bluuebunny/crossref_metadata_2025_split huggingface dataset:
Insights into the domestication of avocado and potential genetic contributors to heterodichogamy
Authors: Solares Edwin , Morales-Cruz Abraham , Balderas Rosa Figueroa , Focht Eric , Ashworth Vanessa E. T. M. , Wyant Skylar , Minio Andrea , Cantu Dario , Arpaia Mary Lu , Gaut Brandon S. 
Published: April 2022

SUMMARYThe domestication history of avocado (Persea americana) remains unclear, in part due to a lack of suitable genomic tools.We created a reference genome from the Gwen varietal, which is closely related to the economically dominant Hass varietal. We also compiled a database of 34 resequenced accessions that represented the three botanical races of P. americana.Our genome assembly had an N50 of 3.37 megabases, a BUSCO score of 91% and was scaffolded with a genetic map, producing 12 pseudo-chromosomes with 49,450 genes. We used the Gwen genome as a reference to investigate the population genomics of avocado. Our analyses were consistent with three separate domestication events; we estimated that the Mexican race diverged from the Lowland (formerly known as ‘West Indian’) and Guatemalan races >1 million years ago. We also identified putative targets of selective sweeps in domestication events; within the Guatemalan race, putative candidate genes were enriched for fruit development and ripening. We also investigated divergence between heterodichogamous flowering types.With the help of a new reference genome, we inferred the domestication history of avocado and identified genes that may contribute to heterodichogamy, including genes with functions in pollination and floral development.
An in situ cut-and-paste genome editing platform mediated by CRISPR/Cas9 or Cas12a
Authors: Jiang Ping , Kemper Kevin M. , Chang Kai-Ti , Qian Cheng , Li Yulong , Guan Liying , van Hasselt Peter , Caradonna Salvatore J. , Strich Randy 
Published: April 2022

ABSTRACTRecombinant DNA technology mediated by restriction enzymes and ligases allows in vitro manipulation of a DNA segment isolated from the genome. Short overhangs generated by restriction enzymes facilitate efficient pasting together a DNA sequence and a vector. We adopted this recombinant DNA strategy to develop an in vivo recombinant-genome genome editing approach. Using the programmable endonuclease Cas9 or Cas12a as a restriction enzyme, we devised an in situcut-and-paste (iCAP) genome editing method that was tested in both mouse germline and human cell line platforms. Mouse gene loci Slc35f2 and Slc35f6 were each edited with in-frame insertion of a large APEX2-Cre cassette and concurrent FRT3 insertion at a second location providing proof of principle for the iCAP method. Further, a de nova single nucleotide mutation associated with MED13L syndrome was efficiently corrected in patient cells. Altogether, the iCAP method provides a single genome editing platform with flexibility and multiutility enabling versatile and precise sequence alterations, such as insertion, substitution, and deletion, at single or multiple locations within a genomic segment in mammalian genomes.
Factors Affecting Protein Recovery During Hsp40 Affinity Profiling
Authors: Montoya Maureen R. , Quanrud Guy M. , Mei Liangyong , Moñtano José L. , Hong Caleb , Genereux Joseph C. 
Published: April 2022

ABSTRACTHsp40s, also termed J-domain proteins, play a central role in cellular protein homeostasis by promiscuously surveying the proteome for misfolded proteins. We have exploited this property to develop Hsp40 affinity profiling as a method for identifying proteins that misfold in response to cellular stresses. In this assay, we use the Hsp40FlagDNAJB8H31Qas our recognition element for misfolded proteins. This protein is exogenously introduced into cells, promoting interactions without regard for native protein clients. Herein, we evaluate potential approaches to improve the performance of this assay. We find that although intracellular crosslinking increases recovery of protein interactors, this is not enough to overcome the relative drop in DNAJB8 recovery. While the J-domain promotes Hsp70 association, it does not affect the yield of protein association with DNJAB8 underbasalconditions. By contrast, crosslinking and J-domain ablation both substantially increase relative protein interactor recovery with the structurally distinct Class B Hps40 DNAJB1 but are completely compensated by poorer yield of DNAJB1 itself. Cellular thermal stress promotes increased affinity between DNAJB8H31Qand interacting proteins, as expected for interactions driven by recognition of misfolded proteins. DNAJB8WTdoes not demonstrate such a property, suggesting that under stress misfolded proteins are handed off to Hsp70. Hence, we find that DNAJB8H31Qis still our most effective recognition element for the recovery of destabilized client proteins following cellular stress.Raw data is accessible through the PRIDE Archive at PXD030633.
Phasor-Based Multi-Harmonic Unmixing for In-Vivo Hyperspectral Imaging
Authors: Vallmitjana Alexander , Lepanto Paola , Irigoin Florencia , Malacrida Leonel 
Published: April 2022

AbstractHyperspectral imaging (HSI) is a paramount technique in biomedical science, however, unmixing and quantification of each spectral component is a challenging task. Traditional unmixing relies on algorithms that need spectroscopic parameters from the fluorescent species in the sample. The phasor-based multi-harmonic unmixing method requires only the empirical measurement of the pure species to compute the pixel-wise photon fraction of every spectral component. Using simulations, we demonstrate the feasibility of the approach for up to 5 components and explore the use of adding a 6th unknown component representing autofluorescence. The simulations show that the method can be successfully used in typical confocal imaging experiments (with pixel photon counts between 101and 103). As a proof of concept, we tested the method in living cells, using 5 common commercial dyes for organelle labeling and we easily and accurately separate them. Finally, we challenged the method by introducing a solvatochromic probe, 6-Dodecanoyl-N,N-dimethyl-2-naphthylamine (LAURDAN), intended to measure membrane dynamics on specific subcellular membrane-bound organelles by taking advantage of the linear combination between the organelle probes and LAURDAN. We succeeded in monitoring the membrane order in the Golgi apparatus, Mitochondria, and plasma membrane in the same in-vivo cell and quantitatively comparing them. The phasor-based multi-harmonic unmixing method can help expand the outreach of HSI and democratize its use by the community for it does not require specialized knowledge.
Vaccination decreases the risk of influenza A virus reassortment with a concomitant increase in subgenomic genetic variation in pigs
Authors: Li Chong , Culhane Marie R. , Schroeder Declan C. , Cheeran Maxim C-J. , Pantoja Lucina Galina , Jansen Micah L. , Torremorell Montserrat 
Published: April 2022

AbstractAlthough vaccination is broadly used in North American swine breeding herds, managing swine influenza is challenging primarily due to the continuous evolution of influenza A virus (IAV) and the ability of the virus to transmit among vaccinated pigs. Studies that have simultaneously assessed the impact of vaccination on the emergence of IAV reassortment and genetic variation in pigs are limited. Here we directly sequenced 28 bronchoalveolar lavage fluid (BALF) samples collected from vaccinated and unvaccinated pigs co-infected with H1N1 and H3N2 IAV strains, and characterized 202 individual viral plaques recovered from 13 BALF samples. We identified 54 reassortant viruses that were grouped in 16 distinct and 18 mixed genotypes. Notably, we found that prime-boost vaccinated pigs had less reassortant viruses than non-vaccinated pigs, likely due to a reduction in the number of days pigs were co-infected with both challenge viruses. However, direct sequencing from BALF samples revealed limited impact of vaccination on viral variant frequency, evolutionary rates, and nucleotide diversity in any IAV coding regions. Overall, our results highlight the value of IAV vaccination not only at limiting virus replication in pigs but also at protecting public health by restricting the generation of novel reassortants with zoonotic and/or pandemic potential.
Pulmonary dust foci as rat pneumoconiosis lesion induced by titanium dioxide nanoparticles in 13-week inhalation study
Authors: Yamano Shotaro , Goto Yuko , Takeda Tomoki , Hirai Shigeyuki , Furukawa Yusuke , Kikuchi Yoshinori , Kasai Tatsuya , Misumi Kyohei , Suzuki Masaaki , Takanobu Kenji , Senoh Hideki , Saito Misae , Kondo Hitomi , Umeda Yumi 
Published: April 2022

AbstractBackgroundMost toxicological studies on titanium dioxide (TiO2) particles to date have concentrated on carcinogenicity and acute toxicity, with few studies focusing of pneumoconiosis, which is a variety of airspace and interstitial lung diseases caused by particle-laden macrophages. The present study examined rat pulmonary lesions associated with pneumoconiosis after inhalation exposure to TiO2 nanoparticles (NPs).MethodsMale and female F344 rats were exposed to 6.3, 12.5, 25, or 50 mg/m3 anatase type TiO2 NPs for 6 hours/day, 5 days/week for 13 weeks using a whole-body inhalation exposure system. After the last exposure the rats were euthanized and blood, bronchoalveolar lavage fluid, and all tissues including lungs and mediastinal lymph nodes were collected and subjected to biological and histopathological analyses.ResultsNumerous milky white spots were present in the lungs after exposure 25 and 50 mg/m3 TiO2 NPs. Histopathological analysis revealed that the spots were alveolar lesions, characterized predominantly by the agglomeration of particle-laden macrophages and the presence of reactive alveolar epithelial type 2 cell (AEC2) hyperplasia. We defined this characteristic lesion as pulmonary dust foci (PDF). The PDF is an inflammatory niche, with decreased vascular endothelial cells in the interstitium, and proliferating AEC2 transformed into alveolar epithelial progenitor cells. The AEC2 in the PDF had acquired DNA damage. Based on PDF induction, the lowest observed adverse effect concentration for pulmonary disorders in male and female rats in this study was 12.5 mg/m3 and 6.3 mg/m3, respectively. The no observed adverse effect concentration for male rats was 6.3 mg/m3. There was a sex difference in lung lesion development, with females showing more pronounced lesion parameters than males.ConclusionsInhalation exposure to TiO2 NPs caused PDF, an air-space lesion which is an alveolar inflammatory niche containing particle-laden macrophages and proliferating AEC2. This PDF histopathologically resembles some pneumoconiosis lesions (pulmonary siderosis and hard metal pneumoconiosis) in workers and lung disease in smokers, suggesting that it is an early pneumoconiosis lesion caused by exposure to TiO2 NPs in rats and a common alveolar reaction in mammals.
High temperature molecular motions within a model protomembrane architecture
Authors: Misuraca Loreto , Matsuo Tatsuhito , Cisse Aline , LoRicco Josephine , Caliò Antonio , Zanotti Jean-Marc , Demé Bruno , Oger Philippe , Peters Judith 
Published: April 2022

AbstractModern phospholipid membranes are known to be in a functional, physiological state, corresponding to the liquid crystalline phase, only under very precise external conditions. The phase is characterised by specific lipid motions, which seem mandatory to permit sufficient flexibility and stability for the membrane. It can be assumed that similar principles hold for proto-membranes at the origin of life although they were likely composed of simpler, single chain fatty acids and alcohols. In the present study we investigated molecular motions of four types of model membranes to shed light on the variations of dynamics and structure as a function of temperature as protocells might have existed close to hot vents. We find a clear hierarchy among the flexibilities of the samples, where some structural parameters seem to depend on the lipids used while others do not.
AMPK-p38 axis converts human pluripotent stem cells to naïve state
Authors: Yang Zhennan , Liu Yajing , Xu Huaigeng , Yamane Junko , Hotta Akitsu , Fujibuchi Wataru , Yamashita Jun K 
Published: April 2022

SUMMARYPluripotent stem cells (PSCs) have been reported to exhibit two stages of pluripotency, ‘primed’ and ‘naïve’ states. Typical human PSCs (hPSCs) are in the primed state. Though several methods for conversion from primed to naïve state have been reported, the mechanism of the process is not fully understood. Here, we report that 5’ adenosine monophosphate-activated protein kinase (AMPK) and its downstream p38 is a signaling axis that can induce the naïve conversion of hPSCs with single pathway activation. The simple addition of an AMPK activator, 5-aminoimidazole-4-carboxamide-1-β-D-ribofuranoside (AICAR), or overexpression of a constitutive active form of p38 (CA-p38) alone in primed hPSCs induced naïve hPSCs that satisfied naïve state criteria: differentiation ability to three germ layers and naïve state-specific transcriptional expression, epigenomic resetting, and mitochondrial activity. RNA-seq analysis demonstrated that our AICAR- or CA-p38-induced naïve hPSCs show closely similar gene expression patterns to naïve state human embryonic stem cells (HNES1) derived from human inner cell mass (ICM). This novel and simple naïve conversion method provides new avenues for understanding and elucidating the fundamental mechanism of naïve conversion.
Chaperone Requirements for De Novo Folding of Saccharomyces cerevisiae Septins
Authors: Hassell Daniel , Denney Ashley , Singer Emily , Benson Aleyna , Roth Andrew , Ceglowski Julia , Steingesser Marc , McMurray Michael 
Published: April 2022

ABSTRACTPolymers of septin protein complexes play cytoskeletal roles in eukaryotic cells. The specific subunit composition within complexes controls functions and higher-order structural properties. All septins have globular GTPase domains. The other eukaryotic cytoskeletal NTPases strictly require assistance from molecular chaperones of the cytosol, particularly the cage-like chaperonins, to fold into oligomerization-competent conformations. We previously identified cytosolic chaperones that bind septins and influence the oligomerization ability of septins carrying mutations linked to human disease, but it was unknown to what extent wild-type septins require chaperone assistance for their native folding. Here we use a combination of in vivo and in vitro approaches to demonstrate chaperone requirements for de novo folding and complex assembly by budding yeast septins. Individually purified septins adopted non-native conformations and formed non-native homodimers. In chaperonin- or Hsp70-deficient cells, septins folded slower and were unable to assemble post-translationally into native complexes. One septin, Cdc12, was so dependent on co-translational chaperonin assistance that translation failed without it. Our findings point to distinct translation elongation rates for different septins as a possible mechanism to direct a stepwise, co-translational assembly pathway in which general cytosolic chaperones act as key intermediaries.
The molecular organization of flat and curved caveolae indicates bendable structural units at the plasma membrane
Authors: Matthaeus Claudia , Sochacki Kem A. , Dickey Andrea , Puchkov Dmytro , Haucke Volker , Lehmann Martin , Taraska Justin W. 
Published: April 2022

AbstractCaveolae are small coated inner plasma membrane invaginations found in many cell types. Their diverse functions span from endocytosis to signaling, regulating key cellular processes including lipid uptake, pathogen entry, and membrane tension. Caveolae undergo shape changes from flat to curved. It is unclear which proteins regulate this process. To address this gap, we studied the shapes of caveolae with platinum replica electron microscopy in six common cell types. Next, we developed a correlative multi-color stimulated emission depletion (STED) fluorescence and platinum replica EM imaging (CLEM) method to image caveolae-associated proteins at caveolae of different shapes at the nanoscale. Caveolins and cavins were found at all caveolae, independent of their curvature. EHD2, a classic caveolar neck protein, was strongly detected at both curved and flat caveolae. Both pacsin2 and the regulator EHBP1 were found only at a subset of caveolae. Pacsin2 was localized primarily to areas surrounding flat caveolae, whereas EHBP1 was mostly detected at spheres. Contrary to classic models, dynamin was absent from caveolae and localized only to clathrin-coated structures. Cells lacking dynamin showed no substantial changes to caveolae, suggesting that dynamin is not directly involved in caveolae curvature. Together, we provide a mechanistic map for the molecular control of caveolae shape by eight of the major caveolae-associated coat and regulatory proteins. We propose a model where caveolins, cavins, and EHD2 assemble as a cohesive structural unit regulated by more intermittent associations with pacsin2 and EHBP1. These complexes can flatten and curve, capturing membrane to enable lipid traffic and changes to the surface area of the cell.
RNAinsecta: A tool for prediction of pre-microRNA in insects using machine learning algorithms
Authors: Nath Adhiraj , Bora Utpal 
Published: April 2022

ABSTRACTPre-MicroRNAs are the hairpin loops which produces microRNAs that negatively regulate gene expression in several organisms. In insects, microRNAs participate in several biological processes including metamorphosis, reproduction, immune response, etc. Numerous tools have been designed in recent years to predict pre-microRNA using binary machine learning classifiers where predictive models are trained with true and pseudo pre-microRNA hairpin loops. Currently however, there are no existing tool that is exclusively designed for insect pre-microRNA detection. In this experiment we trained machine learning classifiers such as Random Forest, Support Vector Machine, Logistic Regression and k-Nearest Neighbours to predict pre-microRNA hairpin loops in insects while using Synthetic Minority Over-sampling Technique and Near-Miss to handle the class imbalance. The trained model on Support Vector Machine achieved accuracy of 92.19% while the Random Forest attained an accuracy of 80.28% on our validation dataset. These models are hosted online as web application called RNAinsecta. Further, searching target for the predicted pre-microRNA in insect model organism Drosophila melanogaster has been provided in RNAinsecta using miRanda at the backend where experimentally validated genes regulated by microRNA are collected from miRTarBase as target sites. RNAinsecta is freely available at https://rnainsecta.in
Brain-wide projections and differential encoding of prefrontal neuronal classes underlying learned and innate threat avoidance
Authors: Gongwer Michael W. , Klune Cassandra B. , Couto João , Jin Benita , Enos Alexander S. , Chen Rita , Friedmann Drew , DeNardo Laura A. 
Published: April 2022

AbstractTo understand how the brain produces behavior, we must elucidate the relationships between neuronal connectivity and function. The medial prefrontal cortex (mPFC) is critical for complex functions including decision-making and mood. mPFC projection neurons collateralize extensively, but the relationships between mPFC neuronal activity and brain-wide connectivity are poorly understood. We performed whole-brain connectivity mapping and fiber photometry to better understand the mPFC circuits that control threat avoidance. Using tissue clearing and light sheet fluorescence microscopy we mapped the brain-wide axon collaterals of populations of mPFC neurons that project to nucleus accumbens (NAc), ventral tegmental area (VTA), or contralateral mPFC (cmPFC) in mice. We present DeepTraCE, for quantifying bulk-labeled axonal projections in images of cleared tissue, and DeepCOUNT, for quantifying cell bodies. Anatomical maps produced with DeepTraCE aligned with known axonal projection patterns and revealed class-specific topographic projections within regions. During threat avoidance, cmPFC and NAc-projectors encoded conditioned stimuli, but only when action was required to avoid threats. mPFC-VTA neurons encoded learned but not innate avoidance behaviors. Together our results present new and optimized approaches for quantitative whole-brain analysis and indicate that anatomically-defined classes of mPFC neurons have specialized roles in threat avoidance.
MAIT cells activate dendritic cells to promote T follicular helper cell differentiation and humoral immunity
Authors: Pankhurst Theresa E. , Buick Kaitlin H. , Lange Joshua L. , Marshall Andrew J. , Button Kaileen R. , Palmer Olga R. , Farrand Kathryn J. , Stewart Isabelle F. N. , Bird Thomas , Mason Ngarangi C. , Compton Benjamin J. , Comoletti Davide , Salio Mariolina , Cerundolo Vincenzo , Painter Gavin F. , Hermans Ian F. , Connor Lisa M. 
Published: April 2022

AbstractProtective immune responses against respiratory pathogens, including influenza virus are initiated by the mucosal immune system. However, most licensed vaccines are administered parenterally and are largely ineffective at inducing mucosal immunity. The development of safe and effective mucosal vaccines has largely been hampered by the lack of a suitable mucosal adjuvant. In this study we explore a novel class of adjuvant that harness mucosal-associated invariant T (MAIT) cells. We show evidence that intranasal immunisation of MAIT cell agonists co-administered with protein, including haemagglutinin from influenza A virus induced potent humoral immunity and immunoglobulin (Ig)A production, which protected mice against infection. MAIT cell adjuvant activity was mediated by CD40L-dependent activation of dendritic cells and subsequent priming of CD4+ T follicular helper cells. In summary, we show that MAIT cells are promising vaccine targets that can be utilised as cellular adjuvants in mucosal vaccines.
Innovator or collaborator? A cognitive network perspective to vision formation
Authors: Zasa Federico P. , Verganti Roberto , Bellis Paola 
Published: April 2022

PurposeHaving a shared vision is crucial for innovation. The purpose of this paper is to investigate the effect of individual propensity to collaborate and innovate on the development of a shared vision.Design/methodology/approachThe authors build a network in which each node represents the vision of one individual and link the network structure to individual propensity of collaboration and innovativeness. During organizational workshops in four multinational organizations, the authors collected individual visions in the form of images as well as text describing the approach to innovation from 85 employees.FindingsThe study maps individual visions for innovation as a cognitive network. The authors find that individual propensity to innovate or collaborate is related to different network centrality. Innovators, individuals who see innovation as an opportunity to change and grow, are located at the center of the cognitive network. Collaborators, who see innovation as an opportunity to collaborate, have a higher closeness centrality inside a cluster.Research limitations/implicationsThis paper analyses visions as a network linking recent research in psychology with the managerial longing for a more thorough investigation of group cognition. The study contributes to literature on shared vision creation, suggesting the role which innovators and collaborators can occupy in the process.Originality/valueThis paper proposes how an approach based on a cognitive network can inform innovation management. The findings suggest that visions of innovators summarize the visions of a group, helping the development of an overall shared vision. Collaborators on the other hand are representative of specific clusters and can help developing radical visions.