplings and refined the structure of Ec-Kbp in its potassium-bound state. Guided by this structure, we modified KRaION1, yielding KRaION2, which exhibits an isotonically measured Kd of 96±9 (mM). We identified four Ec-Kbp homologs as potassium binding proteins, which yielded indicators with isotonically measured binding affinities in the 39-112 (mM) range. KRaIONs expressed and functioned in HeLa cells, but exhibited lower Kd values, which were mirrored by lower Kd values measured in vitro when holding sodium constant. Thus, potassium indicator Kd may need to be evaluated in the context of a given experimental goal.
In silico analysis for potential proteins and microRNAs in Glioblastoma and Parkinsonism

In today’s world, neurodegenerative diseases such as Alzheimer’s disease, Parkinson’s Disease, Huntington’s Disease as well as brain cancers such as astrocytomas, ependymomas, glioblastomas have become a great threat to us. In this study, we are trying to find a probable molecular connection associated with two very much different diseases, Glioblastoma, also known as Glioblastoma Multiforme (cancers of microglial cells of our brain) and Parkinson’s disease. We at first downloaded the microarray datasets of these two diseases from Gene Expression Omnibus (GEO) and then analyzed them by the GEO2R tool. After analysis, we found 249 common upregulated differential expressed genes and 135 common downregulated differential expressed genes of these two diseases. Therefore the common differentially expressed genes, both upregulated and downregulated, were imported into STRING online tool to find out the protein-protein interactions. Now, this whole network was subjected to Cytoscape and the top ten hub genes were found by Cyto-Hubba plug-in. The top then hub genes are EGFR, CCNB1, CDK1, CCNA2, CHEK1, RAD51, MAD2L1, KIF20A, BUB1, and CCNB2. These all genes are upregulated in both diseases. To find out the biological processes, molecular functions, cellular components, and pathways associated with these hub genes Enrichr online software was used. We used miRNet software to determine the interactions of hub genes with microRNAs. This study will be useful in the future for drug targets discovery for these diseases.
The current state of knowledge for toxicity of corexit EC9500A dispersant: a review

Abstract Corexit EC9500A is an oil dispersant used prominently in the Deepwater Horizon spill both below water and on the ocean surface. Aquatic tests show that it has low toxicity to many crustaceans, corals and fish but is more toxic to plankton, daphnia and many species early life stages. Human health concerns found low acute toxicities but potentials for chronic effects with large exposures. Dispersant use should be based on many factors, of which toxicity is just one which should be considered. However, freshwater system toxicity requires more study before widespread use is recommended.
Software choice and depth of sequence coverage can impact plastid genome assembly – A case study in the narrow endemic Calligonum bakuense

Most plastid genome sequences are assembled from short-read whole-genome sequencing data, yet the impact that sequence coverage and the choice of assembly software can have on the accuracy of the resulting assemblies is poorly understood. In this study, we test the impact of both factors on plastid genome assembly in the threatened and rare endemic shrub Calligonum bakuense, which forms a distinct lineage in the genus Calligonum. We aim to characterize the differences across plastid genome assemblies generated by different assembly software tools and levels of sequence coverage and to determine if these differences are large enough to affect the phylogenetic position inferred for C. bakuense. Four assembly software tools (FastPlast, GetOrganelle, IOGA, and NOVOPlasty) and three levels of sequence coverage (original depth, 2,000x, and 500x) are compared in our analyses. The resulting assemblies are evaluated with regard to reproducibility, contig number, gene complement, inverted repeat length, and computation time; the impact of sequence differences on phylogenetic tree inference is also assessed. Our results show that software choice can have a considerable impact on the accuracy and reproducibility of plastid genome assembly and that GetOrganelle produced the most consistent assemblies for C. bakuense. Moreover, we found that a cap in sequence coverage can reduce both the sequence variability across assembly contigs and computation time. While no evidence was found that the sequence variability across assemblies was large enough to affect the phylogenetic position inferred for C. bakuense, differences among the assemblies may influence genotype recognition at the population level.
Cloacimonadota metabolisms include adaptations for engineered environments that are reflected in the evolutionary history of the phylum

Phylum Cloacimonadota (previously Cloacimonetes, WWE1) is an understudied bacterial lineage frequently associated with engineered and wastewater systems. Cloacimonadota members were abundant and diverse in metagenomic datasets from a municipal landfill, prompting an examination of phylogenetic relationships, metabolic diversity, and pangenomic dynamics across the phylum, based on 22 publicly available genomes and 24 from landfill samples. Cloacimonadota formed two discrete clades, with one clade’s genomes principally deriving from engineered systems. A few more-divergent genomes were placed basal in the tree, and not associated with either clade. Metabolic reconstructions for metagenome-assembled genomes predict an anaerobic, acetogenic, and fermentative lifestyle for the majority of Cloacimonadota surveyed. Genomes from engineered ecosystems (first clade) encode a unique suite of genes not typically found in genomes from natural environments (second clade). These encoded functions include acetate kinase, the enzyme responsible for the formation of acetate from acetyl phosphate, and carbon utilization enzymes, suggesting different substrate degradation and energy generation strategies in these ecologically and phylogenetically distinct lineages. Originality/Significance Statement Cloacimonadota is a bacterial phylum that is under-described compared to its members’ prevalence in genome repositories. Cloacimonadota are frequently associated with engineered systems, including being identified as abundant and diverse in the municipal landfill site surveyed in this study. We reconstructed twenty-four landfill-associated Cloacimonadota metagenome assembled genomes (MAGs), more than doubling the number of publicly available Cloacimonadota genomes. We combined these MAGs with available reference genomes to predict major metabolic pathways and to describe the conserved features in the lifestyle of phylum Cloacimonadota. We found that Cloacimonadota have distinct evolutionary histories associated with engineered versus natural environments. Prior studies have evaluated metabolism from individual Cloacimonadota genomes – this work is the first to examine trait distribution across a more-complete representation of the phylum, including identification of genomic features and metabolic strategies that correlate to habitat of origin.
CRISPR-Cas9-mediated knockout of CYP79D1 and CYP79D2 in cassava attenuates toxic cyanogen production

Cassava (Manihot esculenta Crantz) is a starchy root crop that supports over a billion people in tropical and subtropical regions of the world. This staple, however, produces toxic cyanogenic compounds and requires processing for safe consumption. Excessive consumption of insufficiently processed cassava, in combination with protein-poor diets, can have neurodegenerative impacts. Reducing the cyanogen content by conventional breeding is problematic due to the heterozygous nature of the crop; recombination will generally disrupt a clonally propagated cultivar’s suite of desirable traits. To reduce cyanide levels in cassava, we used CRISPR-mediated mutagenesis to disrupt the cytochrome P450 genes CYP79D1 and CYP79D2 whose protein products catalyze the first step in cyanogenic glucoside biosynthesis. Knockout of both genes eliminated cyanide in leaves and storage roots of cassava accession 60444 and the West African, farmer-preferred cultivar TME 419. Although knockout of CYP79D2 alone resulted in significant reduction of cyanide, mutagenesis of CYP79D1 did not, indicating these paralogs have diverged in their function. Our work demonstrates cassava genome editing for food safety, reduced processing requirements, and environmental benefits that could be readily extended to other farmer-preferred cultivars.
A robust receptive field code for optic flow detection and decomposition during self-motion

The perception of optic flow is essential for any visually guided behaviour of a moving animal. To mechanistically predict behaviour and understand the emergence of self-motion perception in vertebrate brains, it is essential to systematically characterize the motion receptive fields (RFs) of optic flow processing neurons. Here, we present the fine-scale RFs of thousands of motion-sensitive neurons studied in the diencephalon and the midbrain of zebrafish. We found neurons that serve as linear filters and robustly encode directional and speed information of translation-induced optic flow. These neurons are topographically arranged in pretectum according to translation direction. The unambiguous encoding of translation enables the decomposition of translational and rotational self-motion information from mixed optic flow. In behavioural experiments, we successfully demonstrated the predicted decomposition in the optokinetic and optomotor responses. Together, our study reveals the algorithm and the neural implementation for self-motion estimation in a vertebrate visual system.