bluuebunny/crossref_metadata_2025_split huggingface dataset:
PICASSO: Ultra-multiplexed fluorescence imaging of biomolecules through single-round imaging and blind source unmixing
Authors: Seo Junyoung , Sim Yeonbo , Kim Jeewon , Kim Hyunwoo , Cho In , Yoon Young-Gyu , Chang Jae-Byum 
Published: January 2021

ABSTRACTUltra-multiplexed fluorescence imaging of biomolecules is essential to studying heterogeneous biological systems. However, this is challenging due to fluorophores’ spectral overlap and variation of the emission spectra. Here, we propose a strategy termed PICASSO, which enables more than 15-colour multiplexed imaging of thick tissue slices through a single imaging process and blind unmixing without reference spectra measurement. We show that PICASSO can be used to achieve a high multiplexing capability in diverse applications, such as 3D protein imaging, expansion microscopy, tissue clearing, imaging of clinical specimens, and cyclic immunofluorescence imaging. PICASSO only requires an equal number of images as the number of fluorophores, enabling such a high level of multiplexed imaging even with bandpass filter-based microscopy. As such, PICASSO would be a useful tool for the study of cancer, the immune system, and the brain, as well as for the diagnosis of cancer, as it enables ultra-multiplexed imaging of diverse specimens with minimum instrumental requirements and experimental processes.
Cooperativity boosts affinity and specificity of proteins with multiple RNA-binding domains
Authors: Stitzinger Simon H. , Sohrabi-Jahromi Salma , Söding Johannes 
Published: January 2021

AbstractNumerous cellular processes rely on the binding of proteins with high affinity to specific sets of RNAs. Yet most RNA binding domains display low specificity and affinity, to the extent that for most RNA-binding domains, the enrichment of the best binding motif measured by high-throughput RNA SELEX or RNA bind-n-seq is usually below 10-fold, dramatically lower than that of DNA-binding domains. Here, we develop a thermodynamic model to predict the binding affinity for proteins with any number of RNA-binding domains given the affinities of their isolated domains. For the four proteins in which affinities for individual domains have been measured the model predictions are in good agreement with experimental values. The model gives insight into how proteins with multiple RNA-binding domains can reach affinities and specificities orders of magnitude higher than their individual domains. Our results contribute towards resolving the conundrum of missing specificity and affinity of RNA binding proteins and underscore the need for bioinformatic methods that can learn models for multi-domain RNA binding proteins from high-throughputin-vitroandin-vivoexperiments.
The MEMIC: Anex vivosystem to model the complexity of the tumor microenvironment
Authors: Janská Libuše , Anandi Libi , Kirchberger Nell C. , Marinkovic Zoran S. , Schachtner Logan T. , Guzelsoy Gizem , Carmona-Fontaine Carlos 
Published: January 2021

ABSTRACTThere is an urgent need for accurate, scalable, and cost-efficient models of the complexity and heterogeneity of the tumor microenvironment. Here, we detail how to fabricate and use the Metabolic Microenvironment Chamber (MEMIC) – a 3D-printedex vivomodel of intratumoral heterogeneity. A major driver of the cellular and molecular diversity in tumors is the accessibility to the blood stream that provides key resources such as oxygen and nutrients. While some tumor cells have direct access to these resources, many others must survive under progressively more ischemic environments as they reside further from the vasculature. The MEMIC is designed to simulate the differential access to nutrients and allows co-culturing different cell types, such as tumor and immune cells. This system is optimized for live imaging and other microscopy-based approaches and it is a powerful tool to study tumor features such as the effect of nutrient scarcity on tumor-stroma interactions. Due to its adaptable design and full experimental control, the MEMIC can provide novel insights into the tumor microenvironment that would be difficult to obtain via other methods. As a proof of principle, we show that cells can sense gradual changes in metabolite concentration, and tune intracellular cell signaling to form multicellular spatial patterns of cell proliferation. We also show that ischemic macrophages reduce epithelial features in neighboring tumor cells highlighting the power of this system to study cell-cell interactions and non-cell autonomous effects of the metabolic microenvironment. We propose that the MEMIC can be easily adapted to study early development, ischemic stroke, and other systems where multiple cell types interact within heterogeneous environments.
Leaf-to-whole plant spread bioassay for pepper andRalstonia solanacearuminteraction determines inheritance of resistance to bacterial wilt for further breeding
Authors: Kwon Ji-Su , Nam Jae-Young , Yeom Seon-In , Kang Won-Hee 
Published: January 2021

AbstractBacterial wilt (BW) disease byRalstonia solanacearumis a serious disease and causes severe yield losses in chili peppers worldwide. Resistant cultivar breeding is the most effective in controlling BW. Thus, a simple and reliable evaluation method is required to assess disease severity and to investigate the inheritance of resistance for further breeding programs. Here, we developed a reliable leaf-to-whole plant spread bioassay for evaluating BW disease and then, using this, determined the inheritance of resistance toR. solanacearumin peppers.Capsicum annuum‘MC4’ displayed a completely resistant response with fewer disease symptoms, a low level of bacterial cell growth, and significant up-regulations of defense genes in infected leaves compared to those in susceptible ‘Subicho’. We also observed the spreading of wilt symptoms from the leaves to the whole susceptible plant, which denotes the normal BW wilt symptoms, similar to the drenching method. Through this, we optimized the evaluation method of the resistance to BW. Additionally, we performed genetic analysis for resistance inheritance. The parents, F1and 90 F2progenies, were evaluated, and the two major complementary genes involved in the BW resistance trait were confirmed. These could provide an accurate evaluation to improve resistant pepper breeding efficiency against BW.
Abolished miR158 activity leads to 21-nucleotide tertiary phasiRNA biogenesis that targetsNHX2inArabidopsis thaliana
Authors: Tripathi Abhinandan Mani , Singh Rajneesh , Singh Akanksha , Verma Ashwani Kumar , Mishra Parneeta , Narayan Shiv , Shirke Pramod Arvind , Roy Sribash 
Published: January 2021

ABSTRACTSmall RNAs including microRNAs (miRNAs) are short 20-24-nucleotide non-coding RNAs. They are key regulators of gene expression in plants and other organisms. Some small RNAs, mostly 22-nucleotide long trigger biogenesis of secondary small interfering RNAs (siRNAs). Those siRNAs having distinctive phased configuration are known as phased siRNAs (phasiRNAs) and act either incisortransenhancing silencing cascade. Here, we report natural variants ofMIR158having deletions or insertions led to negligible or reduced expression of miR158. The deletion/insertion events affected processing of primary transcript of miR158 to precursor and to mature miR158. We show that miR158 targets a pseudo-pentatricopeptide gene and its abolished activity led to 21-nucleotide tertiary phasiRNA generation from its target. The biogenesis of these phasiRNAS is triggered byTAS2derived two siRNAs. Accordingly, small RNA analyses of these natural variants, mutants and over-expression lines ofMIR158or its target exhibited enhanced or reduced phasiRNA biogenesis. Finally, we functionally validated the highest expressed tertiary phasiRNA that targetsNHX2thereby regulating transpiration and stomatal conductance. Overall, we deciphered a new module of small RNA network, miRNA-TAS-siRNA-pseudogene-tertiary phasiRNA-NHX2, suggesting an additional layer of gene regulation and larger role of pseudogene in plants.
Improved spatio-temporal measurements of visually-evoked fields using optically-pumped magnetometers
Authors: Gialopsou Aikaterini , Abel Christopher , James Timothy M. , Coussens Thomas , Bason Mark G. , Puddy Reuben , Di Lorenzo Francesco , Rolfs Katharina , Voigt Jens , Sander Tilmann , Cercignani Mara , Krüger Peter 
Published: January 2021

AbstractRecent developments in performance and practicality of optically pumped magnetometers have enabled new capabilities in non-invasive brain function mapping through magnetoencephalography. In particular the lack of need of cryogenic operating conditions allows for more flexible placement of the sensor heads closer to the brain surface, leading to improved spatial measurement resolution and increased source localisation capabilities. Through the recording of visually evoked brain fields (VEF), we demonstrate that the closer sensor proximity can be further exploited to improve the temporal resolution. We use optically pumped magnetometers (OPMs), and for reference superconducting quantum interference devices (SQUIDs), to measure brain responses to standard flash and pattern reversal stimuli. We find highly reproducible signals with consistency across multiple healthy participants, stimulus paradigms and sensor modalities. The temporal resolution advantage of OPMs is manifest in a fourfold improvement of the ratio of magnetic signal peak height to temporal width, compared to SQUIDs. The resulting capability of improved spatio-temporal signal tracing is illustrated by simultaneous vector recordings of VEFs in the primary (V1) and associative (V2) visual cortex, where a time lag on the order of 10-20 ms is consistently found. This paves the way for further studies of spatio-temporal neurophysiological signal tracking in visual stimulus processing and other brain responses with potentially far-reaching consequences for time-critical mapping of functionality in the healthy and pathological brains.
Natural diversity of honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states
Authors: Papp Márton , Békési László , Farkas Róbert , Makrai László , Maróti Gergely , Tőzsér Dóra , Solymosi Norbert 
Published: January 2021

ABSTRACTAs pollinators and producers of numerous human consumed products, honey bees have great ecological, economic and health importance. The composition of their bacteriota, for which the available knowledge is limited, is essential for their body’s functioning. Based on our survey, we performed a metagenomic analysis of samples collected by repeated sampling. We used geolocations that represent the climatic types of the study area over two nutritionally extreme periods (March and May) of the collection season. In bacteriome composition, significant (p=0.002) difference was found between the samples from March and May. The samples’ bacteriome from March showed a significant (p=0.02) composition difference between cooler and the warmer regions. However, there were no significant bacteriome composition differences among the climatic classes of samples taken in May. Based on our results, one may conclude that the composition of healthy core bacteriome in honey bees varies depending on the climatic and seasonal conditions. This is likely due to climatic factors and vegetation states determining the availability and nutrient content of flowering plants. The results of our study prove that in order to gain a thorough understanding of a microbiome’s natural diversity, we need to obtain the necessary information from extreme ranges within the host’s health state.
DROSOPHILAMTOR COMPLEX 2 PRESERVES MITOCHONDRIAL AND CARDIAC FUNCTION UNDER HIGH FAT DIET TREATMENT
Authors: Chang Kai , Requejo Figueroa Guillermo A. , Bai Hua 
Published: January 2021

AbstractHigh fat diet (HFD)-associated lipotoxicity is one of the major causes of cardiovascular diseases. The mechanistic target of rapamycin (mTOR) pathway, especially mTOR complex 1 (mTORC1), has been previously implicated in HFD-induced heart dysfunction. In the present study, we find that unlike mTORC1, mTOR complex 2 (mTORC2) protects hearts from HFD-induced cardiomyopathy and mitochondrial dysfunction inDrosophila. We show that HFD feeding induces contractile dysfunction along with altered mitochondrial morphology and function. Upon HFD feeding, the mitochondria of cardiomyocytes exhibit fragmentation, loss of membrane potential, and calcium overload. Interestingly, HFD feeding also reduces the activity of cardiac mTORC2. In line with this finding, the flies with cardiac-specific knockdown ofrictor, the key subunit of mTORC2, show cardiac and mitochondrial dysfunction similar to what is observed in HFD-fed wild-type flies. Conversely, cardiac-specific activation of mTORC2 by overexpressingrictorattenuates HFD-induced mitochondrial and cardiac dysfunction. Thus, our findings suggest that mTORC2 is a cardioprotective factor and regulates mitochondrial homeostasis upon HFD feeding.
Social and physical environment independently affect oviposition decisions inDrosophila melanogaster
Authors: Churchill Emily R. , Dytham Calvin , Bridle Jon R. , Thom Michael D.F. 
Published: January 2021

AbstractIn response to environmental stimuli, including variation in the presence of conspecifics, animals show highly plastic responses in behavioural and physiological traits influencing reproduction. These responses have been extensively documented in males, but equivalent study of females is so far lacking. We expect females to be highly responsive to environmental variation, with significant impacts on fitness given females’ direct impact on offspring number, size, and developmental conditions. UsingDrosophila melanogasteras a model, we manipulate (a) exposure to conspecific females, expected to influence their expectation of number of potential mates and larval density for their own offspring, and (b) test how prior consexual population density interacts with the spatial distribution of potential oviposition sites, with females expected to prefer clustered food resources that can support a larger number of eggs and larvae. After exposure to competition, females were slower to start copulating and reduced their copulation duration – the opposite effect to that observed in males previously exposed to rivals. There was a parallel and perhaps related effect on egg production, with females previously housed in groups laying fewer eggs than those that were housed in solitude. The spatial distribution of resources also influenced oviposition behaviour: females clearly preferred aggregated patches of substrate, being more likely to lay, and laying on more of the available patches, in the clustered environment. However, we found no significant interaction between prior housing conditions and resource patchiness, indicating that females did not perceive the value of different resource distributions differently when they were expecting either high or low levels of larval competition. While exposure to consexual competition influences copulatory behaviours, it is the distribution of oviposition resources that has a greater impact on oviposition decisions.
In vitroassessment of an engineered tBID-based safety switch system in human T lymphocytes
Authors: Lu Jiamiao , Collins Patrick , Lee Ki Jeong , Li Chi-Ming , Wang Songli 
Published: January 2021

ABSTRACTCell therapy as a promising therapeutic modality to treat cancer has been intensively studied for decades. However, the clinical trials have indicated that patients under T cell therapy may develop severe cytokine release syndrome resulting in hospitalization or even death. Furthermore, genetic modifications to promote proliferation and persistence of T cells could result in high numbers of long-lived engineered cells in patients after treatment. In this study we developed a novel tBID-based safety switch regulated through a small molecule inducible on switch to control undesired toxicity or ablate engineered cells as needed. We compared several tBID-based safety switch constructs with the clinically validated safety switches, HSV-TK (human herpes simplex virus thymidine kinase) and iCasp9 (inducible Caspase 9), few tBID-based safety switch constructs were systematically tested and investigatedin vitroin Jurkat or human primary T cells. We demonstrated that our novel tBID based safety switch, with optimization, was able to eliminate up to ~90% of transduced human primary T cells within 72hr after activation, providing an alternative switch system to manage safety concerns for cell therapy.
Speed-related but not detrended gait variability increases with more sensitive self-paced treadmill controllers at multiple slopes
Authors: Castano Cesar R. , Huang Helen J. 
Published: January 2021

AbstractSelf-paced treadmills are being used more frequently to study humans walking with their self-selected gaits on a range of slopes. There are multiple options to purchase a treadmill with a built-in controller, or implement a custom written self-paced controller, which raises questions about how self-paced controller affect treadmill speed and gait biomechanics on multiple slopes. This study investigated how different self-paced treadmill controller sensitivities affected gait parameters and variability on decline, level, and incline slopes. We hypothesized that increasing self-paced controller sensitivity would increase gait variability on each slope. We also hypothesized that detrended variability could help mitigate differences in variability that arise from differences in speed fluctuations created by the self-paced controllers. Ten young adults walked on a self-paced treadmill using three controller sensitivities (low, medium, and high) and fixed speeds at three slopes (decline, −10°; level, 0°; incline, +10°). Within each slope, average walking speeds and spatiotemporal gait parameters were similar regardless of self-paced controller sensitivity. With higher controller sensitivities on each slope, speed fluctuations, speed variance, and step length variance increased whereas step frequency variance and step width variance were unaffected. Detrended variance was not affected by controller sensitivity suggesting that detrending variability helps mitigate differences associated with treadmill speed fluctuations. Speed-trend step length variances, however, increased with more sensitive controllers. Further, detrended step length variances were similar for self-paced and fixed speed walking, whereas self-paced walking included substantial speed-trend step length variance not present in fixed speed walking. In addition, regardless of the self-paced controller, subjects walked fastest on the level slope with the longest steps, narrowest steps, and least variance. Overall, our findings suggest that separating gait variability into speed-trend and detrended variability could be beneficial for interpreting gait variability among multiple self-paced treadmill studies and when comparing self-paced walking with fixed speed walking.
Caspase3-deficient cells require fibronectin for protection against autophagy-dependent death
Authors: Weir David B. , Boise Lawrence H. 
Published: January 2021

ABSTRACTCaspases are required for execution of apoptosis. However, in their absence, signals that typically induce apoptosis can still result in cell death. Our laboratory previously demonstrated that Casp3-deficient mouse embryonic fibroblasts (MEFs) have increased fibronectin (FN) secretion, and an adhesion-dependent survival advantage compared to wild type (WT) MEFs. Here, we show that FN is required for survival of Casp3-deficient MEFs following serum withdrawal. Furthermore, when FN is silenced, serum withdrawal-induced death is caspase-independent. However, procaspase-7 is cleaved, suggesting that MOMP is taking place. Indeed, in the absence of FN, cytochromecrelease is increased following serum withdrawal in Casp3-deficient MEFs. Yet death does not correspond to cytochromecrelease in Casp3-deficient MEFs. This is true both in the presence and absence of FN. Additionally, caspase-independent death is inhibited by Bcl-XLoverexpression. These findings suggest that Bcl-XLis not inhibiting death through regulation of Bax/Bak insertion into the mitochondria, but through a different mechanism. One such possibility is autophagy and induction of autophagy is associated with caspase-independent death in Casp3-deficient cells. Importantly, when ATG5 is ablated in Casp3-deficient cells, autophagy is blocked and death is largely inhibited. Taken together, our data indicate that Casp3-deficient cells incapable of undergoing canonical serum withdrawal-induced apoptosis, are protected from autophagy-dependent death by FN-mediated adhesion.
Genome and transcriptome of a pathogenic yeast,Candida nivariensis
Authors: Fan Yunfan , Gale Andrew N , Bailey Anna , Barnes Kali , Colotti Kiersten , Mass Michal , Morina Luke B , Robertson Bailey , Schwab Remy , Tselepidakis Niki , Timp Winston 
Published: January 2021

AbstractWe present a highly contiguous genome and transcriptome of the pathogenic yeast,Candida nivariensis. We sequenced both the DNA and RNA of this species using both the Oxford Nanopore Technologies (ONT) and Illumina platforms. We assembled the genome into an 11.8 Mb draft composed of 16 contigs with an N50 of 886 Kb, including a circular mitochondrial sequence of 28 Kb. Using direct RNA nanopore sequencing and Illumina cDNA sequencing, we constructed an annotation of our new assembly, supplemented by lifting over genes fromSaccharomyces cerevisiaeandCandida glabrata.
Modulating short-term auditory memory with focal transcranial direct current stimulation applied to the Supramarginal Gyrus
Authors: Lerud Karl D. , Vines Bradley W. , Shinde Anant B. , Schlaug Gottfried 
Published: January 2021

AbstractPrevious studies have shown that transcranial direct current stimulation (tDCS) can affect performance by decreasing regional excitability in a brain region that contributes to the task of interest. To our knowledge, no research to date has found both enhancing and diminishing effects on performance, depending upon which polarity of current is applied. The supramarginal gyrus (SMG) is an ideal brain region for testing tDCS effects because it is easy to identify using the 10-20 EEG coordinate system, and results of neuroimaging studies have implicated the left SMG in short-term memory for phonological and non-phonological sounds. In the present study, we found that applying tDCS to the left SMG affected pitch memory in a manner that depended upon the polarity of stimulation: cathodal tDCS had a negative impact on performance while anodal tDCS had a positive impact. These effects were significantly different from sham stimulation, which did not influence performance; they were also specific to the left hemisphere – no effect was found when applying cathodal stimulation to the right SMG – and were unique to pitch memory as opposed to memory for visual shapes. Our results provide further evidence that the left SMG is a nodal point for short-term auditory storage and demonstrate the potential of tDCS to influence cognitive performance, and to causally examine hypotheses derived from neuroimaging studies.