bluuebunny/crossref_metadata_2025 huggingface dataset:
LIRcentral: a manually curated online database of experimentally validated functional LIR-motifs
Authors: Chatzichristofi Agathangelos , Sagris Vasileios , Pallaris Aristos , Eftychiou Marios , Kalvari Ioanna , Price Nicholas , Theodosiou Theodosios , Iliopoulos Ioannis , Nezis Ioannis P. , Promponas Vasilis J
Published: June 2022

Several selective macroautophagy receptor and adaptor proteins bind members of the Autophagy-related protein 8 (Atg8) family using short linear motifs (SLiMs), most often referred to as Atg8-interacting motifs (AIM) or LC3-interacting motifs (LIR). AIM/LIR-motifs have been extensively studied during the last fifteen years, since they can uncover the underlying biological mechanisms and possible substrates for this key catabolic process of eukaryotic cells. Prompted by the fact that experimental information regarding LIR-motifs can be found scattered across heterogeneous literature resources, we have developed LIRcentral (https://lircentral.eu), a freely available online repository for user-friendly access to comprehensive, high-quality information regarding LIR-motifs from manually curated publications. Herein, we describe the development of LIRcentral and showcase currently available data and features, along with our plans for the expansion of this resource. Information incorporated in LIRcentral is useful for accomplishing a variety of research tasks, including: (i) guiding wet biology researchers for the characterization of novel instances of LIR-motifs, (ii) giving bioinformaticians/computational biologists access to high-quality LIR-motifs for building novel prediction methods for LIR-motifs and LIR containing proteins (LIRCPs) and (iii) performing analyses to better understand the biological importance/features of functional LIR-motifs. We welcome feedback on the LIRcentral content and functionality by all interested researchers and anticipate this work to spearhead a community effort for sustaining this resource which will further promote progress in studying LIR-motifs/LIRCPs.
Nucleosome patterns in circulating tumor DNA reveal transcriptional regulation of advanced prostate cancer phenotypes
Authors: Sarkar Navonil De , Patton Robert D. , Doebley Anna-Lisa , Hanratty Brian , Kreitzman Adam J. , Sarthy Jay F. , Ko Minjeong , Adil Mohamed , Brahma Sandipan , Meers Michael P. , Janssens Derek H. , Ang Lisa A. , Coleman Ilsa , Bose Arnab , Dumpit Ruth F. , Lucas Jared M. , Nunez Talina A. , Nguyen Holly M. , McClure Heather M. , Pritchard Colin C. , Schweizer Michael T. , Morrissey Colm , Choudhury Atish D. , Baca Sylvan C. , Berchuck Jacob E. , Freedman Matthew L. , Ahmad Kami , Haffner Michael C. , Montgomery Bruce , Corey Eva , Henikoff Steven , Nelson Peter S. , Ha Gavin
Published: June 2022

Advanced prostate cancers comprise distinct phenotypes, but tumor classification remains clinically challenging. Here, we harnessed circulating tumor DNA (ctDNA) to study tumor phenotypes by ascertaining nucleosome positioning patterns associated with transcription regulation. We sequenced plasma ctDNA whole genomes from patient-derived xenografts representing a spectrum of androgen receptor active (ARPC) and neuroendocrine (NEPC) prostate cancers. Nucleosome patterns associated with transcriptional activity were reflected in ctDNA at regions of genes, promoters, histone modifications, transcription factor binding, and accessible chromatin. We identified the activity of key phenotype-defining transcriptional regulators from ctDNA, including AR, ASCL1, HOXB13, HNF4G, and NR3C1. Using these features, we designed a prediction model which distinguished NEPC from ARPC in patient plasma samples across three clinical cohorts with 97-100% sensitivity and 85-100% specificity. While phenotype classification is typically assessed by immunohistochemistry or transcriptome profiling, we demonstrate that ctDNA provides comparable results with numerous diagnostic advantages for precision oncology.

STATEMENT OF SIGNIFICANCE

This study provides key insights into the dynamics of nucleosome positioning and gene regulation associated with cancer phenotypes that can be ascertained from ctDNA. The new methods established for phenotype classification extend the utility of ctDNA beyond assessments of DNA alterations with important implications for molecular diagnostics and precision oncology.
Validating the representation of distance between infarct diseases using Word2Vec word embedding
Authors: Yokokawa Daiki , Noda Kazutaka , Yanagita Yasutaka , Uehara Takanori , Ohira Yoshiyuki , Shikino Kiyoshi , Tsukamoto Tomoko , Ikusaka Masatomi
Published: June 2022

Objective

To determine if inter-disease distances between word embedding vectors using the picot-and-cluster strategy (PCS) are a valid quantitative representation of similar disease groups in a limited domain.

Materials and Methods

Abstracts were extracted from the Ichushi-Web database and subjected to morphological analysis and training using the Word2Vec. From this, word embedding vectors were obtained. For words including “infarction”, we calculated the cophenetic correlation coefficient (CCC) as an internal validity measure and the adjusted rand index (ARI), normalized mutual information (NMI), and adjusted mutual information (AMI) with ICD-10 codes as the external validity measures. This was performed for each combination of metric and hierarchical clustering method.

Results

Seventy-one words included “infarction”, of which 38 diseases matched the ICD-10 standard with the appearance of 21 unique ICD-10 codes. The CCC was most significant at 0.8690 (metric and method: euclidean and centroid), while the AMI was maximal at 0.4109 (metric and method: cosine and correlation, and average and weighted). The NMI and ARI were maximal at 0.8463 and 0.3593, respectively (metric and method: cosine and complete).

Discussion

The metric and method that maximized the internal validity measure were different from those that maximized the external validity measures; both produced different results. The Cosine distance should be used when considering ICD-10, and the Euclidean distance when considering the frequency of word occurrence.

Conclusion

The distributed representation, when trained by Word2Vec on the “infarction” domain from a Japanese academic corpus, provides an objective inter-disease distance used in PCS.
Co-occurrences enhance our understanding of aquatic fungal metacommunity assembly and reveal potential host–parasite interactions
Authors: Vass Máté , Eriksson Karolina , Carlsson-Graner Ulla , Wikner Johan , Andersson Agneta
Published: June 2022

Our knowledge of aquatic fungal communities, their assembly, distributions and ecological roles in marine ecosystems is scarce. Hence, we aimed to investigate fungal metacommunities of coastal habitats in a subarctic zone (northern Baltic Sea, Sweden). Using a novel joint species distribution model and network approach, we quantified the importance of biotic associations contributing to the assembly of mycoplankton, further, detected potential biotic interactions between fungi–algae pairs, respectively. Our long-read metabarcoding approach identified 504 fungal taxa, of which a dominant fraction (44.8 %) was assigned as early-diverging fungi (i.e., Cryptomycota and Chytridiomycota). Alpha diversity of mycoplankton declined and community compositions changed along inlet–bay– offshore transects. The distributions of most fungi were rather influenced by spatial factors than by environmental drivers, and the influence of biotic associations was pronounced when environmental filtering was weak and spatial patterning lessened. We found great number of co-occurrences (138) among the dominant fungal groups, and the forty associations between fungal and algal OTUs suggested potential host–parasite/saprotroph links, supporting a Cryptomycota-based mycoloop pathway. We emphasize that the contribution of biotic associations to mycoplankton assembly are important to consider in future studies as it helps to improve predictions of species distributions in aquatic ecosystems.
Pancreatic tumors activate arginine biosynthesis to adapt to myeloid-driven amino acid stress
Authors: Apiz-Saab Juan J. , Dzierozynski Lindsey N. , Jonker Patrick B. , Zhu Zhou , Chen Riona N. , Oh Moses , Sheehan Colin , Macleod Kay F. , Weber Christopher R. , Muir Alexander
Published: June 2022

Nutrient stress in the tumor microenvironment requires cancer cells to adopt adaptive metabolic programs to maintain survival and proliferation. Therefore, knowledge of microenvironmental nutrient levels and how cancer cells cope with such nutrition is critical to understand the metabolism underpinning cancer cell biology. Previously, we performed quantitative metabolomics of the interstitial fluid (the local perfusate) of murine pancreatic ductal adenocarcinoma (PDAC) tumors to comprehensively characterize nutrient availability in the microenvironment of these tumors (Sullivan et al., 2019a). Here, we developTumorInterstitialFluidMedium (TIFM), a cell culture medium that contains nutrient levels representative of the PDAC microenvironment, enabling study of PDAC metabolism under physiological nutrition. We show that PDAC cells cultured in TIFM, compared to standard laboratory models, adopt a cellular state more similar to PDAC cells in tumors. Further, using the TIFM model we identified arginine biosynthesis as a metabolic adaptation PDAC cells engage to cope with microenvironmental arginine starvation driven by myeloid cells in PDAC tumors. Altogether, these data show that nutrient availability in tumors is an important determinant of cancer cell metabolism and behavior, and cell culture models that incorporate physiological nutrient availability have improved fidelity and enable the discovery of novel cancer metabolic phenotypes.
Octopamine affects gustatory responsiveness and associative learning performance in bumble bees
Authors: Muth Felicity , Breslow Emily , Leonard Anne S.
Published: June 2022

Octopamine has broad roles within invertebrate nervous systems as a neurohormone, neurotransmitter and neuromodulator. It orchestrates foraging behavior in many insect taxa via effects on feeding, gustatory responsiveness and appetitive learning. Knowledge of how this biogenic amine regulates bee physiology and behavior is based largely on study of a single species, the honey bee,Apis mellifera. Until recently, its role in the foraging ecology and social organization of diverse bee taxa had been unexplored. Bumble bees (Bombusspp.) are a model for the study of foraging and learning, and its neural basis, but whether octopamine similarly affects sensory and cognitive performance in this genus is not known. To address this gap, we explored the effects of octopamine on sucrose response thresholds and associative learning inBombus impatiensvia conditioning of the Proboscis Extension Reflex (PER) using a visual (color) cue. We found that octopamine had similar effects on bumble bee behavior as honey bees, however, higher doses were required to induce these effects. At this higher dose, octopamine lowered bees’ sucrose response thresholds and appeared to enhance associative learning performance. Adding to recent studies on stingless bees (Meliponini), these findings support the idea that octopamine’s role in reward processing and learning is broadly conserved across Apidae, while pointing towards some differences across systems worth exploring further.
Adaptive, maladaptive, neutral, or absent plasticity: Hidden caveats of reaction norms
Authors: Eriksson Martin , Kinnby Alexandra , De Wit Pierre , Rafajlović Marina
Published: June 2022

Adaptive phenotypic plasticity may improve the response of individuals when faced with new environmental conditions. Typically, empirical evidence for plasticity is based on phenotypic reaction norms obtained in reciprocal transplant experiments. In such experiments, individuals from their native environment are transplanted into a different environment, and a number of trait values, potentially implicated in individuals’ response to the new environment, are measured. However, the interpretations of reaction norms may differ depending on the nature of the assessed traits, which may not be known beforehand. For example, for traits that contribute to local adaptation, adaptive plasticity implies non-zero slopes of reaction norms. By contrast, for traits that are correlated to fitness, high tolerance to different environments (possibly due to adaptive plasticity in traits that contribute to adaptation) may, instead, result in flat reaction norms. Here we investigate reaction norms for adaptive versus fitness-correlated traits, and how they may affect the conclusions regarding the contribution of plasticity. To this end, we first simulate range expansion along an environmental gradient where plasticity evolves to different values locally and then perform reciprocal transplant experimentsin silico. We show that reaction norms alone cannot inform us whether the assessed trait exhibits locally adaptive, maladaptive, neutral or no plasticity, without any additional knowledge of the traits assessed and species’ biology. We use the insights from the model to analyse and interpret empirical data from reciprocal transplant experiments involving the marine isopodIdotea balthicasampled from two geographical locations with different salinities, concluding that the low-salinity population likely has reduced adaptive plasticity relative to the high-salinity population. Overall, we conclude that, when interpreting results from reciprocal transplant experiments, it is necessary to consider whether traits assessed are locally adaptive with respect to the environmental variable accounted for in the experiments, or correlated to fitness.
Electrophysiological characterization of medial preoptic neurons in lactating rats and its modulation by hypocretin-1
Authors: Rivas Mayda , Serantes Diego , Pascovich Claudia , Peña Florencia , Ferreira Annabel , Torterolo Pablo , Benedetto Luciana
Published: June 2022

The medial preoptic area (mPOA) undergoes through neuroanatomical changes across the postpartum period, during which its neurons play a critical role in the regulation of maternal behavior. In addition, this area is also crucial for sleep-wake regulation. We have previously shown that hypocretins (HCRT) within the mPOA facilitate active maternal behaviors in postpartum rats, while the blockade of endogenous HCRT in this area promotes nursing and sleep. To explore the mechanisms behind these HCRT actions, we aimed to evaluate the effects of juxta-cellular HCRT-1 administration on mPOA neurons in urethane-anesthetized postpartum and virgin female rats. We recorded mPOA single units and the electroencephalogram (EEG) and applied HCRT-1 juxta-cellular by pressure pulses. Our main results show that the electrophysiological characteristics of the mPOA neurons and their relationship with the EEG of postpartum rats did not differ from virgin rats. Additionally, neurons that respond to HCRT-1 had a slower firing rate than those that did not. In addition, administration of HCRT increased the activity in one group of neurons while decreasing it in another, both in postpartum and virgin rats. The mechanisms by which HCRT modulate functions controlled by the mPOA involve different cell populations.
Gender impacts the relationship between mood disorder symptoms and effortful avoidance performance
Authors: Forys Brandon J. , Tomm Ryan J. , Stamboliyska Dayana , Terpstra Alex R. , Clark Luke , Chakrabarty Trisha , Floresco Stan B. , Todd Rebecca M.
Published: June 2022

We must often decide how much effort to exert or withhold to avoid undesirable outcomes or obtain rewards. In depression and anxiety, levels of avoidance can be excessive and reward-seeking may be reduced. Yet outstanding questions remain about the links between motivated action/inhibition and anxiety and depression levels, and whether they differ between men and women. Here we examined the relationship between anxiety and depression scores, and performance on effortful active and inhibitory avoidance (Study 1) and reward seeking (Study 2) in humans. Undergraduates and paid online workers (NAvoid= 545,NReward= 310;NFemale= 368,NMale= 450,MAge= 22.58,RangeAge= 17-62) were assessed on the Beck Depression Inventory II (BDI) and the Beck Anxiety Inventory (BAI) and performed an instructed online avoidance or reward-seeking task. Participants had to make multiple presses on active trials and withhold presses on inhibitory trials to avoid an unpleasant sound (Study 1) or obtain points towards a monetary reward (Study 2). Overall, men deployed more effort than women in both avoidance and reward-seeking, and anxiety scores were negatively associated with active reward-seeking performance based on sensitivity scores. Gender interacted with anxiety scores and inhibitory avoidance performance, such that women with higher anxiety showed worse avoidance performance. Our results illuminate effects of gender in the relationship between anxiety and depression levels and the motivation to actively and effortfully respond to obtain positive and avoid negative outcomes.

Significance statement

We must often take or withhold effortful action to avoid unpleasant outcomes or obtain rewards. Depression and anxiety can impact these behaviours’ effectiveness, but the roles of avoidance in depression and reward-seeking in anxiety are not fully understood. Gender differences in avoidance and reward-seeking have also not been examined. We present a task in which community participants with a range of anxiety and depression levels made or withheld button presses to avoid hearing an unpleasant sound or obtain a reward. Men deployed more effort than women in avoidance, and women with higher anxiety scores had lower avoidance performance than men. We illuminate gender differences in how depressive and anxiety scores impact our ability to avoid threats and obtain rewards.
Early exposure to high-fat diet impairs central and peripheral metabolic function: Impacts on cognition and mitochondrial function
Authors: Vilela Wembley Rodrigues , Bellozi Paula Maria Quaglio , Picolo Victor Luna , Cavadas Bruna Neves , Silva Marques Keila Valentina , Pereira Louise Tavares Garcia , Amato Angélica Amorim , Magalhães Kelly Grace , Mortari Márcia Renata , Goulart Jair Trapé , de Bem Andreza Fabro
Published: June 2022

The impact of overnutrition early in life is not restricted to the onset of cardiovascular and metabolic diseases, but also affects critical brain functions related to cognition. This study aimed to evaluate the relationship between peripheral metabolic and bioenergetic changes induced by high-fat diet (HFD) and their impact on hippocampal cognitive functions in juvenile mice. To this purpose, three-week-old male C57BL/6 mice received a HFD or control diet for seven weeks, associated with two low doses of streptozotocin (STZ) or vehicle, to accelerate the metabolic dysfunction. HFD induced metabolic changes in mice, particularly related to glucose metabolism, in spite of the absence of obesity and changes in lipid profile. HFD exposure starting from weaning impaired recognition and spatial memories in mice, without inducing a depressive-like behavior. Increased immunoreactivity for GFAP and a trend towards a decrease in NeuN staining were verified in the hippocampus of HFD-fed mice. HFD caused a bioenergetic impairment in the hippocampus, characterized by a decrease in both O2 consumption related to ATP production and in the maximum respiratory capacity. The thermogenic capacity of brown adipose tissue was impaired by HFD, here verified through the absence of a decrease in O2 consumption after UCP-1 inhibition and increase in the reserve respiratory capacity. Impaired mitochondria function was also observed in the liver of HFD mice, while no changes were verified in O2 consumption in the heart of juvenile mice. These results indicate that the introduction of a HFD early in life has a detrimental impact on bioenergetic and mitochondrial function of tissues with metabolic and thermogenic activities, which is likely related to hippocampal metabolic changes and cognitive impairment.

Highlights

HFD introduced early in life impacts mitochondrial function

Dietary shift early in life leads hippocampal dysfunction

Early life HFD exposure disrupts BAT thermogenic acitivity

HFD-induced hippocampal and BAT mitochondrial dysfunction impacts cognition
Cell wall extensin arabinosylation is required for root directional response to salinity
Authors: Zou Yutao , Gigli-Bisceglia Nora , Zelm Eva van , Kokkinopoulou Pinelopi , Julkowska Magdalena M. , Besten Maarten , Nguyen Thu-Phuong , Li Hongfei , Lamers Jasper , Zeeuw Thijs de , Dongus Joram A. , Zeng Yuxiao , Cheng Yu , Koevoets Iko T. , Jørgensen Bodil , Giesbers Marcel , Vroom Jelmer , Ketelaar Tijs , Petersen Bent Larsen , Engelsdorf Timo , Sprakel Joris , Zhang Yanxia , Testerink Christa
Published: June 2022

Soil salinity is a major contributor to crop yield losses. To improve our understanding of root responses to salinity, we developed and exploit here a real-time salt-induced tilting assay (SITA). This method follows root growth upon both gravitropic and salt challenges, revealing that root bending upon tilting is modulated by salinity, but not by osmotic stress. Next, this salt-specific response was measured in 345 natural Arabidopsis accessions and we discovered a genetic locus, encoding for the cell-wall modifying enzyme EXTENSIN ARABINOSE DEFICIENT TRANSFERASE (ExAD), to be associated with root bending in salt. Extensins are a class of structural cell wall glycoproteins [hydroxyproline-rich glycoproteins (HRGPs)] which are post-translationally modified by O-glycosylation mostly in the form of hydroxyproline (Hyp)-arabinosylation. We show that salt induces ExAD-dependent Hyp-arabinosylation, influencing root bending responses and cell wall thickness. We report that roots ofexadmutants, which lack extensin Hyp-Araf4modifications, display increased root epidermal cell wall thickness and porosity and altered gravitropic root bending in salt, as well as a reduced salt avoidance response. Our results suggest that extensin modification via Hyp-arabinosylation represents a novel salt-specific cellular process that is required for the directional response of roots exposed to salinity.
Plasma levels of Ceramides and their association with Hematocrit and Thrombocytopenia in Severe and Non-severe dengue
Authors: Jeanpierre Aashika Raagavi , Mariappan Vignesh , Green Siva Ranganathan , Mutheneni Srinivasa Rao , P Shashikala , Pillai Agieshkumar Balakrishna
Published: June 2022

Background

Plasma leakage due to endothelial permeability is regarded as a hallmark process in the pathophysiology of severe dengue. In recent years, the importance of ceramide in regulating vascular tone during viral infection and metabolic diseases has gained attention. The present study aimed to evaluate the plasma levels of ceramide and its association with plasma leakage in dengue patients.

Methods

The study involved 30 dengue samples involving severe dengue (SD-10), Dengue with Warning sign (DWW-10), Dengue without Warning Sign (DWOW-10), along with other febrile illness (OFI-10) controls. Samples were collected on the day of admission (DOA), day of defervescence (DOD), and day of convalescence (DOC). Total plasma ceramides (d18:1/22:0) were quantified using RP-HPLC. The correlation between ceramides and hematocrit/platelet count was evaluated using Spearman Rho Correlation. All the statistical analyses were performed using SPSS software.

Results

During the febrile phase, a significant (P≤0.05) decrease in the levels of ceramides was observed in dengue compared to OFI (control). Towards the defervescences, the ceramides levels were substantially (P ≤ 0.001) elevated in dengue groups compared to baseline. Most importantly, the ceramide levels were found to be higher in SD patients compared to non-severe dengue (DWW & DWOW) and OFI, particularly at the critical phase of infection. We observed a significant negative correlation (r = -0.867, P ≤0.001) between the platelet count and ceramide levels in SD subjects. Notably, a negative correlation was observed between ceramide and hematocrit during the defervescence phase (R = -0.355, P≤0.05) in the AD group.

Conclusion

Elevated levels of circulating plasma ceramides during the defervescence phase of severe dengue show an essential role of ceramides in disease pathogenesis, however further studies are required to ascertain it.
KPop: Accurate and scalable comparative analysis of microbial genomes by sequence embeddings
Authors: Didelot Xavier , Ribeca Paolo
Published: June 2022

The recent explosion in the amount of available sequencing data challenges existing analysis techniques. Here we introduce KPop, a novel versatile method based on fullk-mer spectra and dataset-specific transformations, through which thousands of assembled or unassembled microbial genomes can be quickly compared. Unlike minimizer-based methods that produce distances and have lower resolution, KPop is able to accurately map sequences onto a low-dimensional space. Extensive validation on simulated and real-life viral and bacterial datasets shows that KPop can correctly separate sequences at both species and sub-species levels even when the overall genomic diversity is low. KPop also rapidly identifies related sequences and systematically outperforms minimizer-based methods. KPop’s code is open-source and available on GitHub athttps://github.com/PaoloRibeca/KPop.
The Effects of Nonlinear Signal on Expression-Based Prediction Performance
Authors: Heil Benjamin J. , Crawford Jake , Greene Casey S.
Published: June 2022

Those building predictive models from transcriptomic data are faced with two conflicting perspectives. The first, based on the inherent high dimensionality of biological systems, supposes that complex non-linear models such as neural networks will better match complex biological systems. The second, imagining that complex systems will still be well predicted by simple dividing lines prefers linear models that are easier to interpret. We compare multi-layer neural networks and logistic regression across multiple prediction tasks on GTEx and Recount3 datasets and find evidence in favor of both possibilities. We verified the presence of non-linear signal for transcriptomic prediction tasks by removing the predictive linear signal with Limma, and showed the removal ablated the performance of linear methods but not non-linear ones. However, we also found that the presence of non-linear signal was not necessarily sufficient for neural networks to outperform logistic regression. Our results demonstrate that while multi-layer neural networks may be useful for making predictions from gene expression data, including a linear baseline model is critical because while biological systems are highdimensional, effective dividing lines for predictive models may not be.
Defining the Ligand-dependent Interactome of the Sigma 1 Receptor
Authors: Zhao Jing , Veeranan-Karmegam Rajalakshmi , Baker Frederick C. , Mysona Barbara A. , Bagchi Pritha , Liu Yutao , Smith Sylvia B. , Gonsalvez Graydon B. , Bollinger Kathryn E.
Published: June 2022

Sigma 1 Receptor (S1R) is a therapeutic target for a wide spectrum of pathological conditions ranging from neurodegenerative diseases to cancer and COVID-19. S1R is ubiquitously expressed throughout the visceral organs, nervous, immune and cardiovascular systems. It is proposed to function as a ligand-dependent molecular chaperone that modulates multiple intracellular signaling pathways. The purpose of this study was to define the S1R interactome under native conditions and upon binding to well-characterized ligands. This was accomplished by fusing the biotin ligase, Apex2, to the C terminus of S1R. Cells stably expressing S1R-Apex or a GFP-Apex control were used to map specific protein interactions. Biotinylated proteins were labeled under native conditions and in a ligand dependent manner, then purified and identified using quantitative mass spectrometry. Under native conditions, S1R biotinylates over 200 novel proteins, many of which localize within the endomembrane system (ER, Golgi, secretory vesicles) and function within the secretory pathway. Under conditions of cellular exposure to either S1R agonist or antagonist, results show enrichment of proteins integral to secretion, extracellular matrix formation, and cholesterol biosynthesis. Notably, Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9) displays increased binding to S1R under conditions of treatment with Haloperidol, a well-known S1R antagonist; whereas Low density lipoprotein receptor (LDLR) binds more efficiently to S1R upon treatment with (+)-Pentazocine ((+)-PTZ), a classical S1R agonist. Our results are consistent with the postulated role of S1R as an intracellular chaperone and further suggest important and novel functionalities related to cholesterol metabolism and biosynthesis.
Community composition shapes microbial-specific phenotypes in a cystic fibrosis polymicrobial model system
Authors: Jean-Pierre Fabrice , Hampton Thomas H. , Schultz Daniel , Hogan Deborah A. , Groleau Marie-Christine , Déziel Eric , O’Toole George A.
Published: June 2022

Interspecies interactions can drive the emergence of unexpected microbial phenotypes that are not observed when studying monocultures. The cystic fibrosis (CF) lung consists of a complex environment where particular microbes, living as polymicrobial biofilm-like communities, are associated with negative clinical outcomes for persons with CF (pwCF). However, the current lack of in vitro models integrating the microbial diversity observed in the CF airway hampers our understanding of why polymicrobial communities are recalcitrant to therapy in this disease. Here, integrating computational approaches informed by clinical data, we built a mixed community of clinical relevance to the CF lung composed of Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinis and Prevotella melaninogenica. We developed and validated this model biofilm community with multiple isolates of these four genera. When challenged with tobramycin, a front-line antimicrobial used to treat pwCF, the microorganisms in the polymicrobial community show altered sensitivity to this antibiotic compared to monospecies biofilms. We observed that wild-type P. aeruginosa is sensitized to tobramycin in a mixed community versus monoculture, and this observation holds across a range of community relative abundances. We also report that LasR loss-of-function, a variant frequently detected in the CF airway, induces tolerance of P. aeruginosa to tobramycin specifically in the mixed community. The molecular basis of this community-specific recalcitrance to tobramycin for the LasR mutant variant is the increased production of redox-active phenazines. Our data support the importance of studying clinically-relevant model polymicrobial biofilms to understand community-specific traits relevant to infections.

SIGNIFICANCE STATEMENT

The CF lung is colonized by biofilm-like microbial communities that exhibit both resistance and tolerance (collectively called “recalcitrance”) to antimicrobials used in the clinic. Here, we leveraged clinical data from pwCF to inform our understanding of communities exhibiting recalcitrance. We developed and validated an in vitro model that revealed novel, community-specific phenotypes relevant to the clinic. We used this model to explore the underlying mechanism associated with a community-specific emergent behavior. We posit that in vitro models of polymicrobial communities may help in developing new antimicrobial strategies to improve patient outcomes, and that the approach used here can be applied to other polymicrobial models.
CSPP1 stabilizes growing microtubule ends and damaged lattices from the luminal side
Authors: van den Berg Cyntha M. , Volkov Vladimir A. , Schnorrenberg Sebastian , Huang Ziqiang , Stecker Kelly E. , Grigoriev Ilya , Patzke Sebastian , Zimmermann Timo , Dogterom Marileen , Akhmanova Anna
Published: June 2022

Microtubules are dynamic cytoskeletal polymers, and their organization and stability are tightly regulated by numerous cellular factors. While regulatory proteins controlling formation of interphase microtubule arrays and mitotic spindles have been extensively studied, the biochemical mechanisms responsible for generating stable microtubule cores of centrioles and cilia are poorly understood. Here, we used in vitro reconstitution assays to investigate microtubule-stabilizing properties of CSPP1, a centrosome and cilia-associated protein mutated in the neurodevelopmental ciliopathy Joubert syndrome. We found that CSPP1 preferentially binds to polymerizing microtubule ends that grow slowly or undergo growth perturbations and, in this way, resembles microtubule-stabilizing compounds such as taxanes. Fluorescence microscopy and cryo-electron tomography showed that CSPP1 is deposited in the microtubule lumen and inhibits microtubule growth and shortening through two separate domains. CSPP1 also specifically recognizes and stabilizes damaged microtubule lattices. These data help to explain how CSPP1 regulates elongation and stability of ciliary axonemes and other microtubule-based structures.
Membrane contact site detection (MCS-DETECT) reveals dual control of rough mitochondria-ER contacts
Authors: Cardoen Ben , Vandevoorde Kurt , Gao Guang , Alan Parsa , Liu William , Tiliakou Ellie , Vogl A. Wayne , Hamarneh Ghassan , Nabi Ivan R.
Published: June 2022

Identification and morphological analysis of mitochondria-ER contacts (MERCs) by fluorescent microscopy is limited by sub-pixel resolution inter-organelle distances. Application of a Membrane Contact Site (MCS) detection algorithm, MCS-DETECT, to 3D STED super-resolution image volumes reconstructs sub-resolution MERCs. MCS-DETECT shows that elongated ribosome-studded riboMERCs, present in HT-1080 but not COS-7 cells, are morphologically distinct from smaller smooth contacts and larger contacts induced by mitochondria-ER linker expression in COS-7 cells. riboMERC expression is reduced in Gp78 knockout HT-1080 cells and induced by Gp78 ubiquitin ligase activity in COS-7 cells. Knockdown of the riboMERC tether RRBP1 eliminates riboMERCs in both wild-type and Gp78 knockout HT-1080 cells. By MCS-DETECT, Gp78-dependent riboMERCs present complex tubular shapes that intercalate between and contact multiple mitochondria, that are lost upon RRBP1 knockdown. MCS-DETECT of 3D whole cell super-resolution image volumes therefore identifies a novel dual regulatory mechanism for tubular riboMERCs, whose formation is dependent on RRBP1 and size modulated by Gp78 E3 ubiquitin ligase activity.

eTOC Summary

Application of the sub-pixel resolution Membrane Contact Site (MCS) detection algorithm, MCS-DETECT, to 3D STED super-resolution image volumes identifies a novel dual regulatory mechanism for tubular riboMERCs, whose formation is dependent on RRBP1 and size modulated by Gp78 E3 ubiquitin ligase activity.
Chitin utilization by marine picocyanobacteria and the evolution of a planktonic lifestyle
Authors: Capovilla Giovanna , Braakman Rogier , Fournier Gregory , Hackl Thomas , Schwartzman Julia , Lu Xinda , Yelton Alexis , Longnecker Krista , Soule Melissa Kido , Thomas Elaina , Swarr Gretchen , Mongera Alessandro , Payette Jack , Waldbauer Jacob , Kujawinski Elizabeth B. , Cordero Otto X. , Chisholm Sallie W.
Published: June 2022

Marine picocyanobacteria (Prochlorococcus and Synechococcus), the most abundant photosynthetic cells in the oceans, are generally thought to have a primarily single-celled and free-living lifestyle. However, we find that genes for breaking down chitin - an abundant source of organic carbon that primarily exists as particles - are widespread in this group. We further show that cells with a chitin degradation pathway display chitin degradation activity, attach to chitin particles and show enhanced growth under low light conditions when exposed to chitosan, a partially deacetylated form of chitin. Marine chitin is largely derived from arthropods, whose roots lie in the early Phanerozoic, 520-535 million years ago, close to when marine picocyanobacteria began colonizing the ocean. We postulate that attachment to chitin particles allowed benthic cyanobacteria to emulate their mat-based lifestyle in the water column, initiating their expansion into the open ocean, seeding the rise of modern marine ecosystems. Transitioning to a constitutive planktonic life without chitin associations along a major early branch within the Prochlorococcus tree led to cellular and genomic streamlining. Our work highlights how coevolution across trophic levels creates metabolic opportunities and drives biospheric expansions.
Grk7 but not Grk1 undergoes cAMP-dependent phosphorylation in zebrafish cone photoreceptors in the dark and mediates recovery of the cone photoresponse in response to forskolin
Authors: Chrispell Jared D. , Xiong Yubin , Weiss Ellen R.
Published: June 2022

In the vertebrate retina, phosphorylation of photoactivated visual pigments in rods and cones by G protein-coupled receptor kinases is essential for sustained visual function. In vitro analysis demonstrates that GRK1 and GRK7 are phosphorylated by PKA and that phosphorylation is associated with a decreased capacity to phosphorylate rhodopsin, while in vivo observations show that GRK phosphorylation is cAMP-dependent. In many vertebrates, including humans, GRK1 is expressed in both rods and cones while GRK7 is expressed only in cones. However, mice express only GRK1 in both rods and cones and lack GRK7. We recently reported that a mutation deleting the phosphorylation site, Ser21, in GRK1 is associated with a delay in dark adaptation in mouse rods but not in cones, suggesting that GRK1 may serve a different role depending upon the photoreceptor cell type in which it is expressed. Here, we present immunochemical and electrophysiological studies using zebrafish as a model. Since zebrafish display a retinal GRK expression profile similar to humans, these studies will allow us to further evaluate the role of cAMP-dependent GRK phosphorylation in cone photoreceptor recovery that may be relevant to human physiology. ERG analyses of wildtype and Grk-knockout zebrafish larvae treated with forskolin show that elevated intracellular cAMP significantly decreases recovery of the cone photoresponse, which is mediated by Grk7a rather than Grk1b. Using a cone-specific dominant negative PKA transgenic zebrafish, we show for the first time that PKA is required for Grk7a phosphorylation in vivo. Lastly, immunoblot analyses in rod grk1a and cone grk1b knockout zebrafish, as well as the ‘all cone’ Nrl-/- mouse, show that cone-expressed Grk1 does not undergo cAMP-dependent phosphorylation in vivo. These results provide a better understanding of the function of Grk phosphorylation in the context of cone adaptation and recovery.
Restoration of β-GC trafficking improves the lysosome function in Gaucher’s disease
Authors: Patel Saloni , Radhakrishnan Dhwani , Kumari Darpan , Bhansali Priyanka , Setty Subba Rao Gangi
Published: June 2022

Lysosomes function as a primary site for catabolism and cellular signaling. These organelles digest a variety of substrates received through endocytosis, secretion and autophagy with the help of resident acid hydrolases. Lysosomal enzymes are folded in the endoplasmic reticulum (ER) and trafficked to lysosomes via Golgi and endocytic route. The inability of hydrolase trafficking due to mutations or mutations in its receptor or cofactor leads to cargo accumulation (storage) in lysosomes, resulting in lysosome storage disorder (LSD). In Gaucher’s disease (GD), the lysosomes accumulate glucosylceramide due to a lack of β-glucocerebrosidase (β-GC) activity that causes lysosome enlargement/dysfunction. We hypothesize that improving the trafficking of mutant β-GC to lysosomes may delay the progression of GD. RNAi screen using high throughput based lysosomal enzyme activity assay followed by reporter trafficking assay utilizing β-GC-mCherry lead to the identification of nine potential phosphatases. Depletion of these phosphatases in HeLa cells enhanced the β-GC activity by increasing the folding and trafficking of Gaucher’s mutants to the lysosomes. Consistently, the lysosomes in primary fibroblasts from GD patients restored their function upon the knockdown of these phosphatases. Thus, these studies provide evidence that altering phosphatome activity possibly delays the GD and forms an alternative therapeutic strategy for this genetic disease.

Key points

Phosphatome RNAi screen identified both activators and inhibitors of cellular glucocerebrosidase activity

Depletion of selective phosphatases in HeLa cells improved the folding and trafficking of mutant β-glucocerebrosidase to lysosomes

Knockdown of selective phosphatases restored the low basal β-glucocerebrosidase activity to that of wild-type in primary cells derived from Gaucher’s disease patients

Depletion of selective phosphatases displayed variable β-GC activity in neuropathic and non-neuropathic Gaucher’s disease patient cells
Fine-grained deconvolution of cell-type effects from human bulk brain data using a large single-nucleus RNA sequencing based reference panel
Authors: van den Oord Edwin J.C.G. , Aberg Karolina A.
Published: June 2022

Brain disorders are leading causes of disability worldwide. Gene expression studies provide promising opportunities to better understand their etiology. When studying bulk tissue, cellular diversity may cause many genes that are differentially expressed in cases and controls to remain undetected. Furthermore, identifying the specific cell-types from which association signals originate is key to formulating refined hypotheses of disease etiology, designing proper follow-up experiments and, eventually, developing novel clinical interventions. Cell-type effects can be deconvoluted statistically from bulk expression data using cell-type proportions estimated with the help of a reference panel. To create a fine-grained reference panel for the human prefrontal cortex, we analyzed data from the seven largest single nucleus RNA-seq (snRNA-seq) studies. Seventeen cell-types were robustly detected across all seven studies. To estimate the cell-type proportions, we proposed an empirical Bayes estimator that is suitable for the new panel that involves multiple low abundant cell-types. Furthermore, to avoid the use of a very large reference panel and prevent challenges with public access of nuclei level data, our estimator uses a panel comprising mean expression levels rather than the nuclei level snRNA-seq data. Evaluations show that our empirical Bayes estimator produces highly accurate and unbiased cell-type proportion estimates. Transcriptome-wide association studies performed with permuted bulk RNA-seq data showed that it is possible to perform TWASs for even the rarest cell-types without an increased risk of false positives. Furthermore, we determined that for optimal statistical power the best approach is to analyze all cell-types in the panel as opposed to grouping or omitting (rare) cell-types.
OligoFlow: rapid and sensitive virus quantification using flow cytometry and oligonucleotide hybridization
Authors: Paterson James S. , Dann Lisa M. , Carlson-Jones Jessica , Giles Sarah , McIvor Connor , Speck Peter G. , Mitchell James G.
Published: June 2022

Flow cytometry is an established method for the detection and enumeration of viruses. However, the technique is unable to target specific viral species. Here, we present OligoFlow, a novel method for the rapid detection and enumeration of viruses by incorporating flow cytometry with species specific oligonucleotide hybridization. Using Ostried herpesvirus and dengue virus as model organisms, we demonstrate high-level detection and specificity. Our results represent a significant advancement in viral flow cytometry, opening the possibilities for the rapid identification of viruses in time critical settings.
Differentials in clinical severity and other patient activity indicators amongst Black and South Asian cancer patients in England
Authors: Willis Steffan , Aparicio Pedro Figueiredo , Steel Rhoda , Leblay Gaetan
Published: June 2022

The link between ethnicity, deprivation and health inequalities is well-established. The relationship between ethnicity and cancer is more complex and influenced by a variety of socio-economic, cultural and physiological factors. Understanding the relationship between ethnicity and patient care indicators for specific cancer types is vital if NHS England is to meet the UK government’s stated priority to reduce health inequalities as it recovers from COVID-19.

This paper explores the impact of ethnicity on clinical severity, treatment costs and a range of patient activity indicators across three cancer types – chronic lymphocytic leukaemia, multiple myeloma and prostate cancer.

The paper uses a dataset derived from the Hospital Episodes Statistics (secondary care) database covering 2016/17 to 2020/21,. This enabled the differential impact of the pandemic on ethnic minority patients to be considered. The data was aggregated by ethnicity and deprivation quintile at a national and Integrated Care System (ICS) level. Clinical severity was proxied using co-morbidity and complications (CC) scores. Multivariate linear regression (OLS) models were used to explore the associations with ethnicity.

Black and South Asian patients CC scores were 12.2% and 15.8% higher than the population average (4.1). Controlling for socio-economic deprivation, South Asian patients had higher average clinical severity (+0.57, p<0.01). In addition, ICSs with large South Asian populations were associated with higher CC scores (+0.69, p<0.01). Treatment costs were higher for Black prostate cancer patients with interventions (+£842, p<0.001) and South Asian multiple myeloma patients (+£1686, p<0.001). Both Black and South Asian patients tend to have more spells in hospital. COVID-19 saw total inpatient admissions fall by 18.9%. Black and South Asian inpatient admissions fell by 1.9 and 2.9 percentage points more than the national average respectively. Average clinical severity increased by 7.1% with the largest increase amongst South Asian (+11.5%) and Black (+8.1%) patients.

The higher clinical severity in South Asian patients and higher treatment costs in Black patients observed in this study are not accompanied by significant variations in patient activity indicators, which may point to drivers associated with delays to diagnosis or barriers to access to primary care.
Insulin receptor turnover in fasting is dependent on β-dystroglycan deglycosylation
Authors: Joseph Sunu , Zbidat Sewar , Volodin Alexandra , Kasiviswanathan Dharanibalan , Fried Adina I. , Armani Andrea , Gilda Jennifer E. , Cohen Shenhav
Published: June 2022

Fasting exerts various physiological effects, most notably, reduced signaling through the insulin receptor. We showed that insulin receptor activity requires association with Dystrophin Glycoprotein Complex (DGC). Here, we demonstrate that insulin receptor turnover by lysosomes during fasting is dependent on deglycosylation of the principal DGC component, β-dystroglycan. We show that the lysosomal enzymes HexA and Man2b1, which specifically remove N-linked glycans, mediate β-dystroglycan deglycosylation and consequently insulin receptor-DGC loss. Surprisingly, the lysosomal enzyme NAGLU, which cannot process N-linked glycosylation, also facilitated β-dystroglycan deglycosylation and insulin receptor loss. NAGLU enhances the activity of the transcriptional complex PPAR-γ/RXR-α, which in turn promotes Man2b1 and HexA induction and the resulting β-dystroglycan deglycosylation. Accordingly, downregulation of HexA, Man2b1, NAGLU or RXR-α during fasting blocked β-dystroglycan deglycosylation, and caused accumulation of insulin receptor-DGC assemblies on the membrane. Thus, NAGLU mediates physiological adaptation to fasting by promoting indirectly β-dystroglycan deglycosylation.