Miracle-dz/UniFAR-FTUs huggingface dataset:
Nitrogen isotope ratio analysis of small samples: sample preparation and calibration

A method for the preparation of samples in the range of 14-100 . mu.g of organic and precipitated N for mass spectrometric isotope ratio analysis is described. In vacuo combustion and molecular sieve trapping of the sample gas into a 0.5 mL mass spectrometer inlet volume are employed. Samples can be processed at a rate of two to three per hour. The standard deviation of 12 analyses of a peptone preparation was 0.10%. The results of an interlaboratory calibration effort are presented. The materials tested were peptone, thiourea, histidine, kerogen, and two (NH/sub 4/)/sub 2/SO/sub 4/ standards. The results of these comparisons were with the range +/-0.12 delta/sup 15/N or less. Peptone was found to provide a more rigorous test of the combustion and preparation system than nitrogen salts and organic compounds of lower molecular weight. 20 references, 1 figure, 1 table.
Divergence in bidirectional plant-soil feedbacks between montane annual and coastal perennial ecotypes of yellow monkeyflower (Mimulus guttatus)

Understanding the physiological and genetic mechanisms underlying plant variation in interactions with root-associated biota (RAB) requires a micro-evolutionary approach. We use locally adapted montane annual and coastal perennial ecotypes of Mimulus guttatus (yellow monkeyflower) to examine population-scale differences in plant-RAB-soil feedbacks. We characterized fungal communities for the two ecotypes in-situ and used a full-factorial greenhouse experiment to investigate the effects of plant ecotype, RAB source, and soil origin on plant performance and endophytic root fungal communities. The two ecotypes harbored different fungal communities and responsiveness to soil biota was highly context-dependent. Soil origin, RAB source, and plant ecotype all affected the intensity of biotic feedbacks on plant performance. Feedbacks were primarily negative, and we saw little evidence of local adaptation to either soils or RAB. Both RAB source and soil origin significantly shaped fungal communities in roots of experimental plants. Further, the perennial ecotype was more colonized by arbuscular mycorrhizal fungi (AMF) than the montane ecotype, and preferentially recruited home AMF taxa. Our results suggest life history divergence and distinct edaphic habitats shape plant responsiveness to RAB and influence specific associations with potentially mutualistic root endophytic fungi. Our results advance the mechanistic study of intraspecific variation in plant–soil–RAB interactions.
NOTCH-YAP1/TEAD-DNMT1 axis regulates hepatocyte reprogramming into intrahepatic cholangiocarcinoma

Intrahepatic cholangiocarcinoma (ICC), a disease of poor prognosis, has increased in incidence. It is challenging to treat due to intra- and inter-tumoral heterogeneity, which in part is attributed to diverse cellular origin. Indeed, co-expression of AKT and NICD in hepatocytes (HCs) yielded ICC, with similarity to proliferative, Notch-activated, and stem cell-like subclasses of clinical ICC. NICD regulated SOX9 and YAP1 during ICC development. Yap1 deletion or TEAD inhibition impaired HC-to-biliary epithelial cell (BEC) reprogramming and ICC proliferation; Sox9 loss repressed tumor growth; and Yap1-Sox9 combined loss abolished ICC development in AKT-NICD model. DNMT1 was discovered as a novel downstream effector of YAP1-TEAD complex that directed HC-to-BEC/ICC fate-switch. DNMT1 loss prevented Notch-dependent HC-to-ICC development, and DNMT1 re-expression restored ICC development following TEAD repression. Coexpression of DNMT1 with AKT was sufficient to induce hepatic tumor development including ICC. Thus, we have identified a novel NOTCH-YAP1/TEAD-DNMT1 axis essential for HC-driven ICC development. SIGNIFICANCE We evaluated the clinical relevance of hepatocyte-driven ICC model and revealed critical but distinct roles of YAP1 and SOX9 in AKT-NICD-driven hepatocyte-derived ICC. We also identified NOTCH-YAP1/TEAD-DNMT1 axis as a critical driver for hepatocyte-to-ICC reprogramming, which might have biological and therapeutic implications in ICC subsets.
Gating mechanism of cardiac ryanodine receptor 2 upon calcium ion binding

Cardiac ryanodine receptor (RyR2) is a large Ca2+ release channel in the sarcoplasmic reticulum and indispensable for excitation-contraction coupling in the heart. RyR2 is activated by Ca2+ and RyR2 mutations have been implicated in severe arrhythmogenic heart diseases. Yet, the structural basis underlying channel opening and how mutations affect the channel remain unknown. Here, we combined high-resolution structures determined by cryo-electron microscopy with quantitative functional analysis of channels carrying various mutations in specific residues. We demonstrated that interactions close to the channel pore are important for stabilizing the channel in the closed state and those in the surrounding regions are essential for channel opening. Our results reveal mechanisms underlying channel opening upon Ca2+ binding and alterations by pathogenic mutations of RyR2 at the atomic level. One Sentence SummaryKey movements and interactions in RyR2 during cardiac Ca2+ channel opening are clarified at the atomic level.
Phosphorylation of AMPA receptor subunit GluA1 regulates clathrin-mediated receptor endocytosis

Synaptic strength is altered during synaptic plasticity by controlling the number of AMPA receptors (AMPARs) at excitatory synapses. In particular, during long-term potentiation and synaptic up-scaling, AMPARs are accumulated at synapses to increase synaptic strength. Neuronal activity leads to activity-dependent phosphorylation of AMPAR subunit GluA1, and subsequent increases in GluA1 surface expression, which can be achieved by either an increase in exocytosis or a decrease in endocytosis of the receptors. However, the molecular pathways underlying GluA1 phosphorylation-induced elevation of surface AMPAR expression are not completely understood. Here, we first employ fluorescence recovery after photobleaching (FRAP) to reveal that phosphorylation of GluA1 Serine 845 (S845) plays a more important role in receptor endocytosis than exocytosis during synaptic plasticity. Notably, endocytosis of AMPARs depends upon the clathrin adaptor, AP2, which recruits cargo proteins into endocytic clathrin coated pits. Importantly, the KRMK (Lysine-Arginine-Methionine-Lysine) motif in the carboxyl-terminus of GluA1 is suggested to be an AP2 binding site, but the exact function has not been defined. Moreover, the GluA1 KRMK motif is closely located to one of GluA1 phosphorylation sites, serine 845 (S845), and GluA1 S845 dephosphorylation is suggested to enhance endocytosis during long-term depression. In fact, we show that an increase in GluA1 S845 phosphorylation by two distinct forms of synaptic plasticity, long-term potentiation and synaptic up-scaling, diminishes the binding of the AP2 adaptor. This reduces endocytosis, resulting in elevation of GluA1 surface expression. We thus demonstrate a mechanism of GluA1 phosphorylation-regulated clathrin-mediated endocytosis of AMPARs.
How efficient is cloud droplet formation of organic aerosols?

Based on laboratory findings that small amounts of a soluble aerosol, such as ammonium sulfate (AS), drastically decrease the activation diameter of moderately soluble organic aerosols, we performed studies with an adiabatic parcel model for cloud droplet nucleation. Moderately soluble organics, such as adipic acid (AA), which represents a class of partially soluble aerosols as found in atmospheric aerosols, require a larger supersaturation and result in fewer cloud droplets as compared to pure AS and vice versa when compared to a completely insoluble species such as dust. Adding only 10% AS to AA dramatically increases its ability to become activated resulting in 36–92% of the cloud droplets that would be obtained from pure AS, whereas the droplet concentration in the almost pure AA aerosol is only 11–47% of that of AS. Addition of a surface active species, such as nonanoic acid, instead of AS to AA reduces its activated fraction by 3–34% as compared to the AA/AS system.
The Bardet-Biedl Syndrome complex component BBS1 regulates proteasome-dependent F-actin clearance from the centrosome to enable its translocation to the T cell immune synapse

Components of the intraflagellar transport (IFT) system that regulates the assembly of the primary cilium are exploited by the non-ciliated T cell to orchestrate polarized endosome recycling to sustain signaling during immune synapse formation. Here we have investigated the potential role of BBS1, an essential core component of the Bardet-Biedl syndrome complex that cooperates with the IFT system in ciliary protein trafficking, in the assembly of the T cell synapse. We show that BBS1 allows for centrosome polarization towards the immune synapse by promoting its untethering from the nuclear envelope. This function is achieved through the clearance of centrosomal F-actin and its positive regulator WASH, a process that we demonstrate to be dependent on the proteasome. We show that BBS1 regulates this process by coupling the 19S proteasome regulatory subunit to the microtubule motor dynein for its transport to the centrosome. Our data identify the ciliopathy-related protein BBS1 as a new player in T cell synapse assembly that acts upstream of the IFT system to set the stage for polarized vesicular trafficking and sustained signaling.
Emetine as an antiviral agent suppresses SARS-CoV-2 replication by inhibitinginteraction of viral mRNAwith eIF4E: An in vitro study

Emetine is a FDA-approved drug for the treatment of amebiasis. In the recent times we had also demonstrated the antiviral efficacy of emetine against some RNA and DNA viruses. Following emergence of the COVID-19, we further evaluated thein vitro antiviral activity of emetine against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The therapeutic index of emetine was determined to be 10910.4, at a cytotoxic concentration 50 (CC50) of 1603.8 nM and effective concentration 50 (EC50) of 0.147 nM.Besides, we also demonstrated the protective efficacy of emetine against lethal challenge with infectious bronchitis virus (IBV; a chicken coronavirus) in the embryonated chicken egg infection model. Emetine treatment was shown to decrease viral RNA and protein synthesis without affecting other steps of viral life cycle such as attachment, entry and budding.In a chromatin immunoprecipitation (CHIP) assay, emetine was shown to disrupt the binding of SARS-CoV-2 RNA with eIF4E (eukaryotic translation initiation factor 4E, a cellular cap-binding protein required for initiation ofprotein translation). Further, SARS-CoV-2 was shown to exploit ERK/MNK1/eIF4E signalling pathwayfor its effective replication in the target cells. To conclude, emetine targets SARS-CoV-2 protein synthesis which is mediated via inhibiting the interaction of SARS-CoV-2 RNA with eIF4E. This is a novel mechanistic insight on the antiviral efficacy of emetine. In vitro antiviral efficacy against SARS-CoV-2 and its ability to protect chicken embryos against IBV suggests that emetine could be repurposed to treat COVID-19.
Human retrosplenial theta and alpha modulation in active spatial navigation

Spatial navigation is a complex cognitive process based on multiple senses that are integrated and processed by a wide network of brain areas. Previous studies have revealed the retrosplenial complex (RSC) to be modulated in a task-related manner during navigation. However, these studies restricted participants’ movement to stationary setups, which might have impacted heading computations due to the absence of vestibular and proprioceptive inputs. Here, we investigated neural dynamics of RSC in an active spatial navigation task where participants actively ambulated from one location to several other points while the position of a landmark and the starting location were updated. The results revealed theta power in the RSC to be pronounced during heading changes but not during translational movements, indicating that physical rotations induce human RSC theta activity. This finding provides a potential evidence of head-direction computation in RSC in healthy humans during active spatial navigation.
Muscle specific translational control of Cand2 by mTORC1 regulates adverse cardiac remodeling

The mechanistic target of rapamycin (mTOR) is a key regulator of pathological remodeling in the heart by activating ribosomal biogenesis and mRNA translation. Inhibition of mTOR in cardiomyocytes is protective, however, a detailed role of mTOR in translational regulation of specific mRNA networks in the diseased heart is largely unknown. A cardiomyocyte genome-wide sequencing approach was used to define mTOR-dependent post-transcriptional gene expression control at the level of mRNA translation. This approach identified the muscle-specific protein Cullin-associated NEDD8-dissociated protein 2 (Cand2) as a translationally upregulated gene, dependent on the activity of mTOR. Deletion of Cand2 protects the myocardium against pathological remodeling. Mechanistically, we found that Cand2 links mTOR signaling to pathological cell growth by increasing Grk5 protein expression. Our data suggest that cell-type-specific targeting of mTOR might have therapeutic value for adverse pathological cardiac remodeling.
Aperture: Accurate detection of structural variations and viral integrations in circulating tumor DNA using an alignment-free algorithm

Background The identification of structural variations (SV) and viral integrations in circulating tumor DNA (ctDNA) is a key step in precision oncology that may assist clinicians for treatment selection and monitoring. However, it is challenging to accurately detect low frequency SVs or SVs involving complex junctions in ctDNA sequencing data due to the short fragment size of ctDNA. Results Here, we describe Aperture, a new fast SV caller that applies a unique strategy of k-mer based searching, breakpoint detection using binary labels and candidates clustering to detect SVs and viral integrations in high sensitivity, especially when junctions span repetitive regions, followed by a barcode-based filter to ensure specificity. We evaluated the performance of Aperture in stimulated, reference and real datasets. Aperture demonstrates superior sensitivity and specificity in all tests, especially for low dilution test, compared with existing methods. In addition, Aperture is able to predict sites of viral integration and identify complex SVs involving novel insertions and repetitive sequences in real patient data. Conclusions Using a novel alignment-free algorithm, Aperture achieves sensitive, specific and fast detection of structural variations and viral integrations, which may enhance the diagnostic value of ctDNA in clinical application. The executable file and source code are freely available at https://github.com/liuhc8/Aperture.
Design especulativo como mediador de atores humanos e não humanos dentro de um contexto de controvérsias

Este trabalho visa compreender como projetar atraves da especulacao e controversia. Para isso, o projeto compreende a natureza do design especulativo, e pela perspectiva da Teoria Ator-Rede, o conceito de Mediacao e Controversia. A pesquisa exploratoria baseou-se no mapeamento das controversias proposto por Venturini (2010) para explorar o contexto do Complexo Industrial Maesa em Caxias do Sul RS. A partir disto, a controversia foi representada e apresentada para um grupo de projeto para a criacao das especulacoes. A trajetoria da especulacao, a partir de entao, foi: Apresenta-la para participantes selecionados no contexto da controversia Maesa atraves de um grupo focal. Ao todo foram 3 grupos focais formados por grupos variados. A cada grupo focal, foi observado os topicos principais entre os atores e a especulacao pela perspectiva da Teoria Ator-Rede e do Design Especulativo. Posteriormente os topicos principais eram levados para uma nova sessao de projeto com o grupo de projeto, que em conjunto como autor desta pesquisa, modificava a trajetoria da especulacao no contexto da controversia. Ao todo, foram realizados 3 grupos focais, onde a Especulacao original no contexto da controversia foi alterada a cada ciclo. Compreende-se que o papel da controversia, se observado pela Teoria Ator-Rede permite explorar diferentes caminhos para a criticidade da especulacao. Com isso, o Design Especulativo inserido dentro da controversia e mais um ator em seu contexto, no entanto, sua pratica projetual possui o papel de agenciar diversos atores e perspectivas. Criando novos enredos e conexoes improvaveis.
Multiple variants of the blast fungus effector AVR-Pik bind the HMA domain of the rice protein OsHIPP19 with high affinity

Microbial plant pathogens secrete effector proteins which manipulate the host to promote infection. Effectors can be recognised by plant intracellular nucleotide-binding leucine-rich repeat (NLR) receptors, initiating an immune response. The AVR-Pik effector from the rice blast fungus Magnaporthe oryzae is recognised by a pair of rice NLR receptors, Pik-1 and Pik-2. Pik-1 contains a non-canonical integrated heavy metal-associated (HMA) domain, which directly binds AVR-Pik to activate plant defences. Non-canonical integrated domains are widespread in plant NLRs and are thought to resemble the host target of the recognised effector. AVR-Pik interacts with specific rice HMA domain-containing proteins, namely heavy metal-associated isoprenylated plant proteins (HIPPs) and heavy metal-associated plant proteins (HPPs). Here, we define the biochemical and structural basis of the interaction between AVR-Pik and OsHIPP19, and compare the interaction with the HMA domain of Pik-1. Using analytical gel filtration and surface plasmon resonance, we show that multiple AVR-Pik variants, including the stealthy variants AVR-PikC and AVR-PikF which do not interact with any characterised Pik-1 alleles, bind to OsHIPP19 with nanomolar affinity. The crystal structure of OsHIPP19 in complex with AVR-PikF reveals differences at the interface that underpin high-affinity binding of OsHIPP19-HMA to a wider set of AVR-Pik variants than achieved by the integrated HMA domain of Pik-1. Our results provide a foundation for engineering the HMA domain of Pik-1 to extend binding to currently unrecognised AVR-Pik variants and expand disease resistance in rice to divergent pathogen strains.
The tumor suppressor protein PTEN undergoes amyloid-like aggregation in tumor cells

Protein aggregation is an underappreciated mechanism that may contribute to the loss- and oncogenic-gain-of-function of mutant tumor suppressors such as p53 and axin. In the present study, we describe amyloid-like aggregation behaviour of the second most frequently mutated tumor suppressor in human cancer, PTEN. In silico analysis revealed a particularly high aggregation vulnerability for this protein, which was corroborated by in vitro aggregation assays. In cultured tumor cells, we found that under stress conditions, PTEN readily undergoes amyloid-like aggregation as a result of mutation. However, we also show that severe dysregulation of protein homeostasis may lead to aggregation of wild-type PTEN. These observations were supported by a small survey of patient-derived uterine tumor tissues, which found that more than 25% of tumors analyzed displayed wild-type PTEN aggregation. Finally, in an exploratory clinical study we found that PTEN aggregation status was correlated with a decline in clinical outcome. Our findings establish that the tumor suppressor PTEN is highly aggregation-prone and our work suggests that protein aggregation might be an underestimated but prevalent component of cancer cell biology.
Constructing ab initio models of ultra-thin Al–AlOx–Al barriers

The microscopic structure of ultra-thin oxide barriers often plays a major role in modern nano-electronic devices. In the case of superconducting electronic circuits, their operation depends on the electrical nonlinearity provided by one or more such oxide layers in the form of ultra-thin tunnel barriers (also known as Josephson junctions). Currently available fabrication techniques manufacture an amorphous oxide barrier, which is attributed as a major noise source within the device. The nature of this noise is currently an open question and requires both experimental and theoretical investigation. Here, we present a methodology for constructing atomic-scale computational models of Josephson junctions using a combination of molecular mechanics, empirical and ab initio methods. These junctions consist of ultra-thin amorphous aluminium-oxide layers sandwiched between crystalline aluminium. The stability and structure of these barriers as a function of density and stoichiometry are investigated, which we compare with experimentally observed parameters.
The de novo genome of the “Spanish” slug Arion vulgaris Moquin-Tandon, 1855 (Gastropoda: Panpulmonata): massive expansion of transposable elements in a major pest species

Background The “Spanish” slug, Arion vulgaris Moquin-Tandon, 1855, is considered to be among the 100 worst pest species in Europe. It is common and invasive to at least northern and eastern parts of Europe, probably benefitting from climate change and the modern human lifestyle. The origin and expansion of this species, the mechanisms behind its outstanding adaptive success and ability to outcompete other land slugs are worth to be explored on a genomic level. However, a high-quality chromosome-level genome is still lacking. Findings The final assembly of A. vulgaris was obtained by combining short reads, linked reads, Nanopore long reads, and Hi-C data. The genome assembly size is 1.54 Gb with a contig N50 length of 8.6 Mb. We found a recent expansion of transposable elements (TEs) which results in repetitive sequences accounting for more than 75% of the A. vulgaris genome, which is the highest among all known gastropod species. We identified 32,518 protein coding genes, and 2,763 species specific genes were functionally enriched in response to stimuli, nervous system and reproduction. With 1,237 single-copy orthologs from A. vulgaris and other related mollusks with whole-genome data available, we reconstructed the phylogenetic relationships of gastropods and estimated the divergence time of stylommatophoran land snails (Achatina) and Arion slugs at around 126 million years ago, and confirmed the whole genome duplication event shared by them. Conclusions To our knowledge, the A. vulgaris genome is the first land slug genome assembly published to date. The high-quality genomic data will provide valuable genetic resources for further phylogeographic studies of A. vulgaris origin and expansion, invasiveness, as well as molluscan aquatic-land transition and shell formation.
An expanded growth model for grasses

Abstract A growth model is needed which will account for time of planting and stage of growth for annual grasses and for time of season and harvest interval for perennial grasses. A linear intrinsic growth function was assumed previously which described response of dry matter accumulation to harvest interval for a warm‐season perennial. Field data indicated that this model was appropriate for intervals up to about six weeks. Beyond this range yields peaked and then declined with increased interval. This article assumes a linear‐exponential intrinsic growth function which more accurately describes the data and removes the restriction on harvest interval. The model describes dependence of dry matter accumulation on time of season and harvest interval for a warm‐season perennial Coastal bermudagrass (Cynodon dactylon). Mean time and standard deviation of the distribution are independent of harvest interval. The model also accounts for time of planting and time in the season for the warm‐season annual corn (Z.