bluuebunny/crossref_metadata_2025 huggingface dataset:
Functional alterations in cortical processing of speech in glioma-infiltrated cortex
Authors: Aabedi Alexander A. , Lipkin Benjamin , Kaur Jasleen , Kakaizada Sofia , Reihl Sheantel , Young Jacob S. , Lee Anthony T. , Krishna Saritha , Chang Edward F. , Brang David , Hervey Jumper Shawn L.
Published: May 2021

Recent developments in the biology of malignant gliomas have demonstrated that glioma cells interact with neurons through both paracrine signaling and electrochemical synapses. Glioma-neuron interactions consequently modulate the excitability of local neuronal circuits, and it is unclear the extent to which glioma-infiltrated cortex can meaningfully participate in neural computations. For example, gliomas may result in a local disorganization of activity that impedes the transient synchronization of neural oscillations. Alternatively, glioma-infiltrated cortex may retain the ability to engage in synchronized activity, in a manner similar to normal-appearing cortex, but exhibit other altered spatiotemporal patterns of activity with subsequent impact on cognitive processing. Here, we use subdural electrocorticography to sample both normal-appearing and glioma-infiltrated cortex during speech. We find that glioma-infiltrated cortex engages in synchronous activity during task performance in a manner similar to normal-appearing cortex, but recruits a diffuse spatial network. On a temporal scale, we show that glioma-infiltrated cortex has lower capacity for information encoding when performing nuanced tasks such as speech production of monosyllabic versus polysyllabic words. As a result, temporal decoding strategies for distinguishing monosyllabic from polysyllabic words were feasible for signals arising from normal-appearing cortex, but not from glioma-infiltrated cortex. These findings inform our understanding of cognitive processing in chronic disease states and have implications for neuromodulation and prosthetics in patients with malignant gliomas.

Significance Statement

As gliomas proliferate, they infiltrate healthy brain tissue. Often, patients with such tumors in the language areas of the brain develop aphasia. Understanding how gliomas interact with normal neural circuits is critical for developing neuroprostheses that restore speech. Recent evidence demonstrates that glioma cells interact synaptically with neurons, and thus can modulate neural circuits. However, it is unclear the extent to which glioma-infiltrated cortex participates in cognitive processing. Using electrocorticography to record both glioma-infiltrated and normal-appearing cortex during speech, we found that glioma-infiltrated cortex is capable of coordinated neural responses, but has reduced capacity for information encoding. Instead, glioma-infiltrated cortex recruits a broader network of cortical regions during speech, which may represent a compensatory mechanism with implications for future neuroprostheses.
Joint inference of migration and reassortment patterns for viruses with segment genomes
Authors: Stolz Ugnė , Stadler Tanja , Müller Nicola F. , Vaughan Timothy G.
Published: May 2021

The structured coalescent allows inferring migration patterns between viral sub-populations from genetic sequence data. However, these analyses typically assume that no genetic recombination process impacted the sequence evolution of pathogens. For segmented viruses, such as influenza, that can undergo reassortment this assumption is broken. Reassortment reshuffles the segments of different parent lineages upon a coinfection event, which means that the shared history of viruses has to be represented by a network instead of a tree. Therefore, full genome analyses of such viruses is complex or even impossible. While this problem has been addressed for unstructured populations, it is still impossible to account for population structure, such as induced by different host populations, while also accounting for reassortmentWe address this by extending the structured coalescent to account for reassortment and present a framework for investigating possible ties between reassortment and migration (host jump) events. This method can accurately estimate sub-population dependent effective populations sizes, reassortment and migration rates from simulated data. Additionally, we apply the new model to avian influenza A/H5N1 sequences, sampled from two avian host types, Anseriformes and Galliformes. We contrast our results with a structured coalescent without reassortment inference, which assumes independently evolving segments. This reveals that taking into account segment reassortment and using sequencing data from several viral segments for joint phylodynamic inference leads to different estimates for effective population sizes, migration and clock rates.

This new model is implemented as the Structured Coalescent with Reassortment (SCoRe) package for BEAST 2.5 and is available at https://github.com/jugne/SCORE.
Condensin-driven loop extrusion on supercoiled DNA
Authors: Kim Eugene , Gonzalez Alejandro Martin , Pradhan Biswajit , van der Torre Jaco , Dekker Cees
Published: May 2021

Condensin, a structural maintenance of chromosomes (SMC) complex, has been shown to be a molecular motor protein that organizes chromosomes by extruding loops of DNA. In cells, such loop extrusion is challenged by many potential conflicts, e.g., the torsional stresses that are generated by other DNA-processing enzymes. It has so far remained unclear how DNA supercoiling affects loop extrusion. Here, we use time-lapse single-molecule imaging to study condensin-driven DNA loop extrusion on supercoiled DNA. We find that condensin binding and DNA looping is stimulated by positive supercoiled DNA where it preferentially binds near the tips of supercoiled plectonemes. Upon loop extrusion, condensin collects all nearby plectonemes into a single supercoiled loop that is highly stable. Atomic force microscopy imaging shows that condensin generates supercoils in the presence of ATP. Our findings provide insight into the topology-regulated loading and formation of supercoiled loops by SMC complexes and clarify the interplay of loop extrusion and supercoiling.
Calcium dependence of neurotransmitter release at a high fidelity synapse
Authors: Eshra Abdelmoneim , Schmidt Hartmut , Eilers Jens , Hallermann Stefan
Published: May 2021

The Ca2+-dependence of the recruitment, priming, and fusion of synaptic vesicles are fundamental parameters controlling neurotransmitter release and synaptic plasticity. Despite intense efforts, these important steps in the synaptic vesicles’ cycle remain poorly understood because disentangling recruitment, priming, and fusion of vesicles is technically challenging. Here, we investigated the Ca2+-sensitivity of these steps at cerebellar mossy fiber synapses, which are characterized by fast vesicle recruitment mediating high-frequency signaling. We found that the basal free Ca2+ concentration (<200 nM) critically controls action potential-evoked release, indicating a high-affinity Ca2+ sensor for vesicle priming. Ca2+ uncaging experiments revealed a surprisingly shallow and non-saturating relationship between release rate and intracellular Ca2+ concentration up to 50 μM. Sustained vesicle recruitment was Ca2+-independent. Finally, quantitative mechanistic release schemes with five Ca2+ binding steps incorporating rapid vesicle recruitment via parallel or sequential vesicle pools could explain our data. We thus show that co-existing high and low-affinity Ca2+ sensors mediate recruitment, priming, and fusion of synaptic vesicles at a high-fidelity synapse.
Impact of α-synuclein fibrillar strains and ß-amyloid assemblies on the endolysosomal logistics of mouse cortical neurons
Authors: Chou Qiao-Ling , Alik Ania , Marquier François , Melki Ronald , Treussart François , Simonneau Michel
Published: May 2021

Endosomal transport and positioning are involved in establishing neuronal compartment architecture, dynamics and function, contributing to neuronal intracellular logistics. Furthermore, endo-lysosomal dysfunction has been identified as a common mechanism in neurodegenerative diseases. Here, we analyzed endolysosomal transport following the external application of α-synuclein (α-syn) fibrillar polymorphs, ß-amyloid (Aß) fibrils and oligomers on primary cultures of mouse cortical neurons. We used a simple readout to measure this transport: the spontaneous endocytosis of fluorescent nanodiamonds — a perfectly stable nano-emitter — in cultured neurons. We then performed a high-throughput automatic extraction and quantification of the directed motions of these nanodiamonds. α-syn fibrillar polymorphs, Aß fibrils and oligomers halved the proportion of nanodiamonds transported along microtubules, but only slightly decreased their interactions with cortical neurons. This large decrease in endosomal transport would be expected to have a huge impact on neuronal homeostasis. We then assessed lysosomal dynamics with Lysotracker. The exposure of neurons to Aß oligomers led to an increase in the number of lysosomes, a decrease in the fraction of moving lysosomes and an increase in their size, reminiscent of findings for the APP transgenic model of Alzheimer’s disease. We then analyzed the effect of α-syn fibrillar polymorphs, Aß fibrils and oligomers on endosomal and lysosomal transport and quantified the directed transport of these assemblies within cortical neurons. We report different impacts on endosomal and lysosomal transport parameters and differences in trajectory length for cargoes loaded with pathogenic protein assemblies. Our results suggest that the internalization and transport of intraneuronal pathogenic protein aggregates are potential targets for novel neuroprotective treatment strategies.

Significance Statement

Neurodegenerative diseases (NDs) are characterized by the deposition of protein aggregates with broad-range neuronal toxicity. Defects of endolysosomal trafficking are increasingly being seen as key pathological features of NDs, probably contributing to synaptic dysfunction and ultimate neuronal death. We used fast fluorescence videomicroscopy to investigate endosomal and lysosomal dynamics in the branches of mouse cortical neurons in primary cultures following the application of α-syn fibrillar polymorphs (fibrils and ribbons) and Aß assemblies (oligomers and fibrils). We provide new insight into the differential effects of these pathogenic protein assemblies on endosomal and lysosomal transport, and reveal differences in the transport characteristics of the compartments loaded with these protein assemblies relative to endosomes.
GP2-enriched pancreatic progenitors give rise to functional beta cells in vivo and eliminate the risk of teratoma formation
Authors: Aghazadeh Yasaman , Sarangi Farida , Poon Frankie , Nkennor Blessing , McGaugh Emily C. , Nunes Sara S. , Nostro M. Cristina
Published: May 2021

Human pluripotent stem cell (hPSC)-derived pancreatic progenitors (PPs) can be differentiated into beta-like cells in vitro and in vivo, and therefore have therapeutic potential for type 1 diabetes (T1D) treatment. However, the purity of PPs varies across different hPSC lines, differentiation protocols and laboratories. The uncommitted cells may give rise to non-pancreatic endodermal, mesodermal, or ectodermal derivatives in vivo, hampering the safety of hPSC-derived PPs for clinical applications. Recently, proteomics and transcriptomics analyses identified glycoprotein 2 (GP2) as a PP-specific cell surface marker. The GP2-enriched PPs generate higher percentages of beta-like cells in vitro compared to unsorted and GP2− fractions, but their potential in vivo remains to be elucidated. Here, we demonstrate that the GP2-enriched-PPs give rise to all pancreatic cells in vivo, including functional beta-like cells. Remarkably, GP2 enrichment eliminated the formation of teratoma in vivo. This study establishes that the GP2-enriched PPs represent a safe option for T1D treatment.
KLFDAPC: A Supervised Machine Learning Approach for Spatial Genetic Structure Analysis
Authors: Qin Xinghu , Chiang Charleston W. K. , Gaggiotti Oscar E.
Published: May 2021

Geographic patterns of human genetic variation provide important insights into human evolution and disease. A commonly used tool to detect geographic patterns from genetic data is principal components analysis (PCA) or the supervised linear discriminant analysis of principal components (DAPC). However, genetic features produced from both approaches could fail to correctly characterize population structure for complex scenarios involving admixture. In this study, we introduce Kernel Local Fisher Discriminant Analysis of Principal Components (KLFDAPC), a supervised nonlinear approach for inferring individual geographic genetic structure that could rectify the limitations of these approaches by preserving the multimodal space of samples. We tested the power of KLFDAPC to infer population structure and to predict individual geographic origin using neural networks. Simulation results showed that KLFDAPC significantly improved the population separability compared with PCA and DAPC. The application to POPRES and CONVERGE datasets indicated that the first two reduced features of KLFDAPC correctly recapitulated the geography of individuals, and significantly improved the accuracy of predicting individual geographic origin when compared to PCA and DAPC. Therefore, KLFDAPC can be useful for geographic ancestry inference, design of genome scans and correction for spatial stratification in GWAS that link genes to adaptation or disease susceptibility.
Engineering Gelation Kinetics in Living Silk Hydrogels by Differential Dynamic Microscopy Microrheology and Machine Learning
Authors: Martineau Rhett L. , Bayles Alexandra V. , Hung Chia-Suei , Reyes Kristofer G. , Helgeson Matthew E. , Gupta Maneesh K.
Published: May 2021

Microbes embedded in hydrogels comprise one form of living material. Discovering formulations that balance potentially competing mechanical and biological properties in living hydrogels—for example gel time of the hydrogel formulation and viability of the embedded organisms—can be challenging. In this work, a pipeline is developed to automate characterization of the gel time of hydrogel formulations. Using this pipeline, living materials comprised of enzymatically crosslinked silk and embedded E. coli—formulated from within a 4D parameter space—are engineered to gel within a pre-selected timeframe. Gelation time is estimated using a novel adaptation of microrheology analysis using differential dynamic microscopy (DDM). In order to expedite the discovery of gelation regime boundaries, Bayesian machine learning models are deployed with optimal decision-making under uncertainty. The rate of learning is observed to vary between AI-assisted planning and human planning, with the fastest rate occurring during AI-assisted planning following a round of human planning. For a subset of formulations gelling within a targeted timeframe of 5-15 minutes, fluorophore production within the embedded cells is substantially similar across treatments, evidencing that gel time can be tuned independent of other material properties—at least over a finite range—while maintaining biological activity.
Phase-specific RNA accumulation and duplex thermodynamics in multiphase coacervate models for membraneless organelles
Authors: Choi Saehyun , Bevilacqua Philip C. , Keating Christine D.
Published: May 2021

Liquid-liquid phase separation has emerged as an important means of intracellular RNA compartmentalization. Some membraneless organelles host two or more compartments serving different putative biochemical roles; the mechanisms for, and functional consequences of, this subcompartmentalization are not yet well understood. Here, we show that adjacent phases of decapeptide-based multiphase model membraneless organelles differ markedly in their interactions with RNA. Additionally, their coexistence introduces new equilibria that alter RNA duplex stability and RNA sorting by hybridization state. These effects require neither biospecific RNA binding sites nor full-length proteins. As such, they are general and point to more primitive versions of mechanisms operating in extant biology that could aid understanding and enable design of functional artificial membraneless organelles.
Temporal and spatial topography of cell proliferation in cancer
Authors: Gaglia Giorgio , Kabraji Sheheryar , Argyropoulou Danae , Dai Yang , Wang Shu , Bergholz Johann , Coy Shannon , Lin Jia-Ren , Jeselsohn Rinath , Metzger Otto , Winer Eric P. , Dillon Deborah A. , Zhao Jean J. , Sorger Peter K , Santagata Sandro
Published: May 2021

Proliferation is a fundamental trait of cancer cells but is poorly characterized in tumors by classical histologic methods. We use multiplexed tissue imaging to quantify the abundance of multiple cell cycle regulating proteins at single-cell level and develop robust multivariate proliferation metrics. Across cancers, the proliferative architecture is organized at two distinct spatial scales: large domains, and local niches enriched for specific immune lineages. A subset of tumor cells express cell cycle regulators in canonical patterns consistent with unrestrained proliferation, a phenomenon we refer to as “cell cycle coherence”. By contrast, the cell cycles of other tumor cell populations are skewed toward a specific phase or characterized by non-canonical (incoherent) marker combinations. Coherence varies across space, with changes in oncogene activity, and with therapeutic intervention, and is associated with aggressive behavior. Multivariate measures capture clinically significant features of cancer proliferation, a fundamental step in enabling more precise use of anti-cancer therapies.
Climatic suitability predictions for the cultivation of macadamia in Malawi using climate change scenarios
Authors: Zuza Emmanuel Junior , Araya Yoseph Negusse , Maseyk Kadmiel , Bhagwat Shonil A , de Sousa Kauê , Emmott Andrew , Rawes Will
Published: May 2021

Global climate change is altering the suitable areas of crop species worldwide, with cascading effects on people and animals reliant upon those crop species as food sources. Macadamia is one of these essential lucrative crop species that grows in Malawi. Here, we used an ensemble model approach to determine the current distribution of macadamia production areas across Malawi in relation to climate. For future distribution of suitable areas, we used the climate outputs of 17 general circulation models based on two climate change scenarios (RCP 4.5 and RCP 8.5). The precipitation of the driest month and isothermality were the climatic variables that strongly influenced macadamia’s suitability in Malawi. We found that these climatic requirements were fulfilled across many areas in Malawi under the current conditions. Future projections indicated that vast parts of Malawi’s macadamia growing regions will remain suitable for macadamia, amounting to 36,910 km2 (39.1%) and 33,511 km2 (35.5%) of land based on RCP 4.5 and RCP 8.5, respectively. Alarmingly, suitable areas for macadamia production are predicted to shrink by −18% (17,015 km2) and −21.6% (20,414 km2) based on RCP 4.5 and RCP 8.5, respectively, with much of the suitability shifting northwards. This means that some currently productive areas will become unproductive in the future, while current unproductive areas will become productive. Notably, suitable areas will increase in Malawi’s central and northern highlands, while the southern region will lose most of its suitable areas. Our study, therefore, shows that there is potential for expanding macadamia production in Malawi. Most, importantly our future projections provide critical evidence on the potential negative impacts of climate change on the suitability of macadamia production in the country. We recommend developing area-specific adaptation strategies to build resilience in the macadamia sector in Malawi under climate change.
Genomic context sensitivity of insulator function
Authors: Ribeiro-dos-Santos André M. , Hogan Megan S. , Luther Raven D. , Maurano Matthew T.
Published: May 2021

Compartmentalization of interactions between genomic regulatory elements and potential target genes is influenced by the binding of insulator proteins such as CTCF, which act as potent enhancer blockers when interposed between an enhancer and a promoter in a reporter assay. But only a minority of CTCF sites genome-wide function as boundary elements, depending on cellular and genomic context. To dissect the influence of genomic context on enhancer blocker activity, we integrated reporter constructs with promoter-only, promoter and enhancer, and enhancer blocker configurations at hundreds of thousands of genomic sites using the Sleeping Beauty transposase. Deconvolution of reporter activity by genomic position revealed strikingly different patterns of reporter function, including a compartment of enhancer blocker reporter integrations with robust expression. The high density of integration sites permits quantitative delineation of characteristic genomic context sensitivity profiles, and their decomposition into sensitivity to both local and distant DNaseI hypersensitive sites. Furthermore, a single-cell expression approach permits direct linkage of reporters integrated into the same clonal lineage with differential endogenous gene expression, revealing that CTCF insulator activity does not completely abrogate reporter effects on endogenous gene expression. Collectively, our results lend new insight to genomic regulatory compartmentalization and its influence on the determinants of promoter-enhancer specificity.
High-throughput mapping of single-neuron projection and molecular features by retrograde barcoded labelling
Authors: Xu Peibo , Peng Jian , Yuan Tingli , Chen Zhaoqin , He Hui , Wu Ziyan , Li Ting , Li Xiaodong , Wang Luyue , Wei Wu , Li Chengyu T. , Luo Zhen-Ge , Chen Yuejun
Published: May 2021

Deciphering patterns of connectivity between neurons in the brain is a critical step toward understanding brain function. Imaging-based neuroanatomical tracing identifies area-to-area or sparse neuron-to-neuron connectivity patterns, but with limited throughput. Barcode-based connectomics maps large numbers of single-neuron projections, but remains a challenge for jointly analyzing single-cell transcriptomics. Here, we established a rAAV2-retro barcode-based multiplexed tracing method that simultaneously characterizes the projectome and transcriptome at the single neuron level. We uncovered dedicated and collateral projection patterns of ventromedial prefrontal cortex (vmPFC) neurons to five downstream targets and found that projection-defined vmPFC neurons are molecularly heterogeneous. We identified transcriptional signatures of projection-specific vmPFC neurons, and verifiedPou3f1as a marker gene of neurons extending collateral branches to dorsomedial striatum and lateral hypothalamus. In summary, we have developed a new multiplexed technique whose paired connectome and gene expression data can help reveal organizational principles that form neural circuits and process information.
A tandem segmentation-classification approach for the localization of morphological predictors of C. elegans lifespan and motility
Authors: Yakimovich Artur , Galimov Evgeniy
Published: May 2021

C. elegans is an established model organism for studying genetic and drug effects on ageing, many of which are conserved in humans. It is also an important model for basic research, and C. elegans pathologies is a new emerging field. Here we develop a proof-of-principal convolutional neural network-based platform to segment C. elegans and extract features that might be useful for lifespan prediction. We use a dataset of 734 worms tracked throughout their lifespan and classify worms into long-lived and short-lived. We designed WormNet - a convolutional neural network (CNN) to predict the worm lifespan class based on young adult images (day 1 – day 3 old adults) and showed that WormNet, as well as, InceptionV3 CNN can successfully classify lifespan. Based on U-Net architecture we develop HydraNet CNNs which allow segmenting worms accurately into anterior, mid-body and posterior parts. We combine HydraNet segmentation, WormNet prediction and the class activation map approach to determine the segments most important for lifespan classification. Such a tandem segmentation-classification approach shows posterior part of the worm might be more important for classifying long-lived worms. Our approach can be useful for the acceleration of anti-ageing drug discovery and for studying C. elegans pathologies.
Neuro-musculoskeletal Upper Limb in-silico as virtual patient
Authors: Kapardi Mallampalli , Pithapuram Madhav Vinodh , Rangayyan Yashaswini Mandayam , Iyengar Raghu Sesha , Singh Avinash Kumar , Sripada Sirisha , Raghavan Mohan
Published: May 2021

Virtual patients and physiologies allow experimentation, design, and early-stage clinical trials in-silico. Virtual patient technology for human movement systems that encompasses musculoskeleton and its neural control are few and far in between. In this work, we present one such neuro-musculoskeletal upper limb in-silico model. This upper limb is both modular in architecture and generates movement as an emergent phenomenon out of a multiscale co-simulation of spinal cord neural control and musculoskeletal dynamics. It is developed on the NEUROiD movement simulation platform that enables a co-simulation of popular neural simulator NEURON and the musculoskeletal simulator OpenSim. In this work, we describe the design and development of the upper limb in a modular fashion, while reusing existing models and modules. We further characterize and demonstrate the use of this model in generating a range of commonly observed movements by means of a spatio temporal stimulation pattern delivered to the cervical spinal cord. We believe this work enables a first and small step towards an in-silico paradigms for understanding upper limb movement, disease pathology, medication, and rehabilitation.
Verification of SARS-CoV-2-Encoded small RNAs and contribution to Infection-Associated lung inflammation
Authors: Cheng Zhang , Cheng Liu , Lin Jiang , Lunbiao Cui , Chunyu Li , Guoxin Song , Rui Xu , Xiangnan Geng , Changxing Luan , Yan Chen , Baoli Zhu , Wei Zhu
Published: May 2021

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus that causes coronavirus disease 2019 (COVID-19), the respiratory illness responsible for the COVID-19 pandemic. SARS-CoV-2 is a positive-stranded RNA virus belongs toCoronaviridaefamily. The viral genome of SARS-CoV-2 contains around 29.8 kilobase with a 5′-cap structure and 3′-poly-A tail, and shows 79.2% nucleotide identity with human SARS-CoV-1, which caused the 2002-2004 SARS outbreak. As the successor to SARS-CoV-1, SARS-CoV-2 now has circulated across the globe. There is a growing understanding of SARS-CoV-2 in virology, epidemiology, and clinical management strategies. In this study, we verified the existence of two 18-22 nt small viral RNAs (svRNAs) derived from the same precursor in human specimens infected with SARS-CoV-2, including nasopharyngeal swabs and formalin-fixed paraffin-embedded (FFPE) explanted lungs from lung transplantation of COVID-19 patients. We then simulated and confirmed the formation of these two SARS-CoV-2-Encoded small RNAs in human lung epithelial cells. And the potential pro-inflammatory effects of the splicing and maturation process of these two svRNAs in human lung epithelial cells were also explored. By screening cytokine storm genes and the characteristic expression profiling of COVID-19 in the explanted lung tissues and the svRNAs precursor transfected human lung epithelial cells, we found that the maturation of these two small viral RNAs contributed significantly to the infection associated lung inflammation, mainly via the activation of the CXCL8, CXCL11 and type I interferon signaling pathway. Taken together, we discovered two SARS-CoV-2-Encoded small RNAs and investigated the pro-inflammatory effects during their maturation in human lung epithelial cells, which might provide new insight into the pathogenesis and possible treatment options for COVID-19.
Versatile and multiplexed mass spectrometry-based absolute quantification with cell-free-synthesized internal standard peptides
Authors: Masuda Keiko , Kasahara Keiko , Narumi Ryohei , Shimojo Masaru , Shimizu Yoshihiro
Published: May 2021

Preparation of stable isotope-labeled internal standard peptides is crucial for mass spectrometry (MS)-based targeted proteomics. Herein, we developed versatile and multiplexed absolute protein quantification method using MS. A previously developed method based on the cell-free peptide synthesis system, termed MS-based quantification by isotope-labeled cell-free products (MS-QBiC), was improved for multiple peptide synthesis in one-pot reaction. We pluralized the quantification tags used for the quantification of synthesized peptides and thus, made it possible to use cell-free synthesized isotope-labeled peptides as mixtures for the absolute quantification. The improved multiplexed MS-QBiC method was proved to be applied to clarify ribosomal proteins stoichiometry in the ribosomal subunit, one of the largest cellular complexes. The study demonstrates that the developed method enables the preparation of several dozens and even several hundreds of internal standard peptides within a few days for quantification of multiple proteins with only a single-run of MS analysis.
Sustained Enzymatic Activity and Flow in Crowded Protein Droplets
Authors: Testa Andrea , Dindo Mirco , Rebane Aleksander A. , Nasouri Babak , Style Robert W. , Golestanian Ramin , Dufresne Eric R. , Laurino Paola
Published: May 2021

Living cells harvest energy from their environments to drive the chemical processes that enable life. We introduce a minimal system that operates at similar protein concentrations, metabolic densities, and length scales as living cells. This approach takes advantage of the tendency of phase-separated protein droplets to strongly partition enzymes, while presenting minimal barriers to transport of small molecules across their interface. By dispersing these microreactors in a reservoir of substrate-loaded buffer, we achieve steady states at metabolic densities that match those of the hungriest microorganisms. We further demonstrate the formation of steady pH gradients, capable of driving microscopic flows. Our approach enables the investigation of the function of diverse enzymes in environments that mimic cytoplasm, and provides a flexible platform for studying the collective behavior of matter driven far from equilibrium.
Genetic code degeneracy is established by the decoding center of the ribosome
Authors: Ye Shixin , Lehmann Jean
Published: May 2021

The degeneracy of the genetic code confers a wide array of properties to coding sequences. Yet, its origin is still unclear. A structural analysis has shown that the stability of the Watson-Crick base pair at the second position of the anticodon-codon interaction is a critical parameter controlling the extent of non-specific pairings accepted at the third position by the ribosome, a flexibility at the root of degeneracy. Based on recent cryo-EM analyses, the present work shows that residue A1493 of the decoding center provides a significant contribution to the stability of this base pair, revealing that the ribosome is directly involved in the establishment of degeneracy. Building on existing evolutionary models, we show the evidence that the early appearance of A1493 and A1492 established the basis of degeneracy when an elementary kinetic scheme of translation was prevailing. Logical considerations on the expansion of this kinetic scheme indicate that the acquisition of the peptidyl transferase center was the next major evolutionary step, while the induced-fit mechanism, that enables a sharp selection of the tRNAs, necessarily arose later when G530 was acquired by the decoding center.
Key informant perceptions on wildlife hunting in India during the COVID-19 lockdown
Authors: Mendiratta Uttara , Khanyari Munib , Velho Nandini , Suryawanshi Kulbhushansingh Ramesh , Kulkarni Nirmal
Published: May 2021

Lockdowns intended to control the COVID-19 pandemic resulted in major socioeconomic upheavals across the world. While there were numerous reports of these lockdowns benefiting wildlife by reducing human movement and habitat disturbance, increased hunting during these lockdowns emerged as a conservation concern, particular in tropical Asia and Africa. We used online interviews with key informants including wildlife researchers, enforcement staff and NGO employees (N=99), and media reports (N=98), to examine the impacts of India’s COVID-19 lockdown (March-May 2020) on wildlife hunting across the country. We asked whether and how hunting patterns changed during the lockdown, and explored socioeconomic and institutional factors underlying these changes. Over half the interviewees spread over 43 administrative districts perceived hunting (mammals, in particular) to have increased during the lockdown relative to a pre-lockdown reference period. Interviewees identified household consumption (53% of respondents) and sport and recreation (34%) as main motivations for hunting during the lockdown, and logistical challenges for enforcement (36%), disruption of food supply (32%), and need for recreational opportunities (32%) as key factors associated with hunting during this period. These insights were corroborated by statements by experts extracted from media articles. Collectively, our findings suggest that the COVID-19 lockdown potentially increased hunting across much of India, and emphasize the role of livelihood and food security in mitigating threats to wildlife during such periods of acute socioeconomic perturbation.
Mind the gap: performance metric evaluation in brain-age prediction
Authors: de Lange Ann-Marie G. , Anatürk Melis , Rokicki Jaroslav , Han Laura K.M. , Franke Katja , Alnæs Dag , Ebmeier Klaus P. , Draganski Bogdan , Kaufmann Tobias , Westlye Lars T. , Hahn Tim , Cole James H.
Published: May 2021

Estimating age based on neuroimaging-derived data has become a popular approach to developing markers for brain integrity and health. While a variety of machine-learning algorithms can provide accurate predictions of age based on brain characteristics, there is significant variation in model accuracy reported across studies. We predicted age based on neuroimaging data in two population-based datasets, and assessed the effects of age range, sample size, and age-bias correction on the model performance metrics r, R2, Root Mean Squared Error (RMSE), and Mean Absolute Error (MAE). The results showed that these metrics vary considerably depending on cohort age range; r and R2 values are lower when measured in samples with a narrower age range. RMSE and MAE are also lower in samples with a narrower age range due to smaller errors/brain age delta values when predictions are closer to the mean age of the group. Across subsets with different age ranges, performance metrics improve with increasing sample size. Performance metrics further vary depending on prediction variance as well as mean age difference between training and test sets, and age-bias corrected metrics indicate high accuracy - also for models showing poor initial performance. In conclusion, performance metrics used for evaluating age prediction models depend on cohort and study-specific data characteristics, and cannot be directly compared across different studies. Since age-bias corrected metrics in general indicate high accuracy, even for poorly performing models, inspection of uncorrected model results provides important information about underlying model attributes such as prediction variance.
Social Housing Status Impacts Rhesus Monkeys’ Affective Responding in Classic Threat Processing Tasks
Authors: Charbonneau Joey A. , Amaral David G. , Bliss-Moreau Eliza
Published: May 2021

The established literature clearly demonstrates that whether or not monkeys are socially reared has long term consequences for their affective behavior. Yet, in the context of behavioral neuroscience and pharmacological studies, social context of adult animals is often ignored. When social context has been studied in adult monkeys, such studies have typically focused on welfare-related issues, as social isolation often leads to the development of abnormal behavior, rather than the impact on outcomes in behavioral neuroscience studies. Variation in social housing conditions for adult animals could have an impact on affective responding and may have significant implications for the interpretation of data from biopsychiatry and behavioral neuroscience studies. We evaluated the affective reactivity of rhesus monkeys (Macaca mulatta) maintained in one of four housing conditions (individually-housed, grate-paired, intermittently-paired, and continuously-paired) using two classic threat processing tasks—a test of responsivity to objects and the Human Intruder Test. Individually-housed monkeys exhibited consistently blunted sensitivity to ostensibly threatening stimuli as compared to socially-housed monkeys. Within the three socially-housed conditions, intermittently- and continuously-paired monkeys behaved similarly to each other and grate-paired monkeys exhibited relatively enhanced sensitivity to threatening stimuli. These findings suggest that the adult housing conditions of monkeys can robustly modulate affective responding in a way that may be consistent with behavioral phenotypes observed in human psychiatric conditions. Results are considered in the context of the broad behavioral and psychiatric neuroscience literatures, which have historically used individually-housed animals, pointing to the potential need to reconsider inferences drawn from those studies.
Flexibility of Functional Neuronal Assemblies Supports Human Memory
Authors: Umbach Gray , Tan Ryan , Jacobs Joshua , Pfeiffer Brad E. , Lega Bradley
Published: May 2021

Summary Paragraph

Episodic memories, or consciously accessible memories of unique events, represent a key aspect of human cognition. Evidence from rodent models suggests that the neural representation of these complex memories requires cooperative firing of groups of neurons on short time scales1, organized by gamma oscillations2, 3. These co-firing groups, termed “neuronal assemblies,”4 represent a fundamental neurophysiological unit supporting memory. Using microelectrode data from neurosurgical patients5, we identify neuronal assemblies in the human MTL and show that they exhibit consistent organization in their firing pattern based on gamma phase information. We connect these properties to memory performance across recording sessions. Finally, we describe how human neuronal assemblies flexibly adjust6-9 over longer time scales. Our findings provide key evidence linking assemblies to human episodic memory for the first time.
Rho Kinase regulates neutrophil NET formation that is involved in UVB-induced skin inflammation
Authors: Li Minghui , Lyu Xing , Liao James , Werth Victoria P. , Liu Ming-Lin
Published: May 2021

Objective

Ultraviolet B (UVB) is an important trigger of skin inflammation and lupus with leukocyte recruitment to inflamed skin. We recently reported the involvement of neutrophil NETosis in UVB-induced skin inflammation, and that NETotic nuclear envelope rupture is driven by PKCα-mediated nuclear lamin B disassembly. To address the role of Actin cytoskeleton in NETosis, we investigated the effects of Rho kinase (ROCK) and its downstream actomyosin cytoskeletal networks on PKCα nuclear translocation and NET formation, as well as their involvement in UVB-induced skin inflammation.

Methods

We studied the dynamic changes of ROCK and actomyosin cytoskeletal networks during NETosis induction and their involvement in PKCα nuclear translocation. Using mice with hematopoietic-specific ROCK1 deficiency, we investigated the effects of ROCK1 deficiency on NETosis, and its involvement in UVB-induced skin inflammation.

Results

Our time course studies demonstrated the dynamic changes of actin polymerization and ROCK activation, support the role of actin cytoskeleton in nuclear translocation of cytosolic PKCα in early stage of NETosis induction. Inhibition of actin polymerization or key molecules of the ROCK/MLCK/myosin pathway decreased PKCα nuclear translocation and NET formation. Genetic deficiency of ROCK1, inhibited NETosisex vivoandin vivo, decreased extracellular display of NET-associated IL-17A, TNFα, IFNγ, and IFNα in inflamed skin, which were correlated with the ameliorated skin inflammation in UVB-irradiated mice with hematopoietic-specific ROCK1 deficiency.

Conclusions

ROCK regulated NETosis through modulation of PKCα nuclear translocation via actomyosin cytoskeletal networks in neutrophils. ROCK1 deficiency ameliorated UVB- induced skin inflammation by attenuation of NETosis and NET-associated cytokines.
Positive and negative effects of land abandonment on butterfly communities revealed by a hierarchical sampling design across climatic regions
Authors: Sugimoto Naoki , Fukasawa Keita , Asahara Akio , Kasada Minoru , Matsuba Misako , Miyashita Tadashi
Published: May 2021

Land abandonment may decrease biodiversity but also provides an opportunity for rewilding. It is therefore necessary to identify areas that may benefit from traditional land management practices and those that may benefit from a lack of human intervention. In this study, we conducted comparative field surveys of butterfly occurrence in abandoned and inhabited settlements in 18 regions of diverse climatic zones in Japan to test the hypotheses that species-specific responses to land abandonment correlate with climatic niches and habitat preferences. Hierarchical models that unified species occurrence and habitat preferences revealed that negative responses to land abandonment were associated with species that have cold climatic niches and utilize open habitats, suggesting that species negatively impacted by land abandonment will decline more due to future climate warming. Maps representing species gains and losses due to land abandonment, which were created from the model estimates, showed similar geographic patterns, but some areas exhibited high species losses relative to gains. Our hierarchical modelling approach was useful for scaling up local-scale effects of land abandonment to a macro-scale assessment, which is crucial to developing spatial conservation strategies in the era of depopulation.
The bitter end: T2R bitter receptor agonists elevate nuclear calcium and induce apoptosis in non-ciliated airway epithelial cells
Authors: McMahon Derek B. , Kuek Li Eon , Johnson Madeline E. , Johnson Paige O. , Horn Rachel L.J. , Carey Ryan M. , Adappa Nithin D. , Palmer James N. , Lee Robert J.
Published: May 2021

Bitter taste receptors (T2Rs) localize to airway motile cilia and initiate innate immune responses in retaliation to bacterial quorum sensing molecules (acyl-homoserine lactones and quinolones). Activation of T2Rs leads to calcium-driven NO production that increases cilia beating and directly kills bacteria. Several airway diseases, including chronic rhinosinusitis, COPD, and cystic fibrosis, are characterized by epithelial remodeling, including loss of motile cilia and/or squamous metaplasia. To understand the function of T2Rs within the altered landscape of airway disease, we studied T2Rs in non-ciliated airway cell lines and primary cells de-differentiated to a squamous phenotype. In differentiated cells, T2Rs localize to cilia, however in de-differentiated, non-ciliated cells they localize to the nucleus. Cilia and nuclear import utilize many shared proteins, thus in the absence of motile cilia some T2Rs may target to the nucleus. T2R agonists selectively elevated both nuclear and mitochondrial calcium through a G-protein-coupled receptor, phospholipase C, and InsP3receptor-dependent mechanism. Additionally, T2R agonists decreased nuclear cAMP, increased nitric oxide, and increased cGMP, consistent with T2R signaling. Furthermore, exposure to T2R agonists led to nuclear calcium-induced mitochondrial depolarization and caspase activation. T2R agonists induced apoptosis in primary bronchial and nasal cells differentiated at air-liquid interface but then induced to a squamous phenotype by apical submersion. Air-exposed well-differentiated cells did not die. This T2R-induced apoptosis may be a last-resort defense against infection, possibly when bacteria have breached the epithelial barrier and reach non-ciliated cells below. However, it may also increase susceptibility of de-differentiated or remodeled epithelia to damage by bacterial metabolites. Moreover, the T2R-activated apoptosis pathway occurs in airway cancer cells. T2Rs may thus contribute to microbiome-tumor cell crosstalk in airway cancers. T2R agonists may also be useful topical therapeutics (e.g., delivered by nasal rinse or nebulizer) for activating airway cancer cell apoptosis without killing surrounding differentiated tissue.
DISCA: high-throughput cryo-ET structural pattern mining by deep unsupervised clustering
Authors: Zeng Xiangrui , Kahng Anson , Xue Liang , Mahamid Julia , Chang Yi-Wei , Xu Min
Published: May 2021

Cryo-electron tomography directly visualizes heterogeneous macromolecular structures in complex cellular environments, but existing computer-assisted sorting approaches are low-throughput or inherently limited due to their dependency on available templates and manual labels.

We introduce a high-throughput template-and-label-free deep learning approach that automatically discovers subsets of homogeneous structures by learning and modeling 3D structural features and their distributions.

Diverse structures emerging from sorted subsets enable systematic unbiased recognition of macro-molecular complexes in situ.
Growth and division mode plasticity is dependent on cell density in marine-derived black yeasts
Authors: Goshima Gohta
Published: May 2021

The diversity and ecological contribution of the fungus kingdom in the marine environment remain under-studied. A recent survey in the Atlantic (Woods Hole, MA, USA) brought to light the diversity and unique biological features of marine fungi. The study revealed that black yeast species undergo an unconventional cell division cycle, which has not been documented in conventional model yeast species such as Saccharomyces cerevisiae (budding yeast) and Schizosaccharomyces pombe (fission yeast). The prevalence of this unusual property is unknown. Here, I collected and identified 65 marine fungi species across 40 genera from the surface ocean water, sediment, and the surface of macroalgae (seaweeds) in the Pacific (Sugashima, Toba, Japan). The Sugashima collection largely did not overlap with the Woods Hole collection and included several unidentifiable species, further illustrating the diversity of marine fungi. Three black yeast species were isolated, two of which were commonly found in Woods Hole (Aureobasidium pullulans, Hortaea werneckii). Surprisingly, their cell division mode was dependent on cell density, and the previously reported unconventional division mode was reproduced only at a certain cell density. For all three black yeast species, cells underwent filamentous growth with septations at low cell density and immediately formed buds at high cell density. At intermediate cell density, two black yeasts (H. werneckii and an unidentifiable species) showed rod cells undergoing septation at the cell equator. In contrast, all eight budding yeast species showed a consistent division pattern regardless of cell density. This study suggests the plastic nature of the growth/division mode of marine-derived black yeast.