bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-destructive extraction of DNA from preserved tissues in medical collections
Authors: Rayo Enrique , Ferrari Giada , Neukamm Judith , Akgül Gülfirde , Breidenstein Abagail M. , Cooke Martyn , Phillips Carina , Bouwman Abigail S. , Rühli Frank J. , Schuenemann Verena J. 
Published: February 2021

AbstractMuseum and medically fixed material are valuable samples for the study of historical soft tissues and represent a pathogen-specific source for retrospective molecular investigations. However, current methods for the molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology thus damaging the sample - or conserving the material for future investigations. Here we present an unprecedented non-destructive alternative that facilitates the genetic analysis of fixed wet tissues while avoiding tissue damage. We extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. Our results prove that human ancient DNA can be retrieved from the fixative material of stored medical specimens and provide new options for the sampling of valuable curated collections.Method summaryWe compared the metagenomic content of historical tissues and their embedding liquid to retrieve DNA from the host and specified pathogens based on the diagnosis of the sample. We applied ancient DNA research techniques, including in-solution hybridization capture with DNA baits for human mitochondrial DNA,Mycobacterium tuberculosis, Mycobacterium leprae, andTreponema pallidum.
Structural basis for the specificity of PPM1H phosphatase for Rab GTPases
Authors: Waschbüsch Dieter , Berndsen Kerryn , Lis Pawel , Knebel Axel , Lam Yuko P. Y. , Alessi Dario R. , Khan Amir R. 
Published: February 2021

AbstractLRRK2 serine/threonine kinase is associated with inherited Parkinson’s disease. LRRK2 phosphorylates a subset of Rab GTPases within their switch 2 motif to control their interactions with effectors. Recent work has shown that the metal-dependent protein phosphatase PPM1H counteracts LRRK2 by dephosphorylating Rabs. PPM1H is highly selective for LRRK2 phosphorylated Rabs, and closely related PPM1J exhibits no activity toward substrates such as Rab8a phosphorylated at Thr72 (pThr72). Here we have identified the structural determinant of PPM1H specificity for Rabs. The crystal structure of PPM1H reveals a structurally conserved phosphatase fold that strikingly has evolved a 110-residue flap domain adjacent to the active site. The flap domain distantly resembles tudor domains that interact with histones in the context of epigenetics. Cellular assays, crosslinking and 3-D modelling suggest that the flap domain encodes the docking motif for phosphorylated Rabs. Consistent with this hypothesis, a PPM1J chimera with the PPM1H flap domain dephosphorylates pThr72 of Rab8a both in vitro and in cellular assays. Therefore, PPM1H has acquired a Rab-specific interaction domain within a conserved phosphatase fold.
Tetrazoles as PPARγ ligands: A Structural and Computational Investigation
Authors: de Paula Karina , Santos Jademilson C. , Mafud Ana Carolina , Nascimento Alessandro S. 
Published: February 2021

AbstractDiabetes is an important chronic disease affecting about 10% of the adult population in the US and over 420 million people worldwide, resulting in 1.6 million deaths every year, according to the World Health Organization. The most common type of the disease, type 2 diabetes, can be pharmacologically managed using oral hypoglycemic agents or thiazolidinediones (TZDs), such as pioglitazone, which act by activating the Peroxisome Proliferated-Activated Receptor γ. Despite their beneficial effects in diabetes treatment, TZDs like rosiglitazone and troglitazone were withdrawn due to safety reasons, creating a void in the pharmacological options for the treatment of this important disease. Here, we explored a structure-based approach in the screening for new chemical probes for a deeper investigation of the effects of PPARγ activation. A class of tetrazole compounds was identified and the compounds named T1, T2 and T3 were purchased and evaluated for their ability to interact with the PPARγ ligand binding domain (LBD). The compounds were binders with micromolar range affinity, as determined by their IC50values. A Monte Carlo simulation of the compound T2 revealed that the tetrazole ring makes favorable interaction with the polar arm of the receptor binding pocket. Finally, the crystal structure of the PPARγ-LBD-T2 complex was solved at 2.3 Å, confirming the binding mode for this compound. The structure also revealed that, when the helix H12 is mispositioned, an alternative binding conformation is observed for the ligand suggesting an H12-dependent binding conformation for the tetrazole compound.
Psilocybin induces rapid and persistent growth of dendritic spines in frontal cortexin vivo
Authors: Shao Ling-Xiao , Liao Clara , Gregg Ian , Davoudian Pasha A. , Savalia Neil K. , Delagarza Kristina , Kwan Alex C. 
Published: February 2021

SummaryPsilocybin is a serotonergic psychedelic with untapped therapeutic potential. There are hints that the use of psychedelics can produce neural adaptations, although the extent and time scale of the impact in a mammalian brain are unknown. In this study, we used chronic two-photon microscopy to image longitudinally the apical dendritic spines of layer 5 pyramidal neurons in the mouse medial frontal cortex. We found that a single dose of psilocybin led to ∼10% increases in spine size and density, driven by an elevated spine formation rate. The structural remodeling occurred quickly within 24 hours and was persistent 1 month later. Psilocybin also ameliorated stress-related behavioral deficit and elevated excitatory neurotransmission. Overall, the results demonstrate that psilocybin-evoked synaptic rewiring in the cortex is fast and enduring, potentially providing a structural trace for long-term integration of experiences and lasting beneficial actions.
Automated assignment of cell identity from single-cell multiplexed imaging and proteomic data
Authors: Geuenich Michael J. , Hou Jinyu , Lee Sunyun , Jackson Hartland W. , Campbell Kieran R. 
Published: February 2021

AbstractThe creation of scalable single-cell and highly-multiplexed imaging technologies that profile the protein expression and phosphorylation status of heterogeneous cellular populations has led to multiple insights into disease processes including cancer initiation and progression. A major analytical challenge in interpreting the resulting data is the assignment of cells to a priori known cell types in a robust and interpretable manner. Existing approaches typically solve this by clustering cells followed by manual annotation of individual clusters or by strategies that gate protein expression at predefined thresholds. However, these often require several subjective analysis choices such as selecting the number of clusters and do not automatically assign cell types in line with prior biological knowledge. They further lack the ability to explicitly assign cells to an unknown or uncharacterized type, which exist in most highly multiplexed imaging experiments due to the limited number of markers quantified. To address these issues we present Astir, a probabilistic model to assign cells to cell types by integrating prior knowledge of marker proteins. Astir uses deep recognition neural networks for fast Bayesian inference, allowing for cell type annotations at the million-cell scale and in the absence of previously annotated reference data across multiple experimental modalities and antibody panels. We demonstrate that Astir outperforms existing approaches in terms of accuracy and robustness by applying it to over 2.1 million single cells from several suspension and imaging mass cytometry and microscopy datasets in multiple tissue contexts. We further showcase that Astir can be used for the fast analysis of the spatial architecture of the tumour microenvironment, automatically quantifying the immune influx and spatial heterogeneity of patient samples. Astir is freely available as an open source Python package at https://www.github.com/camlab-bioml/astir.
HES1 protein oscillations are necessary for neural stem cells to exit from quiescence
Authors: Marinopoulou Elli , Sabherwal Nitin , Biga Veronica , Desai Jayni , Adamson Antony D. , Papalopulu Nancy 
Published: February 2021

SummaryQuiescence is a dynamic process of reversible cell-cycle arrest. High-level sustained expression of the HES1 transcriptional repressor, which oscillates with an ultradian periodicity in proliferative neural stem cells (NSCs), is thought to mediate quiescence. However, it is not known whether this is due to a change in levels or in dynamics. Here, we induce quiescence in NSCs with BMP4, which does not increase HES1 level, and we find that HES1 continues to oscillate. To assess the role of HES1 dynamics, we express sustained HES1 under a moderate-strength promoter, which overrides the endogenous oscillations while maintaining the total HES1 level within physiological range. We find that sustained HES1 does not affect proliferation or entry into quiescence, however, exit from quiescence is impeded. Thus, oscillatory expression of HES1 is specifically required for NSCs to exit quiescence, a finding of potential importance for controlling reactivation of stem cells in tissue regeneration and cancer.
A method to estimate effective population size from linkage disequilibrium when generations overlap
Authors: Cortés Luis Alberto García , Austerlitz Frédéric , de Cara M. Ángeles R. 
Published: February 2021

AbstractEffective population size (Ne) is a key parameter in evolutionary and conservation studies. It represents the number of individuals of an ideal panmictic population that would have the same genetic drift as the observed population and can be used to establish management programmes. Several methods have been developed to estimate this parameter. Currently, for studies with one sample in time, the simplest methods are based on linkage disequilibrium. These methods rely on simple models, and biases have been shown when populations deviate from the assumptions made in those models. This occurs in particular when populations are age-structured or have overlapping generations. Recently, several methods have been developed to correct such biases. Here, we develop analytical equations to predict linkage disequilibrium within age groups, and use such results to infer cohort size from samples of newborn individuals. We can in turn use these equations to estimateNeaccurately for a variety of species. Furthermore, using publicly available data, we apply our method to the white-crowned sparrow (Zonotrichia leucophrys).
GATA3 is essential for separating patterning domains during facial morphogenesis
Authors: Abe Makoto , Firulli Anthony B. , Kanai Stanley M. , Lim Kim-Chew , Engel J Douglas , Clouthier David E. 
Published: February 2021

AbstractNeural crest cells (NCCs) within the mandibular and maxillary portions of the first pharyngeal arch are initially competent to respond to signals from either region. However, mechanisms that are only partially understood establish developmental tissue boundaries to ensure spatially correct patterning. In the Hinge and Caps model of facial development, signals from both ventral prominences, referred to as the caps, pattern the adjacent tissues while the intervening region, known as the hinge, maintains separation of the mandibular and maxillary domains. One cap signal is GATA3, a member of the GATA family of zinc-finger transcription factors with a distinct expression pattern in the ventral-most part of the mandibular and maxillary portions of the first arch. Here we show that disruption ofGata3in mouse embryos leads to hemifacial microsomia, facial bone hypoplasia and syngnathia (bony fusion of the upper and lower jaws). These changes are preceded by gene expression changes in post-migratory NCCs around the maxillomandibular junction (the hinge). GATA3 is thus a crucial component in establishing the network of factors that functionally separate the upper and lower jaws during development.Summary StatementLoss ofGata3leads to BMP-mediated disruption ofFgf8expression at the maxillomandibular junction during development, resulting in later fusion of the upper and lower jaws.
Eukaryotic translation initiation factor 2A protects pancreatic beta cells during endoplasmic reticulum stress while rescuing translation inhibition
Authors: Panzhinskiy Evgeniy , Skovsø Søs , Cen Haoning Howard , Chu Kwan Yi , MacDonald Kate , Soukhatcheva Galina , Dionne Derek A. , Hallmaier-Wacker Luisa K. , Wildi Jennifer S. , Marcil Stephanie , Noursadeghi Nilou , Taghizadeh Farnaz , Verchere C. Bruce , Jan Eric , Johnson James D. 
Published: February 2021

ABSTRACTThe endoplasmic reticulum (ER) stress-induced unfolded protein response (UPR) helps decide β cell survival in diabetes. The alternative eukaryotic initiation factor 2A (EIF2A) has been proposed to mediate EIF2S1-independent translation during cellular stress and viral infection, but its role in β cells is unknown. EIF2A abundance is high in human and mouse islets relative to other tissues, and both thapsigargin and palmitate significantly increasedEIF2AmRNA and EIF2A protein levels in MIN6 cells, mouse islets and human islets. Knockdowns of EIF2A, the related factor EIF2D, or both EIF2A and EIF2D, were not sufficient to cause apoptosis. On the other hand, transient or stable EIF2A over-expression protected MIN6 cells, primary mouse islets, and human islets from ER stress-induced, caspase-3-dependent apoptosis. Mechanistically, EIF2A overexpression decreased ERN1 (also known as IRE1α) expression in thapsigargin-treated MIN6 cells or human islets.In vivo, β cell specific EIF2A viral overexpression reduced ER stress, improved insulin secretion, and abrogated hyperglycemia inIns2Akita/WTmice. EIF2A overexpression significantly increased expression of genes involved in protein translation and reduced expression of pro-apoptotic genes (e.g. ALDH1A3). Remarkably, the decrease in global protein synthesis during UPR was prevented by EIF2A, despite ER stress-induced EIF2S1 phosphorylation. The protective effects of EIF2A were additive to those of ISRIB, a drug that counteracts the effects of EIF2S1 phosphorylation. Cells overexpressing EIF2A showed higher expression of translation factor EIF2B5, which may contribute to the lack of translational inhibition in these cells. We conclude that EIF2A is a novel target for β cell protection and the circumvention of EIF2S1-mediated translational repression.
Modeling land use impacts on spatial distribution of floating plastic litter in surface water of Southeast Asian archipelago
Authors: Wibowo Andri 
Published: February 2021

AbstractPlastics are present in many ecosystems including floating in surface water of remote archipelago and this can lead to the increase in plastic litter density. Whereas the spatial model of plastic litter density related to the population inhabits isolated archipelago is still limited. And what are the underlying factors driving the presence of plastic litter is also poorly understood. This study is trying to find the answers of those questions. The study was implemented in Thousand Island archipelago located in North of Java Island, one of populated islands in Southeast Asia. The studied surface water covers an area of 10000 Ha and consists of 10 islands with 3 islands are occupied by settlements and the remaining islands are occupied by vegetation. This study has recorded 3 types of floating macro-litter from water that consist of PET, HDPE, and LDPE litter. The plastic litter was observed concentrated in the east sides of archipelago where the populated islands were located. The spatial models show LDPE litter was distributed in the vast areas in comparison to PET and HDPE litter. Beside land use variables, the model has confirmed that the population density was the main underlying factors contribute to the plastic litter density in Thousand Island archipelago. The model can be applied to estimate PET (AIC = −0.53060) and HDPE (AIC = 18.28828) litter density. While LDPE litter density was influenced by population (AIC = 22.60201) rather than population density factors.
Recurrent Connections in the Primate Ventral Visual Stream Mediate a Tradeoff Between Task Performance and Network Size During Core Object Recognition
Authors: Nayebi Aran , Sagastuy-Brena Javier , Bear Daniel M. , Kar Kohitij , Kubilius Jonas , Ganguli Surya , Sussillo David , DiCarlo James J. , Yamins Daniel L. K. 
Published: February 2021

AbstractThe computational role of the abundant feedback connections in the ventral visual stream (VVS) is unclear, enabling humans and non-human primates to effortlessly recognize objects across a multitude of viewing conditions. Prior studies have augmented feedforward convolutional neural networks (CNNs) with recurrent connections to study their role in visual processing; however, often these recurrent networks are optimized directly on neural data or the comparative metrics used are undefined for standard feedforward networks that lack these connections. In this work, we developtask-optimizedconvolutional recurrent (ConvRNN) network models that more correctly mimic the timing and gross neuroanatomy of the ventral pathway. Properly chosen intermediate-depth ConvRNN circuit architectures, which incorporate mechanisms of feedforward bypassing and recurrent gating, can achieve high performance on a core recognition task, comparable to that of much deeper feedforward networks. We then develop methods that allow us to compare both CNNs and ConvRNNs to fine-grained measurements of primate categorization behavior and neural response trajectories across thousands of stimuli. We find that high performing ConvRNNs provide a better match to this data than feedforward networks of any depth, predicting the precise timings at which each stimulus is behaviorally decoded from neural activation patterns. Moreover, these ConvRNN circuits consistently produce quantitatively accurate predictions of neural dynamics from V4 and IT across the entire stimulus presentation. In fact, we find that the highest performing ConvRNNs, which best match neural and behavioral data, also achieve a strong Pareto-tradeoff between task performance and overall network size. Taken together, our results suggest the functional purpose of recurrence in the ventral pathway is to fit a high performing network in cortex, attaining computational power through temporal rather than spatial complexity.
Fluorescence Imaging-Based Discovery of Membrane Domain-Associated Proteins inMycobacterium smegmatis
Authors: Rokicki Corelle A. Z. , Brenner James R. , Dills Alexander , Judd Julius J. , Kester Jemila C. , Puffal Julia , Wade Joseph T. , Gray Todd A. , Derbyshire Keith M. , Fortune Sarah M. , Morita Yasu S. 
Published: February 2021

AbstractMycobacteria spatially organize their plasma membrane, and many enzymes involved in envelope biosynthesis associate with a membrane compartment termed the intracellular membrane domain (IMD). The IMD is concentrated in the polar regions of growing cells and becomes less polarized under non-growing conditions. Because mycobacteria elongate from the poles, the observed polar localization of the IMD during growth likely supports the localized envelope biosynthesis. While we have identified more than 300 IMD-associated proteins by proteomic analyses, only a handful of these have been verified by other experimental methods. Furthermore, we speculate that some IMD-associated proteins may have escaped proteomic identification and remain to be identified. Here, we visually screened an arrayed library of 523Mycobacterium smegmatisstrains each expressing a Dendra2-FLAG-tagged recombinant protein. We identified 29 fusion proteins that showed fluorescence patterns similar to those of IMD proteins and, consistent with this co-localization, we had previously identified 20 of these using a proteomics approach. Of the nine remaining IMD candidate proteins, three were confirmed to be associated with the IMD while some others appear to be lipid droplet-associated. Taken together, our newly devised strategy is effective in verifying the IMD association of proteins found by proteomic analyses, while facilitating the discovery of additional IMD-associated proteins.ImportanceThe intracellular membrane domain (IMD) is a membrane subcompartment found inMycobacterium smegmatiscells. Proteomic analysis of purified IMD identified more than 300 proteins, including enzymes involved in cell envelope biosynthesis, that likely contribute to the function of the IMD. How can we find more IMD-associated proteins that escaped proteomic detection? Here, as an alternative approach, fluorescence microscope images of 523 proteins were screened to identify IMD-associated proteins. We confirmed the IMD association of previously identified proteins and discovered three additional proteins associated with the IMD. Together, subcellular fractionation, proteomics, and fluorescence microscopy form a robust combination to more rigorously define IMD proteins, which will aid future investigations to decipher the synthesis, maintenance and functions of this membrane domain.
Relict groups of spiny frogs indicate Late Paleogene-Early Neogene trans-Tibet dispersal of thermophile faunal elements
Authors: Hofmann Sylvia , Jablonski Daniel , Litvinchuk Spartak , Masroor Rafaqat , Schmidt Joachim 
Published: February 2021

AbstractBackgroundThe Himalaya-Tibet orogen (HTO) presents an outstanding geologically active formation that contributed to, and fostered, modern Asian biodiversity. However, our concepts of the historical biogeography of its biota are far from conclusive, as are uplift scenarios for the different parts of the HTO. Here, we revisited our previously published data set of the tribe Paini extending it with sequence data from the most western Himalayan spiny frogsAllopaaandChrysopaaand using them as an indirect indicator for the paleoecological development of Tibet.MethodsWe obtained sequence data of two mitochondrial loci (16S rRNA, COI) and one nuclear marker (Rag1) fromAllopaasamples from Kashmir Himalaya as well asChrysopaasequence data from the Hindu Kush available from GenBank to complement our previous data set. A Maximum likelihood and dated Bayesian gene tree were generated based on the concatenated data set. To resolve the inconsistent placement ofAllopaa,we performed different topology tests.ResultsConsistent with previous results, the Southeast Asian genusQuasipaais sister to all other spiny frogs. The results further reveal a basal placement ofChrysopaarelative toAllopaaandNanoranawith an estimated age ofca.26 Mya. Based on the topology tests, the phylogenetic position ofAllopaaas a sister clade toChaparanaseems to be most likely, resulting in a paraphyletic genusNanoranaand a separation from the latter clade around 20 Mya. Both, the placements ofChrysopaaandAllopaasupport the presence of basal Paini lineages in the far north western part of the HTO, which is diametrically opposite end of the HTO with respect to the ancestral area of spiny frogs in Southeast Asia. These striking distributional patterns can be most parsimoniously explained by trans-Tibet dispersal during the late Oligocene (subtropicalChrysopaa) respectively early Miocene (warm temperateAllopaa).Within spiny frogs, only members of the monophyleticNanorana+Paaclade are adapted to the colder temperate climates, indicating that high-altitude environments did not dominate in the HTO beforeca.15 Mya. Our results are consistent with fossil records suggesting that large parts of Tibet were characterized by subtropical to warm temperate climates at least until the early Miocene.