bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of atypical circulating tumor cells with prognostic value in metastatic breast cancer patients
Authors: Lopresti Alexia , Boudin Laurys , Finetti Pascal , Garnier Séverine , Aulas Anaïs , Liberatoscioli Maria-Lucia , Cabaud Olivier , Guille Arnaud , de Nonneville Alexandre , Dacosta Quentin , Denicolai Emilie , Pakradouni Jihane , Goncalves Anthony , Birnbaum Daniel , Acquaviva Claire , Bertucci François , Mamessier Emilie
Published: September 2020

Background

Circulating tumor cells (CTCs) have a strong potential as a quasi-non-invasive tool to set up precision medicine strategy for cancer patients. Tremendous efforts have been made to develop the second-generation of “filtration-based” technologies to detect CTCs, revealing a surprising heterogeneity among those cells. Here, we performed the largest and simultaneous analysis of all atypical circulating tumor cells (aCTCs) detected with a filtration-based technology, in a cohort of metastatic breast cancer (mBC) patients, and correlated their presence with clinicopathological and survival data.

Methods

The PERMED-01 study enrolled patients with mBC refractory to systemic therapy. We prospectively analyzed aCTCs present at the time of inclusion in the study, using the Screencell®Cyto device (n=91). Subsets cut-offs were established and evaluated for correlation with clinicopathological data, including progression-free survival (PFS) and overall survival (OS).

Results

The median number of aCTCs found in mBC was 8.3 per mL of blood. Three subsets of aCTCs, absent from controls, were observed in mBC patients: single (s-aCTCs), circulating tumor micro-emboli (CTM), and giant-aCTCs (g-aCTCs). The presence of g-aCTCs was associated with shorter PFS and OS in multivariate analyses. For 23 cases, the analysis was completed with advanced immunofluorescence staining and showed that CTM and g-aCTCs displayed a hybrid phenotype for epithelial and mesenchymal markers.

Conclusions

This study highlights the heterogeneity of aCTCs in mBC patients both at the cytomorphological and molecular levels when using a Screencell®Cyto device. It reveals the g-aCTC subset as a prognostic factor and a potential stratification tool that might help to orientate late-stage mBC patients’ therapeutic care.
Estimation of the Basic Reproduction Number of SARS-CoV-2 in Bangladesh Using Exponential Growth Method
Authors: Mahmud Riaz , Patwari H. M. Abrar Fahim
Published: September 2020

Objectives

In December 2019, a novel coronavirus (SARS-CoV-2) outbreak emerged in Wuhan, Hubei Province, China. Soon, it has spread out across the world and become an ongoing pandemic. In Bangladesh, the first case of novel coronavirus (SARS-CoV-2) was detected on March 8, 2020. Since then, not many significant studies have been conducted to understand the transmission dynamics of novel coronavirus (SARS-CoV-2) in Bangladesh. In this study, we estimated the basic reproduction number R0 of novel coronavirus (SARS-CoV-2) in Bangladesh.

Methods

The data of daily confirmed cases of novel coronavirus (SARS-CoV-2) in Bangladesh and the reported values of generation time of novel coronavirus (SARS-CoV-2) for Singapore and Tianjin, China, were collected. We calculated the basic reproduction number R0 by applying the exponential growth (EG) method. Epidemic data of the first 76 days and different values of generation time were used for the calculation.

Results

The basic reproduction number R0 of novel coronavirus (SARS-CoV-2) in Bangladesh is estimated to be 2.66 [95% CI: 2.58-2.75], optimized R0 is 2.78 [95% CI: 2.69-2.88] using generation time 5.20 with a standard deviation of 1.72 for Singapore. Using generation time 3.95 with a standard deviation of 1.51 for Tianjin, China, R0 is estimated to be 2.15 [95% CI: 2.09-2.20], optimized R0 is 2.22 [95% CI: 2.16-2.29].

Conclusions

The calculated basic reproduction number R0 of novel coronavirus (SARS-CoV-2) in Bangladesh is significantly higher than 1, which indicates its high transmissibility and contagiousness.
A wake-up call - revealing the oversight of sleep physiology and related translational discrepancies in studies of rapid-acting antidepressants
Authors: Alitalo Okko , Saarreharju Roosa , Zarate Carlos A. , Kohtala Samuel , Rantamäki Tomi
Published: October 2020

Depression and sleep problems go hand-in-hand, while clinical improvement often emerges along the normalization of sleep architecture and realignment of the circadian rhythm. Antidepressant effects of sleep deprivation and cognitive behavioral therapy targeted at insomnia further demonstrate the confluence of sleep and mood. Moreover, recent literature showing that ketamine influences many processes related to sleep-wake neurobiology, have led to novel hypotheses explaining rapid and sustained antidepressant effects. Surprisingly, studies addressing ketamine’s antidepressant effects have had a narrow focus on solely on pharmacological aspects and often ignore the role of physiology. To illustrate this discrepancy, we conducted a literature review on articles around rapid-acting antidepressants published between 2009-2019. A gross keyword check indicated overall ignorance of sleep in most studies. To investigate the topic closer, we focused on the most cited preclinical and clinical research papers. Circadian rhythm, timing of drug administration and behavioral tests relative to light cycles, sleep, and their potential association with experimental observations were mentioned only in a handful of the papers. Most importantly, in preclinical reports the treatments have been preferentially delivered during the inactive period, which is polar opposite to clinical practice and research. We hope this report serves as a wake-up call for sleep in the field and urges (re)examining rapid-acting antidepressant effects from the perspective of wake-sleep physiology.
Reconsider phase reconstruction in signals with dynamic periodicity from the modern signal processing perspective
Authors: Alian Aymen , Lo Yu-Lun , Shelley Kirk , Wu Hau-Tieng
Published: October 2020

Phase is the most fundamental physical quantity when we study an oscillatory time series. There are many tools aiming to estimate phase, most of them are developed based on the analytic function model. Unfortunately, this approach might not be suitable for modern signals withintrinsic nonstartionary structure, including multiple oscillatory components, each with time-varying frequency, amplitude, and non-sinusoidal oscillation, e.g., biomedical signals. Specifically, due to the lack of consensus of model and algorithm, phases estimated from signals simultaneously recorded from different sensors for the same physiological system from the same subject might be different. This fact might challenge reproducibility, communication, and scientific interpretation and thus we need a standardized approach with theoretical support over a unified model. In this paper, after summarizing existing models for phase and discussing the main challenge caused by the above-mentioned intrinsic nonstartionary structure, we introduce theadaptive non-harmonic model (ANHM), provide a definition of phase calledfundamental phase, which is a vector-valued function describing the dynamics of all oscillatory components in the signal, and suggest a time-varying bandpass filter (tvBPF) scheme based on time-frequency analysis tools to estimate the fundamental phase. The proposed approach is validated with a simulated database and a real-world database with experts’ labels, and it is applied to two real-world databases, each of which has biomedical signals recorded from different sensors, to show how to standardize the definition of phase in the real-world experimental environment. Specifically, we report that the phase describing a physiological system, if properly modeled and extracted, is immune to the selected sensor for that system, while other approaches might fail. In conclusion, the proposed approach resolves the above-mentioned scientific challenge. We expect its scientific impact on a broad range of applications.
Soluble mannose receptor induces pro-inflammatory macrophage activation and metaflammation
Authors: Embgenbroich Maria , van der Zande Hendrik J.P. , Hussaarts Leonie , Schulte-Schrepping Jonas , Pelgrom Leonard R. , García-Tardón Noemí , Schlautmann Laura , Stoetzel Isabel , Händler Kristian , Lambooij Joost M. , Zawistowska-Deniziak Anna , Hoving Lisa , de Ruiter Karin , Wijngaarden Marjolein , Pijl Hanno , van Dijk Ko Willems , Everts Bart , van Harmelen Vanessa , Yazdanbakhsh Maria , Schultze Joachim L. , Guigas Bruno , Burgdorf Sven
Published: October 2020

Pro-inflammatory activation of macrophages in metabolic tissues is critically important in induction of obesity-induced metaflammation. Here, we demonstrate that the soluble mannose receptor (sMR) plays a direct, functional role in both macrophage activation and metaflammation. We show that sMR binds CD45 on macrophages and inhibits its phosphatase activity, leading to a Src/Akt/NF-κB-mediated cellular reprogramming towards an inflammatory phenotype bothin vitroandin vivo.Remarkably, increased serum sMR levels were observed in obese mice and humans and directly correlated with body weight. Additionally, MR deficiency lowers pro-inflammatory macrophages in metabolic tissues and protects against hepatic steatosis and whole-body metabolic dysfunctions in high-fat diet-induced obese mice. Conversely, administration of sMR in lean mice increases serum pro-inflammatory cytokines, activates tissue macrophages and promotes insulin resistance. Altogether, our results reveal sMR as novel regulator of pro-inflammatory macrophage activation which could constitute a new therapeutic target for metaflammation and other hyperinflammatory diseases.
Reconfiguring primase DNA-recognition sequences by using a data-driven approach
Authors: Soffer Adam , Ifrach Morya , Ilic Stefan , Afek Ariel , Schussheim Hallel , Vilenchik Dan , Akabayov Barak
Published: October 2020

DNA-protein interactions are essential in all aspects of every living cell. Understanding of how features embedded in the DNA sequence affect specific interactions with proteins is challenging but important, since it may contribute to finding the means to regulate metabolic pathways involving DNA-protein interactions. Using a massive experimental benchmark dataset of binding scores for DNA sequences and a machine learning workflow, we describe the binding to DNA of T7 primase, as a model system for specific DNA-protein interactions. Effective binding of T7 primase to its specific DNA recognition sequences triggers the formation of RNA primers that serve as Okazaki fragment start sites during DNA replication.
Separation of coiled-coil structures in lamin A/C is required for elongation of the filament
Authors: Ahn Jinsook , Jeong Soyeon , Kang So-mi , Jo Inseong , Park Bum-Joon , Ha Nam-Chul
Published: September 2020

Intermediate filaments (IFs) commonly have structural elements of a central α-helical coiled-coil domain consisting of coil 1a, coil 1b, coil 2, and their flanking linkers. Recently, crystal structure of a long lamin A/C fragment was determined and showed detailed features of a tetrameric unit. The structure further suggested a new binding mode between tetramers, designated eA22, where a parallel overlap of coil 1a and coil 2 is the key interaction. In this study, we investigated the biochemical effects of genetic mutations causing human diseases, focusing on the eA22 interaction. The mutant proteins exhibited either weakened or augmented interactions between coil 1a and coil 2. The ensuing biochemical results indicated that the interaction requires the separation of the coiled-coils in N-terminal of coil 1a and C-terminal of coil 2, coupled with the structural transition in the central α-helical rod domain. This study provides insight into the role of coil 1a as a molecular regulator in elongation of the IF proteins.
Carbon for nutrient exchange between the lycophyte,Lycopodiella inundataand Mucoromycotina ‘fine root endophytes’ is unresponsive to high atmospheric CO2concentration
Authors: Hoysted Grace A. , Kowal Jill , Pressel Silvia , Duckett Jeffrey G. , Bidartondo Martin I. , Field Katie J.
Published: October 2020

Background and Aims

Non-vascular plants associating with arbuscular mycorrhizal (AMF) and Mucoromycotina ‘fine root endophyte’ (MFRE) fungi derive greater benefits from their fungal associates under higher atmospheric [CO2] than ambient, however nothing is known about how changes in [CO2] affects MFRE function in vascular plants.

Methods

We measured movement of phosphorus (P), nitrogen (N) and carbon (C) between the lycophyte,Lycopodiella inundataand Mucoromycotina fine root endophyte fungi using33P-orthophosphate,15N-ammonium chloride and14CO2isotope tracers under ambient and elevated atmospheric [CO2] concentrations of 440 and 800 ppm, respectively.

Key Results

Transfer of33P and15N from MFRE to plant were unaffected by changes in [CO2]. There was a slight increase in C transfer from plant to MFRE under elevated [CO2].

Conclusions

Our results demonstrate that the exchange of C-for-nutrients between a vascular plant and Mucoromycotina FRE is largely unaffected by changes in atmospheric [CO2]. Unravelling the role of MFRE in host plant nutrition and potential C-for-N trade changes between symbionts under varying abiotic conditions is imperative to further our understanding of the past, present and future roles of diverse plant-fungal symbioses in global ecosystems.
Genome-wide identification of novel genes involved inCorynebacterialescell envelope biogenesis usingCorynebacterium glutamicumas a model
Authors: de Sousa-d’Auria Célia , Constantinesco-Becker Florence , Constant Patricia , Tropis Maryelle , Houssin Christine
Published: September 2020

CorynebacterialesareActinobacteriathat possess an atypical didermic cell envelope. One of the principal features of this cell envelope is the presence of a large complex made up of peptidoglycan, arabinogalactan and mycolic acids. This covalent complex constitutes the backbone of the cell wall and supports an outer membrane, called mycomembrane in reference to the mycolic acids that are its major component. The biosynthesis of the cell envelope ofCorynebacterialeshas been extensively studied, in particular because it is crucial for the survival of important pathogens such asMycobacterium tuberculosisand is therefore a key target for anti-tuberculosis drugs. In this study, we explore the biogenesis of the cell envelope ofCorynebacterium glutamicum, a non-pathogenicCorynebacteriales, which can tolerate dramatic modifications of its cell envelope as important as the loss of its mycomembrane. For this purpose, we used a genetic approach based on genome-wide transposon mutagenesis. We developed a highly effective immunological test based on the use of anti-arabinogalactan antibodies that allowed us to rapidly identify bacteria exhibiting an altered cell envelope. A very large number (10,073) of insertional mutants were screened by means of this test, and 80 were finally selected, representing 55 different loci. Bioinformatics analyses of these loci showed that approximately 60% corresponded to genes already characterized, 63% of which are known to be directly involved in cell wall processes, and more specifically in the biosynthesis of the mycoloyl-arabinogalactan-peptidoglycan complex. We identified 22 new loci potentially involved in cell envelope biogenesis, 76% of which encode putative cell envelope proteins. A mutant of particular interest was further characterized and revealed a new player in mycolic acid metabolism. Because a large proportion of the genes identified by our study is conserved inCorynebacteriales, the library described here provides a new resource of genes whose characterization could lead to a better understanding of the biosynthesis of the envelope components of these bacteria.
Tumor Necrosis Factor andSchistosoma mansoniegg antigen Omega-1 shape distinct aspects of the early egg-induced granulomatous response
Authors: Takaki Kevin K. , Roca Francisco J. , Schramm Gabriele , Wilbers Ruud H. P. , Ittiprasert Wannaporn , Brindley Paul J. , Rinaldi Gabriel , Berriman Matthew , Ramakrishnan Lalita , Pagán Antonio J.
Published: September 2020

Infections by schistosomes result in granulomatous lesions around parasite eggs entrapped within the host tissues. The host and parasite determinants of theSchistosoma mansoniegg-induced granulomatous response are areas of active investigation. Some studies in mice implicate Tumor Necrosis Factor (TNF) produced in response to the infection whereas others fail to find a role for it. In addition, in the mouse model, theS. mansonisecreted egg antigen omega-1 is found to induce granulomas but the underlying mechanism remains unknown. We have recently developed the zebrafish larva as a model to study macrophage recruitment and granuloma formation in response toSchistosoma mansonieggs. Here we use this model to investigate the mechanisms by which TNF and omega-1 shape the early granulomatous response. We find that TNF, specifically signaling through TNF receptor 1, is not required for macrophage recruitment to the egg and granuloma initiation but does mediate granuloma enlargement. In contrast, omega-1 mediates initial macrophage recruitment, with this chemotactic activity being dependent on its RNase activity. Our findings further the understanding of the role of these host- and parasite-derived factors and show that they impact distinct facets of the granulomatous response to the schistosome egg.
PYL8 ABA receptors ofPhoenix dactyliferaplay a crucial role in response to abiotic stress and are stabilized by ABA (118)
Authors: Garcia-Maquilon Irene , Coego Alberto , Lozano-Juste Jorge , Messerer Maxim , de Ollas Carlos , Julian Jose , Ruiz-Partida Rafael , Pizzio Gaston , Belda-Palazón Borja , Gomez-Cadenas Aurelio , Mayer Klaus F.X. , Geiger Dietmar , Alquraishi Saleh A. , Alrefaei Abdulwahed F. , Ache Peter , Hedrich Rainer , Rodriguez Pedro L.
Published: October 2020

The identification of those prevailing ABA receptors and molecular mechanisms that trigger drought adaptation in crops well adapted to harsh conditions such as date palm (Phoenix dactylifera, Pd) sheds light on plant-environment interactions. We reveal that PdPYL8-like receptors are predominantly expressed under abiotic stress, being Pd27 the most expressed receptor in date palm. Therefore, subfamily I PdPYL8-like receptors have been selected for ABA signaling during abiotic stress response in this crop. Biochemical characterization of PdPYL8-like and PdPYL1-like receptors revealed receptor- and ABA-dependent inhibition of PP2Cs, which triggers activation of thepRD29B-LUCreporter in response to ABA. PdPYLs efficiently abolish PP2C-mediated repression of ABA signaling, but loss of the Trp lock in the seed-specific AHG1-like phosphatase PdPP2C79 markedly impairs its inhibition by ABA receptors. Characterization ofArabidopsistransgenic plants that express PdPYLs shows enhanced ABA signaling in seed, root and guard cells. Specifically, Pd27 overexpressing (OE) plants showed lower ABA content and were more efficient than wild type to lower transpiration at negative soil water potential, leading to enhanced drought tolerance. Finally, PdPYL8-like receptors accumulate after ABA treatment, which suggests that ABA-induced stabilization of these receptors operates in date palm for efficient boosting of ABA signaling in response to abiotic stress.

Highlight

Date palm response to abiotic stress is triggered through PYL8-like ABA receptors that are stabilized by the hormone, which boosts plant adaptation to drought mediated by ABA.
Fitness dependence preserves selection for recombination across diverse mixed mating systems
Authors: Rybnikov Sviatoslav , Weissman Daniel B. , Hübner Sariel , Korol Abraham B.
Published: October 2020

Meiotic recombination and the factors affecting its rate and fate in nature have inspired many theoretical studies in evolutionary biology. Classical theoretical models have inferred that non-zero recombination can be favoured under a rather restricted parameter range. Thus, the ubiquity of recombination in nature remains an open question. However, these models assumed constant (uniform) recombination with an equal rate across all individuals within the population. Models of fitness-dependent recombination, with the rate varying among genotypes according to their fitness have shown that such a strategy can often be favoured over the best constant recombination. Here we use simulations to show that across a range of mating systems with varying frequencies of selfing and clonality, fitness-dependent recombination is often favoured even when any non-zero constant recombination is disfavoured. This recombination-protecting effect of fitness dependence is strongest under intermediate rates of selfing or high rates of clonality.
Sperm acrosome overgrowth and infertility in mice lacking chromosome 18 pachytene piRNA
Authors: Choi Heejin , Wang Zhengpin , Dean Jurrien
Published: September 2020

piRNAs are germline-specific, small non-coding RNAs required to maintain genome integrity and preserve RNA homeostasis during male gametogenesis. In murine adult testes, the highest levels of piRNAs are present in the pachytene stage of meiosis, but their mode of action and function remains incompletely understood. We previously reported that BTBD18 binds to 50 pachytene piRNA-producing loci. Here we show that spermatozoa in gene-edited mice lacking a BTBD18 targeted pachytene piRNA cluster on Chr18 have severe sperm head dysmorphology, poor motility, impaired acrosome exocytosis and are sterile. The absence of Chr18 piRNA results in an imbalance of heat shock proteins associated with renaturing proteins and the ubiquitin-proteasome system involved with protein degradation. The mutant phenotype arises from aberrant formation of proacrosomal vesicles, distortion of thetrans-Golgi network, and up-regulation of GOLGA2 associated with acrosome dysgenesis. Collectively, our findings reveal central role of pachytene piRNAs in controlling spermiogenesis and male fertility.
Mechanisms underlying proximity between oral commensal bacteria
Authors: Perera Dasith , McLean Anthony , Lopez Viviana Morillo , Cloutier-Leblanc Kaileigh , Almeida Eric , Cabana Kiana , Welch Jessica Mark , Ramsey Matthew
Published: September 2020

Complex polymicrobial biofilm communities are abundant in nature particularly in the human oral cavity where their composition and fitness can affect health. While the study of these communities during disease is essential and prevalent, little is known about interactions within the healthy plaque community. Here we describe interactions between two of the most abundant species in this healthy microbiome,Haemophilus parainfluenzaeandStreptococcus mitis. We discovered thatH. parainfluenzaetypically exists adjacent to Mitis group streptococciin vivowith which it also positively correlated based on microbiome data. By comparingin vitrococulture data toex vivomicroscopy we revealed that this co-occurrence is density dependent and further influenced by H2O2production. We discovered thatH. parainfluenzaehas a more redundant, multifactorial response to H2O2than related organisms and that the integrity of this system enhances streptococcal fitness. We also show that Mitis group streptococci can act as anin vivosource of NAD forH. parainfluenzaeand that streptococciin vitroevoke patterns of carbon utilization fromH. parainfluenzaethat are similar to those observedin vivo. Our findings describe mechanistic interactions between two of the most abundant and prevalent members of healthy supragingival plaque that contribute to their survivalin vivo.
Local DNA shape is a general principle of transcription factor binding specificity inArabidopsis thaliana
Authors: Sielemann Janik , Wulf Donat , Schmidt Romy , Bräutigam Andrea
Published: October 2020

A genome encodes two types of information, the “what can be made” and the “when and where”. The “what” are mostly proteins which perform the majority of functions within living organisms and the “when and where” is the regulatory information that encodes when and where DNA is transcribed. Currently, it is possible to efficiently predict the majority of the protein content of a genome but nearly impossible to predict the transcriptional regulation. This regulation is based upon the interaction between transcription factors and genomic sequences at the site of binding motifs1,2,3. Information contained within the motif is necessary to predict transcription factor binding, however, it is not sufficient4, as experimentally verified binding sites are substantially scarcer than the corresponding binding motif. Thus, it remains challenging to derive regulational information from binding motifs. Here we show that a random forest machine learning approach, which incorporates the 3D-shape of DNA, enhances binding prediction for all 216 testedArabidopsis thalianatranscription factors and improves the resolution of differential binding by transcription factor family members which share the same binding motif. Our results contribute to the understanding of protein-DNA recognition and demonstrate the extraction of binding site features beyond the binding sequence. We observed that those features were individually weighted for each transcription factor, even if they shared the same binding sequence. We show that the gained insights enable a more robust prediction of binding behavior regarding novel, not-in-genome motif sequences. Understanding transcription factor binding as a combination of motif sequence and motif shape brings us closer to predicting gene expression from promoter sequence.
The stability landscape ofde novoTIM barrels explored by a modular design approach
Authors: Romero-Romero Sergio , Costas Miguel , Manzano Daniel-Adriano Silva , Kordes Sina , Rojas-Ortega Erendira , Tapia Cinthya , Guerra Yasel , Shanmugaratnam Sooruban , Rodríguez-Romero Adela , Baker David , Höcker Birte , Fernández-Velasco D. Alejandro
Published: October 2020

The ability to design stable proteins with custom-made functions is a major goal in biochemistry with practical relevance for our environment and society. High conformational stability lowers protein sensitivity to mutations and changes in the environment; thus, understanding and manipulating protein stability will expand the applications ofde novoproteins. Since the (β/α)8-barrel or TIM-barrel fold is one of the most common functional scaffolds, in this work we designed a collection of stablede novoTIM barrels (DeNovoTIMs), using a computational fixed-backbone and modular approach based on improved hydrophobic packing of sTIM11, the first validatedde novoTIM barrel. DeNovoTIMs navigate a region of the stability landscape previously uncharted by natural TIM barrels, with variations spanning 60 degrees in melting temperature and 22 kcal per mol in conformational stability throughout the designs. Significant non-additive or epistatic effects were observed when stabilizing mutations from different regions of the barrel were combined. The molecular basis of epistasis in DeNovoTIMs appears to be related to the extension of the hydrophobic cores. This study is an important step towards the fine-tuned modulation of protein stability by design.

Significance Statement

De novoprotein design expands our knowledge about protein structure and stability. The TIM barrel is a highly relevant fold used in nature to host a rich variety of catalytic functions. Here, we follow a modular approach to design and characterize a collection ofde novoTIM barrels and subjected them to a thorough folding analysis. Non-additive effects modulate the increase in stability when different regions of the barrel are mutated, showing a wide variety of thermodynamic properties that allow them to navigate an unexplored region of the stability landscape found in natural TIM barrels. The design of stable proteins increases the applicability ofde novoproteins and provides crucial information on the molecular determinants that modulate structure and stability.

One Sentence Summary

A family of designed TIM barrels with diverse thermodynamic properties shows epistatic effects on its stability landscape.
JIP4 is recruited by the phosphoinositide-binding protein Phafin2 to promote recycling tubules on macropinosomes
Authors: Tan Kia Wee , Nähse Viola , Campsteijn Coen , Brech Andreas , Schink Kay Oliver , Stenmark Harald
Published: October 2020

Macropinocytosis allows cells to take up extracellular material in a non-selective manner. The molecular mechanisms that mediate recycling of membranes and transmembrane proteins from macropinosomes still need to be defined. Here we report that JIP4, a coiled-coil containing protein previously described to bind to microtubule motors, is recruited to retromer- and actin-containing tubulating subdomains on macropinosomes by binding to the PH domain of the phosphatidylinositol 3-phosphate (PtdIns3P)-binding protein Phafin2. This recruitment is not shared by the closely related isoforms JIP3 and Phafin1. Disruption of Phafin2 or PtdIns3P impairs JIP4 recruitment to macropinosomes whereas forced localization of Phafin2 to mitochondria causes mitochondrial targeting of JIP4. While knockout of JIP4 suppresses tubulation, overexpression enhances tubulation from macropinosomes. JIP4 knockout cells display increased retention of macropinocytic cargo in both early and late macropinosomes, consistent with a recycling defect. Collectively, these data identify JIP4 and Phafin2 as components of a tubular recycling pathway that operates from macropinosomes.
Dominant-negative mutations inCBX1cause a neurodevelopmental disorder
Authors: Kuroda Yukiko , Iwata-Otsubo Aiko , Dias Kerith-Rae , Temple Suzanna E.L. , Nagao Koji , De Hayr Lachlan , Zhu Ying , Isobe Shin-Ya , Nishibuchi Gohei , Fiordaliso Sarah K , Fujita Yuki , Rippert Alyssa L. , Baker Samuel W , Leung Marco L. , Koboldt Daniel C. , Harman Adele , Keena Beth A. , Kazama Izumi , Musuwadi Subramanian Gopinath , Manickam Kandamurugu , Schmalz Betsy , Latsko Maeson , Zackai Elaine H , Edwards Matt , Evans Carey-Anne , Dulik Matthew C. , Buckley Michael F. , Yamashita Toshihide , O’Brien W. Timothy , Harvey Robert J. , Obuse Chikashi , Roscioli Tony , Izumi Kosuke
Published: October 2020

Purpose

This study aimed to establish variants inCBX1, encoding heterochromatin protein 1β (HP1β), as a cause of a novel syndromic neurodevelopmental disorder.

Methods

Patients withCBX1variants were identified, and clinician researchers were connected using GeneMatcher and physician referrals. Clinical histories were collected from each patient. To investigate the pathogenicity of identified variants, we performedin vitrocellular assays, neurobehavioral and cytological analyses of neuronal cells obtained from newly generatedCbx1mutant mouse lines.

Results

In three unrelated individuals with developmental delay, hypotonia, and autistic features, we identified heterozygousde novovariants inCBX1. The identified variants were in the chromodomain, the functional domain of HP1 β, which mediates interactions with chromatin.Cbx1chromodomain mutant mice displayed increased latency-to-peak response, suggesting the possibility of synaptic delay or myelination deficits. Cytological and chromatin immunoprecipitation experiments confirmed the reduction of mutant HP1β binding to heterochromatin, while HP1β interactome analysis demonstrated that the majority of HP1β-interacting proteins remained unchanged between the wild-type and mutant HP1β.

Conclusion

These collective findings confirm the role ofCBX1in developmental disabilities through the disruption of HP1β chromatin binding during neurocognitive development. As HP1β forms homodimers and heterodimers, mutant HP1β likely sequesters wild-type HP1β and other HP1 proteins, exerting dominant-negative effects.
A super-resolution protocol to correlate structural underpinnings of fast second-messenger signalling in primary cell types
Authors: Hurley Miriam E. , Sheard Thomas M. D. , Norman Ruth , Kirton Hannah M. , Shah Shihab S. , Pervolaraki Eleftheria , Yang Zhaokang , Gamper Nikita , White Ed , Steele Derek , Jayasinghe Izzy
Published: September 2020

Nanometre-scale cellular information obtained through super-resolution microscopies are often unaccompanied by functional information, particularly transient and diffusible signals through which life is orchestrated in the nano-micrometre spatial scale. We describe a correlative imaging protocol which allows the ubiquitous intracellular second messenger, calcium (Ca2+), to be directly visualised against nanoscale patterns of the ryanodine receptor (RyR) Ca2+channels which give rise to these Ca2+signals in wildtype primary cells. This was achieved by combining total internal reflection fluorescence (TIRF) imaging of the elementary Ca2+signals, with the subsequent DNA-PAINT imaging of the RyRs. We report a straightforward image analysis protocol of feature extraction and image alignment between correlative datasets and demonstrate how such data can be used to visually identify the ensembles of Ca2+channels that are locally activated during the genesis of cytoplasmic Ca2+signals.
Prediction Errors Disrupt Hippocampal Representations and Update Episodic Memories
Authors: Sinclair Alyssa H. , Manalili Grace M. , Brunec Iva K. , Adcock R. Alison , Barense Morgan D.
Published: September 2020

The brain supports adaptive behavior by generating predictions, learning from errors, and updating memories to incorporate new information.Prediction error,or surprise, triggers learning when reality contradicts expectations. Prior studies have shown that the hippocampus signals prediction errors, but the hypothesized link to memory updating has not been demonstrated. In a human fMRI study, we elicited mnemonic prediction errors by interrupting familiar narrative videos immediately before the expected endings. We found that prediction error reversed the relationship between univariate hippocampal activation and memory: greater hippocampal activation predicted memory preservation after expected endings, but memory updating after surprising endings. In contrast to previous studies, we showed that univariate activation was insufficient for understanding hippocampal prediction error signals. We explained this surprising finding by tracking both the evolution of hippocampal activation patterns and connectivity between the hippocampus and neuromodulatory regions. We found that hippocampal activation patterns stabilized as each narrative episode unfolded, suggesting sustained episodic representations. Prediction errors disrupted these sustained representations, and the degree of disruption predicted memory updating. The relationship between hippocampal activation and subsequent memory depended on concurrent basal forebrain activation, supporting the idea that cholinergic modulation regulates attention and memory. We conclude that prediction errors create conditions that favor memory updating, prompting the hippocampus to abandon ongoing predictions and make memories malleable.

Significance

Our brains draw on memories to predict the future; when our predictions are incorrect, we must update our memories to improve future predictions. Past studies have demonstrated that the hippocampus signalsprediction error, or surprise, but have not linked this neural signal to memory updating. Here, we uncover this missing connection: We show that mnemonic prediction errors change the role of the hippocampus, reversing the relationship between hippocampal activation and memory outcomes. We examine the mechanisms of this shift in neural processing, showing that prediction errors disrupt the temporal continuity of hippocampal patterns. We propose that prediction errors disrupt sustained representations and enable memory updating. Our findings bear implications for improving education, understanding eyewitness memory distortion, and treating pathological memories.
High frequency visual stimulation primes gamma oscillations for visually-evoked phase reset and enhances spatial acuity
Authors: Lantz Crystal L. , Quinlan Elizabeth M.
Published: September 2020

The temporal frequency of sensory stimulation is a decisive factor in the bidirectional plasticity of perceptual detection thresholds. However, surprisingly little is known about how distinct temporal parameters of sensory input differentially impact neuronal, circuit, and perceptual function. Here we demonstrate that brief repetitive visual stimulation is sufficient to induce long-term plasticity of visual responses, with the temporal frequency of the visual stimulus determining the location and generalization of visual response plasticity. Brief repetitive low frequency stimulation (LFS, 2 Hz) is sufficient to induce a visual response potentiation that is exclusively expressed in layer 4 in response to the familiar stimulus. In contrast, brief, repetitive high frequency stimulation (HFS, 20 Hz) suppresses the activity of fast-spiking interneurons and primes ongoing gamma oscillatory rhythms for visually-evoked phase reset. Accordingly, visual stimulation subsequent to HFS induces non-stimulus specific visual response plasticity that is expressed in all cortical layers. The generalized visual response enhancement induced by HFS is paralleled by an increase in visual acuity measured by improved performance in a visual detection task.
Functional Landscape of SARS-CoV-2 Cellular Restriction
Authors: Martin-Sancho Laura , Lewinski Mary K. , Pache Lars , Stoneham Charlotte A. , Yin Xin , Pratt Dexter , Churas Christopher , Rosenthal Sara B. , Liu Sophie , De Jesus Paul D. , O’Neill Alan M. , Gounder Anshu P. , Nguyen Courtney , Pu Yuan , Oom Aaron L. , Miorin Lisa , Rodriguez-Frandsen Ariel , Urbanowski Matthew , Shaw Megan L. , Chang Max W. , Benner Christopher , Frieman Matthew B. , García-Sastre Adolfo , Ideker Trey , Hultquist Judd F. , Guatelli John , Chanda Sumit K
Published: October 2020

A deficient interferon response to SARS-CoV-2 infection has been implicated as a determinant of severe COVID-19. To identify the molecular effectors that govern interferon control of SARS-CoV-2 infection, we conducted a large-scale gain-of-function analysis that evaluated the impact of human interferon stimulated genes (ISGs) on viral replication. A limited subset of ISGs were found to control viral infection, including endosomal factors that inhibited viral entry, nucleic acid binding proteins that suppressed viral RNA synthesis, and a highly enriched cluster of ER and Golgi-resident ISGs that inhibited viral translation and egress. These included the type II integral membrane protein BST2/tetherin, which was found to impede viral release, and is targeted for immune evasion by SARS-CoV-2 Orf7a protein. Overall, these data define the molecular basis of early innate immune control of viral infection, which will facilitate the understanding of host determinants that impact disease severity and offer potential therapeutic strategies for COVID-19.
Architecture of the Tuberous Sclerosis Protein Complex
Authors: Ramlaul Kailash , Fu Wencheng , Li Hua , de Martin Garrido Natàlia , He Lin , Cui Wei , Aylett Christopher H S , Wu Geng
Published: October 2020

The Tuberous Sclerosis Complex (TSC) protein complex (TSCC), comprising TSC1, TSC2, and TBC1D7, is widely recognised as a key integration hub for cell growth and intracellular stress signals upstream of the mammalian target of rapamycin complex 1 (mTORC1). The TSCC negatively regulates mTORC1 by acting as a GTPase-activating protein (GAP) towards the small GTPase Rheb. Both human TSC1 and TSC2 are important tumour suppressors, and mutations in them underlie the disease tuberous sclerosis.

We used single-particle cryo-EM to reveal the organisation and architecture of the complete human TSCC. We show that TSCC forms an elongated scorpion-like structure, consisting of a central “body”, with a “pincer” and a “tail” at the respective ends. The “body” is composed of a flexible TSC2 HEAT repeat dimer, along the inner surface of which runs the TSC1 coiled-coil backbone, breaking the symmetry of the dimer. Each end of the body is structurally distinct, representing the N- and C-termini of TSC1; a “pincer” is formed by the highly flexible N-terminal TSC1 core domains and a barbed “tail” makes up the TSC1 coiled-coil-TBC1D7 junction. The TSC2 GAP domain is found abutting the centre of the body on each side of the dimerisation interface, poised to bind a pair of Rheb molecules at a similar separation to the pair in activated mTORC1.

Our architectural dissection reveals the mode of association and topology of the complex, casts light on the recruitment of Rheb to the TSCC, and also hints at functional higher order oligomerisation, which has previously been predicted to be important for Rheb-signalling suppression.
Propagation of Viral Bioaerosols Indoors
Authors: Kudryashova Olga B. , Muravlev Evgeny V. , Antonnikova Alexandra A.
Published: October 2020

Here we look into the spread of aerosols indoors that may potentially carry viruses. Many viruses, including the novel Covid-19, are known to spread via airborne and air-dust pathways. From the literature data and our own research on the propagation of fine aerosols, we simulate herein the carryover of viral aerosols in indoor air. We demonstrate that a great deal of fine droplets released from an infected person’s coughing, sneezing or talking propagate very fast and to large distances indoors, as well as bend around obstacles, lift up and down over staircases, and so on. This study suggests equations to evaluate the concentration of those droplets, depending on time and distance from the source of infection. Estimates are given for the safe distance to the source of infection, and available methods for neutralizing viral aerosols indoors are considered.
Widening the gap: greater racial and ethnic disparities in COVID-19 burden after accounting for missing race/ethnicity data
Authors: Labgold Katie , Hamid Sarah , Shah Sarita , Gandhi Neel R. , Chamberlain Allison , Khan Fazle , Khan Shamimul , Smith Sasha , Williams Steve , Lash Timothy L. , Collin Lindsay J.
Published: October 2020

Black, Hispanic, and Indigenous persons in the United States have an increased risk of SARS-CoV-2 infection and death from COVID-19, due to persistent social inequities. The magnitude of the disparity is unclear, however, because race/ethnicity information is often missing in surveillance data. In this study, we quantified the burden of SARS-CoV-2 infection, hospitalization, and case fatality rates in an urban county by racial/ethnic group using combined race/ethnicity imputation and quantitative bias-adjustment for misclassification. After bias-adjustment, the magnitude of the absolute racial/ethnic disparity, measured as the difference in infection rates between classified Black and Hispanic persons compared to classified White persons, increased 1.3-fold and 1.6-fold respectively. These results highlight that complete case analyses may underestimate absolute disparities in infection rates. Collecting race/ethnicity information at time of testing is optimal. However, when data are missing, combined imputation and bias-adjustment improves estimates of the racial/ethnic disparities in the COVID-19 burden.
Viral genomes reveal patterns of the SARS-CoV-2 outbreak in Washington State
Authors: Müller Nicola F. , Wagner Cassia , Frazar Chris D. , Roychoudhury Pavitra , Lee Jover , Moncla Louise H. , Pelle Benjamin , Richardson Matthew , Ryke Erica , Xie Hong , Shrestha Lasata , Addetia Amin , Rachleff Victoria M. , Lieberman Nicole A. P. , Huang Meei-Li , Gautom Romesh , Melly Geoff , Hiatt Brian , Dykema Philip , Adler Amanda , Brandstetter Elisabeth , Han Peter D. , Fay Kairsten , Ilcisin Misja , Lacombe Kirsten , Sibley Thomas R. , Truong Melissa , Wolf Caitlin R. , Boeckh Michael , Englund Janet A. , Famulare Michael , Lutz Barry R. , Rieder Mark J. , Thompson Matthew , Duchin Jeffrey S. , Starita Lea M. , Chu Helen Y. , Shendure Jay , Jerome Keith R. , Lindquist Scott , Greninger Alexander L. , Nickerson Deborah A. , Bedford Trevor
Published: October 2020

The rapid spread of SARS-CoV-2 has gravely impacted societies around the world. Outbreaks in different parts of the globe are shaped by repeated introductions of new lineages and subsequent local transmission of those lineages. Here, we sequenced 3940 SARS-CoV-2 viral genomes from Washington State to characterize how the spread of SARS-CoV-2 in Washington State (USA) was shaped by differences in timing of mitigation strategies across counties, as well as by repeated introductions of viral lineages into the state. Additionally, we show that the increase in frequency of a potentially more transmissible viral variant (614G) over time can potentially be explained by regional mobility differences and multiple introductions of 614G, but not the other variant (614D) into the state. At an individual level, we see evidence of higher viral loads in patients infected with the 614G variant. However, using clinical records data, we do not find any evidence that the 614G variant impacts clinical severity or patient outcomes. Overall, this suggests that at least to date, the behavior of individuals has been more important in shaping the course of the pandemic than changes in the virus.

One Sentence Summary

Local outbreak dynamics of SARS-CoV-2 in Washington State (USA) were driven by regionally different mitigation measures and repeated introductions of unique viral variants with different viral loads.
Elevated glycoprotein acetyl levels in adolescence and early adulthood predict adverse cardiometabolic profiles and risk of metabolic syndrome in up to 10 year follow-up
Authors: Chiesa Scott T. , Charakida Marietta , Georgiopoulos Georgios , Roberts Justin D. , Stafford Simon J. , Park Chloe , Mykkänen Juha , Kähönen Mika , Lehtimäki Terho , Ala-Korpela Mika , Raitakari Olli , Hughes Alun D. , Sattar Naveed , Timpson Nicholas J. , Deanfield John E.
Published: October 2020

Objective

Low-grade inflammation in the young may contribute to the early development of adverse cardiometabolic risk profiles. We assessed whether measures of glycoprotein acetylation (GlycA) were better able to detect the development of these changes compared to the more commonly used biomarker high-sensitivity C-reactive protein (CRP), and investigated whether these relationships differed in an adolescent compared to young adult cohort.

Research Design and Methods

A total of 3306 adolescents (Avon Longitudinal Study of Parents and Children - ALSPAC; mean age 15.4±0.3; n=1750) and young adults (Cardiovascular Risk in Young Finns Study - YFS; mean age 32.1±5.0; n=1556) were included. Inflammatory biomarkers (GlycA/CRP), body composition (BMI / waist circumference) and cardiometabolic risk factors (blood pressure, triglycerides, HDL-c, glucose, insulin, and homeostasis model of insulin resistance [HOMA_IR]), were measured at baseline and again in 9-10 year follow-up. Metabolic Syndrome (MetS) was defined using adolescent-specific National Cholesterol Education Programme (NCEP) guidelines in ALSPAC and standard NCEP guidelines in YFS.

Results

GlycA levels showed greater within-subject correlation over the 9-10 year duration of follow-up in both cohorts when compared to CRP, particularly in the younger adolescent group. In adjusted models, only GlycA was found to increase in line with cardiometabolic risk factor burden at baseline, and to predict adverse changes in several cardiometabolic risk factors in follow-up. In both cohorts, GlycA predicted future risk of MetS (OR [95%CI] for Q4 vs. Q1 = 1.95 [1.08,3.53] and 2.74 [1.30,5.73] for ALSPAC and YFS, respectively), whereas CRP showed a neutral or even negative relationship in fully-adjusted models (OR [95%CI] = 0.50 [0.29,0.86] and 0.93 [0.53,1.64]).

Conclusions

Chronic inflammation is associated with adverse cardiometabolic risk profiles from as early as adolescence and predicts risk of future cardiometabolic risk and MetS in up to 10 year follow-up. GlycA may be a more sensitive inflammatory biomarker to CRP for detecting early cardiometabolic and cardiovascular risk in the young.