bluuebunny/crossref_metadata_2025 huggingface dataset:
The Anna Karenina model of β cell maturation in development and their dedifferentiation in type 1 and type 2 diabetes
Authors: Nimkulrat Sutichot D. , Ni Zijian , Brown Jared , Kendziorski Christina , Blum Barak
Published: February 2021

Loss of mature β cell function and identity, or β cell dedifferentiation, is seen in all types of diabetes mellitus. Two competing models explain β cell dedifferentiation in diabetes. In the first model, β cells dedifferentiate in the reverse order of their developmental ontogeny. This model predicts that dedifferentiated β cells resemble β cell progenitors. In the second model, β cell dedifferentiation depends on the type of diabetogenic stress. This model, which we call the “Anna Karenina” model, predicts that in each type of diabetes, β cells dedifferentiate in their own way, depending on how their mature identity is disrupted by any particular diabetogenic stress. We directly tested the two models using a β cell-specific lineage-tracing system coupled with RNA-sequencing in mice. We constructed a multidimensional map of β cell transcriptional trajectories during the normal course of β cell postnatal development and during their dedifferentiation in models of both type 1 diabetes (NOD) and type 2 diabetes (BTBR-Lepob/ob). Using this unbiased approach, we show here that despite some similarities between immature and dedifferentiated β cells, β cells dedifferentiation in the two mouse models is not a reversal of developmental ontogeny and is different between different types of diabetes.
Perceptual restoration fails to recover unconscious processing for smooth eye movements after occipital stroke
Authors: Kwon Sunwoo , Fahrenthold Berkeley K. , Cavanaugh Matthew R. , Huxlin Krystel R. , Mitchell Jude F.
Published: February 2021

The visual pathways that guide actions do not necessarily mediate conscious perception. Patients with primary visual cortex (V1) damage lose conscious perception but often retain unconscious abilities (e.g. blindsight). Here, we asked if saccade accuracy and post-saccadic following responses (PFRs) that automatically track target motion upon saccade landing are retained when conscious perception is lost. We contrasted these behaviors in the blind and intact-fields of 11 chronic V1-stroke patients, and in 8 visually-intact controls. Saccade accuracy was relatively normal in all cases. Stroke patients also had normal PFR in their intact-fields, but no PFR in their blind-fields. Thus, V1 damage did not spare the unconscious visual processing necessary for automatic, post-saccadic smooth eye movements. Importantly, visual training that recovered motion perception in the blind-field did not restore the PFR, suggesting a clear dissociation between pathways mediating perceptual restoration and automatic actions in the V1-damaged visual system.
Ezh2 as an epigenetic checkpoint regulator during monocyte differentiation: a potential target to improve cardiac repair after myocardial infarction
Authors: Julie Rondeaux , Déborah Groussard , Sylvanie Renet , Virginie Tardif , Anaïs Dumesnil , Alphonse Chu , Jean-Paul Henry , Zina Badji , Claire Vézier , Delphine Béziau , Dominique Guerrot , Marjorie Brand , Vincent Richard , Eric Durand , Ebba Brakenhielm , Sylvain Fraineau
Published: February 2021

Epigenetic regulation of histone H3K27 methylation has recently emerged as a key step during M2-like macrophage polarization, essential for cardiac repair after Myocardial Infarction (MI). We demonstrate for the first-time that EZH2, responsible for H3K27 methylation, has an ectopic cytoplasmic localization during monocyte differentiation in M2 macrophages. Moreover, we show that pharmacological EZH2 inhibition, with GSK-343, enhances bivalent genes, expression to promote human monocyte repair functions. GSK-343 treatment accelerated cardiac inflammatory resolution preventing infarct expansion and subsequent cardiac dysfunction after MIin vivo. In conclusion, our study reveals that epigenetic modulation of cardiac-infiltrating immune cells may hold promise to limit adverse cardiac remodeling after MI.
The combined influence of viscoelasticity and adhesive cues on fibroblast spreading and focal adhesion formation
Authors: Hui Erica , Moretti Leandro , Barker Thomas H. , Caliari Steven R.
Published: February 2021

Tissue fibrosis is characterized by progressive extracellular matrix (ECM) stiffening and loss of viscoelasticity that ultimately results in reduced organ functionality. Cells bind to the ECM through integrins, where av integrin engagement in particular has been correlated with fibroblast activation into contractile myofibroblasts that drive fibrosis progression. There is a significant unmet need forin vitrohydrogel systems that deconstruct the complexity of native tissues to better understand the individual and combined effects of stiffness, viscoelasticity, and integrin engagement on fibroblast behavior. Here, we developed hyaluronic acid hydrogels with independently tunable cell-instructive properties (stiffness, viscoelasticity, ligand presentation) to address this challenge. Hydrogels with mechanics matching normal or fibrotic lung tissue were synthesized using a combination of covalent crosslinks and supramolecular interactions to tune viscoelasticity. Cell adhesion was mediated through incorporation of either RGD peptide or engineered fibronectin fragments promoting preferential integrin engagement via αvβ3 or α5β1. We showed that preferential αvβ3 engagement enabled human lung fibroblasts to assume a myofibroblast-like phenotype on fibrosis-mimicking stiff elastic hydrogels with increased spreading, actin stress fiber organization, and focal adhesion maturation as indicated by paxillin organization. In contrast, preferential α5β1 binding suppressed these metrics. Viscoelasticity, mimicking the mechanics of healthy tissue, largely curtailed fibroblast spreading and focal adhesion organization independent of adhesive ligand type, highlighting its role in preventing fibroblast activation. Together these results provide new insights into how mechanical and adhesive cues collectively guide disease-relevant cell behaviors.
Phosphatidylinositol phosphate binding domains exhibit complex dissociation properties at the inner leaflet of plasma membrane sheets
Authors: Sponholtz Madeline R. , Senning Eric N.
Published: February 2021

The pleckstrin homology (PH) domain is a lipid targeting motif that binds with high specificity to phosphatidylinositol phosphate (PIP) lipids. Using TIRF microscopy, we followed the dissociation of GFP-tagged PH domains from the plasma membranes of rapidly unroofed cells and found that AKT-PH and PLCδ1-PH dissociation kinetics can be distinguished by their effective koffvalues determined from fitting fluorescence traces to a single exponential equation. Our measurements for the koffof AKT-PH-GFP and PLCδ1-PH-GFP were significantly different (p < 0.05) at 0.39 ± 0.05 s−1and 0.56 ± 0.17 s−1, respectively. Furthermore, we identified substantial rebinding events in our measurements of PLCδ1-PH-GFP dissociation kinetics. By applying inositol triphosphate (IP3) to samples during the unroofing process, we measured a much faster koffof 1.54 ± 0.42 s−1for PLCδ1-PH-GFP, indicating that rebinding events are significantly depressed through competitive action by IP3for the same PH domain binding site as phosphatidylinositol (4,5)-bisphosphate (PIP2). We discuss the complex character of our PLCδ1-PH-GFP fluorescence decays in the context of membrane receptor and ligand theory to address the question of how free PIP2levels modulate the interaction between membrane associated proteins and the plasma membrane.
Nuclear HMGB1 protects from non-alcoholic fatty liver diseases through negative regulation of liver X receptor
Authors: Personnaz Jean , Piccolo Enzo , Dortignac Alizée , Iacovoni Jason S. , Mariette Jérôme , Polizzi Arnaud , Batut Aurélie , Deleruyelle Simon , Paccoud Romain , Moreau Elsa , Martins Frédéric , Clouaire Thomas , Benhamed Fadila , Montagner Alexandra , Wahli Walter A. , Schwabe Robert F. , Yart Armelle , Castan-Laurell Isabelle , Postic Catherine , Moro Cédric , Legube Gaelle , Lee Chih-Hao , Guillou Hervé , Valet Philippe , Dray Cédric , Pradère Jean-Philippe
Published: February 2021

Dysregulations of lipid metabolism in the liver may trigger steatosis progression leading to potentially severe clinical consequences such as non-alcoholic fatty liver diseases (NAFLD). Molecular mechanisms underlying liver lipogenesis are very complex and fine-tuned by chromatin dynamics and the activity of multiple key transcription factors. Here, we demonstrate that the nuclear factor HMGB1 acts as a strong repressor of liver lipogenesis during metabolic stress in NAFLD. Mice with liver-specificHmgb1-deficiency display exacerbated liver steatosis and hepatic insulin resistance when subjected to a high-fat diet or after fasting/refeeding. Global transcriptome and functional analysis revealed that the deletion ofHmgb1gene enhances LXRα activity resulting in increased lipogenesis. HMGB1 repression is not mediated through nucleosome landscape re-organization but rather via a preferential DNA occupation in region carrying genes regulated by LXRα. Together these findings suggest that hepatocellular HMGB1 protects from liver steatosis development. HMGB1 may constitute a new attractive option to therapeutically target LXRα axis during NAFLD.
Timing of selective basal ganglia white matter loss in Huntington’s disease
Authors: Zeun Paul , McColgan Peter , Dhollander Thijs , Gregory Sarah , Johnson Eileanoir B , Papoutsi Marina , Nair Akshay , Scahill Rachael I , Rees Geraint , Tabrizi Sarah J ,   the TrackOn-HD and HD-YAS Investigators
Published: February 2021

Objectives

To investigate the timeframe prior to symptom onset when cortico-basal ganglia white matter (WM) loss begins in premanifest Huntington’s disease (preHD), and which striatal and thalamic sub-region WM tracts are most vulnerable.

Methods

We performed fixel-based analysis, which allows resolution of crossing WM fibres at the voxel level, on diffusion tractography derived WM tracts of striatal and thalamic sub-regions in two independent cohorts; TrackON-HD, which included 72 preHD (approx. 11 years before disease onset) and 85 controls imaged at three time points over two years; and the HD young adult study (HD-YAS), which included 54 preHD (approx. 25 years before disease onset) and 53 controls, imaged at one time point. Group differences in fibre density and cross section (FDC) were investigated.

Results

We found no significant group differences in cortico-basal ganglia sub-region FDC in preHD gene carriers 25 years before onset. In gene carriers 11 years before onset, there were reductions in striatal (limbic and caudal motor) and thalamic (premotor, motor and sensory) FDC at baseline, with no significant change over 2 years. Caudal motor-striatal, pre-motor-thalamic, and primary motor-thalamic FDC at baseline, showed significant correlations with the Unified Huntington’s disease rating scale (UHDRS) total motor score (TMS). Limbic cortico-striatal FDC and apathy were also significantly correlated.

Conclusions

Our findings suggest that the initiation of disease modifying therapies 25 years before onset could protect these important brain networks from undergoing neurodegeneration and highlight selectively vulnerable sub-regions of the striatum and thalamus that may be important targets for future therapies.
Host preferences of coexisting Perkinsea parasitoids during coastal dinoflagellate blooms
Authors: Reñé Albert , Timoneda Natàlia , Sampedro Nagore , Alacid Elisabet , Gallisai Rachele , Gordi Jordina , Fernández-Valero Alan Denis , Pernice Massimo Ciro , Flo Eva , Garcés Esther
Published: February 2021

Parasites in aquatic systems are highly diverse and ubiquitous. In marine environments, parasite-host interactions contribute substantially to shaping microbial communities, but their nature and complexity remain poorly understood. In this study, we examined the relationship between Perkinsea parasitoids and bloom-forming dinoflagellate species. Our aim was to determine whether parasite-host species interactions are specific and whether the diversity and distribution of parasitoids are shaped by their dinoflagellate hosts. Several locations along the Catalan coast (NW Mediterranean Sea) were sampled during the blooms of five dinoflagellate species and the diversity of Perkinsea was determined by combining cultivation-based methods with metabarcoding of the V4 region of 18S rDNA. Most known species of Parviluciferaceae, and others not yet described, were detected, some of them coexisting in the same coastal location, and with a wide distribution. The specific parasite-host interactions determined for each of the studied blooms demonstrated the host preferences exhibited by parasitoids in nature. The dominance of a species within the parasitoid community is driven by the presence and abundances of its preferred host(s).The absence of parasitoid species, often associated with a low abundance of their preferred hosts, suggested that high infection rates are reached only under conditions that favour parasitoid propagation, especially dinoflagellate blooms.
A candidate neuroimaging biomarker for detection of neurotransmission-related functional alterations and prediction of pharmacological analgesic response in chronic pain
Authors: Martins Daniel , Veronese Mattia , Turkheimer Federico , Howard Matthew A. , Williams Steven CR , Dipasquale Ottavia
Published: February 2021

Background

Chronic pain is a world-wide clinical challenge. Response to analgesic treatment is limited and difficult to predict. Functional MRI (fMRI) has been suggested as a potential solution. However, while most analgesics target specific neurotransmission pathways, fMRI-based biomarkers are not specific for any neurotransmitter system, limiting our understanding of how they might contribute to predict treatment response.

Methods

Here, we sought to bridge this gap by applying Receptor-Enriched Analysis of Functional Connectivity by Targets (REACT) to investigate whether neurotransmission-enriched functional connectivity (FC) mapping can provide insights into the brain mechanisms underlying chronic pain and inter-individual differences in analgesic response after a placebo or duloxetine. Chronic knee osteoarthritis (OA) pain patients (n=56) underwent pre-treatment brain scans in two clinical trials. Study 1 (n=17) was a 2-week single-blinded placebo pill trial. Study 2 (n=39) was a 3-month double-blinded randomized trial comparing placebo to duloxetine, a dual serotonin-noradrenaline reuptake inhibitor.

Results

Across two independent studies, we found that chronic pain OA patients present FC alterations in the FC related to the serotonin (SERT) and noradrenaline (NET) transporters, when compared to age-matched healthy controls. Placebo responders presented with higher pre-treatment dopamine transporter (DAT)-enriched FC than non-responders. Duloxetine responders presented with higher pre-treatment SERT and NET-enriched FC than non-responders. Pre-treatment SERT and NET-enriched FC achieved predictive positive values of duloxetine response up to 85.71%.

Conclusion

Neurotransmission-enriched FC mapping might hold promise as a new mechanistic-informed biomarker for functional brain alterations and prediction of response to pharmacological analgesia in chronic pain.
Hot days are associated with short-term adrenocortical responses in a Southern African arid-zone passerine bird
Authors: Moagi Lesedi L. , Bourne Amanda R. , Cunningham Susan J. , Jansen Ray , Ngcamphalala Celiwe A. , Ridley Amanda R. , McKechnie Andrew E.
Published: February 2021

Non-invasive methods for investigating the biological effects of environmental variables are invaluable for understanding potential impacts of climate change on behavioural and physiological stress responses of free-ranging animals. Foraging efficiency, body mass maintenance and breeding success are compromised in Southern pied babblers Turdoides bicolor exposed to air temperatures between ~35°C and ~40°C. We tested the hypothesis that these very hot days are acute stressors for free-ranging babblers by quantifying the relationship between daily maximum air temperature (Tmax) and faecal glucocorticoid metabolite (fGCM) levels. We collected naturally-excreted droppings from free-ranging pied babblers and analysed fGCM levels. Levels of fGCMs in droppings collected after 3pm were independent of same-day Tmax < 38 °C and averaged 140.25 ng g−1 Dry Weight ± 56.92 ng g−1 DW (mean ± SD) over this range. Above an inflection Tmax = 38 °C, however, fGCM levels increased linearly with same-day Tmax and averaged 190.79 ng g−1 DW ± 70.13 ng g−1 DW. There was no relationship between Tmax on the previous day and fGCM levels in droppings collected the following morning. Group size, breeding stage, sex and rank did not predict variation in fGCM levels. These results suggest that very high Tmax may be linked to acute, but not chronic, heat stress responses. The fGCM levels we measured are likely to represent a biologically meaningful response to an environmental stressor (high Tmax), suggesting a physiological mechanism underlying observed changes in behaviour and reproductive success at high temperatures in this species.
Transcriptome analysis and connectivity mapping ofCissampelos pareiraL. provides molecular links of ESR1 modulation to viral inhibition
Authors: Haider Madiha , Dholakia Dhwani , Panwar Aleksha , Garg Parth , Gheware Atish , Singh Dayanidhi , Singhal Khushboo , Burse Shaunak A , Kumari Surekha , Anmol  , Ray Arjun , Medigeshi Guruprasad R. , Sharma Upendra , Prasher Bhavana , Mukerji Mitali
Published: February 2021

Bioactive fractions or compounds obtained from medicinal plants have been used for the treatment of multiple diseases. This effect could be due to common pathways underlying these conditions that are targeted by such medicines. In this study, we explored the molecular basis of action of one such herbal formulationCissampelos pareira, used for the treatment of female hormone disorders and fever. Genome-wide expression studies on MCF7 cell lines treated with Cipa extract were carried out using Affymetrix arrays. Transcriptome analysis revealed a downregulation of signatures of estrogen response governed by estrogen receptor α (ERα). Molecular docking analysis identified 38 constituent molecules in Cipa that potentially bind (ΔG< -7.5) with ERα at the same site as estrogen. Cipa transcriptome signatures show high positive connectivity (https://clue.io/) scores with protein translation inhibitors such as emetine (score: 99.61) and knockdown signatures of genes linked to the antiviral response such as ribosomal protein RPL7 (score: 99.92), which is also an ERα coactivator. Cipa exhibits antiviral activity in dengue infected MCF7 cells that is decreased upon ESR1 (estrogen receptor 1) gene knockdown. This approach reveals a novel pathway involving ESR1-RPL7 axis that could be a potential target in dengue viral infection.
Systemic administration of Ivabradine, an HCN channel inhibitor, blocks spontaneous absence seizures
Authors: Iacone Yasmine , Morais Tatiana P. , David François , Delicata Francis , Sandle Joanna , Raffai Timea , Parri H. Rheinallt , Weisser Johan Juhl , Bundgaard Christoffer , Klewe Ib Vestergaard , Tamás Gábor , Skøtt Thomsen Morten , Crunelli Vincenzo , Lőrincz Magor L.
Published: February 2021

Objective

Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels are known to be involved in the generation of absence seizures (ASs), and there is evidence that cortical and thalamic HCN channel dysfunctions may have a pro-absence role. Many HCN channel blockers are available, but their role in ASs has been investigated only by localized brain injection or inin vitromodel systems due to their limited brain availability. Here, we investigated the effect on ASs of orally administered ivabradine (an HCN channel blocker approved for the treatment of heart failure in humans) following injection of the P-glycoprotein inhibitor elacridar, that is known to increase penetration into the brain of drug substrates for this efflux transporter. The action of ivabradine was also tested followingin vivomicroinjection in the cortical initiation network (CIN) of the somatosensory cortex and in the thalamic ventrobasal nucleus (VB) as well as on cortical and thalamocortical neurons in brain slices.

Methods

We used EEG recordings in freely moving Genetic Absence Epilepsy from Strasbourg Rats (GAERS) to assess the action of oral administration of ivabradine, with and without elacridar, on ASs. Ivabradine was also microinjected in the CIN and VB of GAERSin vivoand applied to Wistar CIN and GAERS VB slices while recording patch-clamped cortical layer 5/6 and thalamocortical neurons, respectively.

Results

Oral administration of ivabradine markedly and dose-dependently reduced ASs. Ivabradine injection in CIN abolished ASs and elicited small-amplitude 4-7 Hz waves (without spikes), whereas in the VB it was less potent. Moreover, ivabradine applied to GAERS VB and Wistar CIN slices selectively decreased HCN-channel-dependent properties of cortical layer 5/6 pyramidal and thalamocortical neurons, respectively.

Significance

These results provide the first demonstration of the anti-absence action of a systemically administered HCN channel blocker, indicating the potential of this class of drugs as a novel therapeutic avenue for ASs.
Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave
Authors: Hohsfield Lindsay A. , Najafi Allison R. , Ghorbanian Yasamine , Soni Neelakshi , Crapser Joshua D. , Figueroa Velez Dario X. , Jiang Shan , Royer Sarah E. , Kim Sung Jin , Anderson Aileen J. , Gandhi Sunil P. , Mortazavi Ali , Inlay Matthew A. , Green Kim N.
Published: February 2021

Microglia, the brain’s resident myeloid cells, play central roles in brain defense, homeostasis, and disease. Using sustained colony-stimulating factor 1 receptor inhibition, we report an unprecedented level of microglial depletion and establish a model system that achieves an empty microglial niche in the adult brain. We identify a myeloid cell that migrates from an important neurogenic niche, the subventricular zone, and associated white matter areas. These cells exhibit tremendous chemotaxis potential, migrating radially and tangentially in a dynamic wave and filling the brain in a distinct pattern, to fully replace the microglial-depleted brain. These repopulating cells are enriched in disease-associated microglia genes and exhibit distinct phenotypic and functional profiles to endogenous microglia. Our findings shed light on the overlapping and distinct functional complexity and diversity of myeloid cells of the CNS and provide new insight into myeloid cell dynamics in an empty microglial niche without contributions from bone marrow-derived cells.
Multistage classification identifies altered cortical phase- and amplitude-coupling in Multiple Sclerosis
Authors: Siems Marcus , Tünnerhoff Johannes , Ziemann Ulf , Siegel Markus
Published: February 2021

Distinguishing groups of subjects or experimental conditions in a high-dimensional feature space is a common goal in modern neuroimaging studies. Successful classification depends on the selection of relevant features as not every neuronal signal component or parameter is informative about the research question at hand. Here, we developed a novel unsupervised multistage analysis approach that combines dimensionality reduction, bootstrap aggregating and multivariate classification to select relevant neuronal features. We tested the approach by identifying changes of brain-wide electrophysiological coupling in Multiple Sclerosis. Multiple Sclerosis is a demyelinating disease of the central nervous system that can result in cognitive decline and physical disability. However, related changes in large-scale brain interactions remain poorly understood and corresponding non-invasive biomarkers are sparse. We thus compared brain-wide phase- and amplitude-coupling of frequency specific neuronal activity in relapsing-remitting Multiple Sclerosis patients (n = 17) and healthy controls (n = 17) using magnetoencephalography. Our analysis approach allowed us to identify systematic and non-redundant changes of both phase- and amplitude-coupling in the diseased brain. Changes included both, increased and decreased neuronal coupling in wide-spread, bilateral neuronal networks across a broad range of frequencies. These changes allowed to successfully classify patients and controls with an accuracy of 84%. Furthermore, classification confidence predicted behavioral scores of disease severity. In sum, our results unravel systematic changes of large-scale phase- and amplitude coupling in Multiple Sclerosis. Furthermore, our results establish a new analysis approach to efficiently contrast high-dimensional neuroimaging data between experimental groups or conditions.

Highlights

A novel multistage approach to analyze high-dimensional neuronal coupling data.

Application to MEG recordings in relapsing-remitting Multiple Sclerosis patients.

Identification of altered phase- and amplitude-coupling in Multiple Sclerosis.

Classification of patients and controls with 84% accuracy.

Classification confidence predicts behavioral scores of disease severity.
Escherichia colirobustly expresses ATP synthase at growth rate maximizing concentrations
Authors: Rabbers Iraes , Bruggeman Frank J
Published: February 2021

Improved protein expression is an important evolutionary adaptation of bacteria. A key question is whether evolution has led to optimal protein expression that maximizes immediate growth rate (short-term fitness) across conditions. Alternatively, fitter genetic variants could display suboptimal short-term fitness, because they cannot do better or because they strive for long-term fitness maximization by, for instance, anticipating future conditions. To answer this question, we focus on the ATP-producing enzyme F1F0H+-ATPase, which is an abundant enzyme and ubiquitously expressed across conditions. We tested the optimality of H+-ATPase expression inEscherichia coliacross 27 different nutrient conditions. In all tested conditions, wild-typeE. coliexpresses its H+- ATPase remarkably close to optimal concentrations that maximize immediate growth rate. This work indicates that bacteria can achieve robust optimal protein expression for immediate growth- rate.
Non-destructive extraction of DNA from preserved tissues in medical collections
Authors: Rayo Enrique , Ferrari Giada , Neukamm Judith , Akgül Gülfirde , Breidenstein Abagail M. , Cooke Martyn , Phillips Carina , Bouwman Abigail S. , Rühli Frank J. , Schuenemann Verena J.
Published: February 2021

Museum and medically fixed material are valuable samples for the study of historical soft tissues and represent a pathogen-specific source for retrospective molecular investigations. However, current methods for the molecular analysis are inherently destructive, posing a dilemma between performing a study with the available technology thus damaging the sample - or conserving the material for future investigations. Here we present an unprecedented non-destructive alternative that facilitates the genetic analysis of fixed wet tissues while avoiding tissue damage. We extracted DNA from the fixed tissues as well as their embedding fixative solution, to quantify the DNA that was transferred to the liquid component. Our results prove that human ancient DNA can be retrieved from the fixative material of stored medical specimens and provide new options for the sampling of valuable curated collections.

Method summary

We compared the metagenomic content of historical tissues and their embedding liquid to retrieve DNA from the host and specified pathogens based on the diagnosis of the sample. We applied ancient DNA research techniques, including in-solution hybridization capture with DNA baits for human mitochondrial DNA,Mycobacterium tuberculosis, Mycobacterium leprae, andTreponema pallidum.
Structural basis for the specificity of PPM1H phosphatase for Rab GTPases
Authors: Waschbüsch Dieter , Berndsen Kerryn , Lis Pawel , Knebel Axel , Lam Yuko P. Y. , Alessi Dario R. , Khan Amir R.
Published: February 2021

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

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

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

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

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

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

Neural crest cells (NCCs) within the mandibular and maxillary portions of the first pharyngeal arch are initially competent to respond to signals from either region. However, mechanisms that are only partially understood establish developmental tissue boundaries to ensure spatially correct patterning. In the Hinge and Caps model of facial development, signals from both ventral prominences, referred to as the caps, pattern the adjacent tissues while the intervening region, known as the hinge, maintains separation of the mandibular and maxillary domains. One cap signal is GATA3, a member of the GATA family of zinc-finger transcription factors with a distinct expression pattern in the ventral-most part of the mandibular and maxillary portions of the first arch. Here we show that disruption ofGata3in mouse embryos leads to hemifacial microsomia, facial bone hypoplasia and syngnathia (bony fusion of the upper and lower jaws). These changes are preceded by gene expression changes in post-migratory NCCs around the maxillomandibular junction (the hinge). GATA3 is thus a crucial component in establishing the network of factors that functionally separate the upper and lower jaws during development.

Summary Statement

Loss ofGata3leads to BMP-mediated disruption ofFgf8expression at the maxillomandibular junction during development, resulting in later fusion of the upper and lower jaws.
Eukaryotic translation initiation factor 2A protects pancreatic beta cells during endoplasmic reticulum stress while rescuing translation inhibition
Authors: Panzhinskiy Evgeniy , Skovsø Søs , Cen Haoning Howard , Chu Kwan Yi , MacDonald Kate , Soukhatcheva Galina , Dionne Derek A. , Hallmaier-Wacker Luisa K. , Wildi Jennifer S. , Marcil Stephanie , Noursadeghi Nilou , Taghizadeh Farnaz , Verchere C. Bruce , Jan Eric , Johnson James D.
Published: February 2021

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

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

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

Mycobacteria spatially organize their plasma membrane, and many enzymes involved in envelope biosynthesis associate with a membrane compartment termed the intracellular membrane domain (IMD). The IMD is concentrated in the polar regions of growing cells and becomes less polarized under non-growing conditions. Because mycobacteria elongate from the poles, the observed polar localization of the IMD during growth likely supports the localized envelope biosynthesis. While we have identified more than 300 IMD-associated proteins by proteomic analyses, only a handful of these have been verified by other experimental methods. Furthermore, we speculate that some IMD-associated proteins may have escaped proteomic identification and remain to be identified. Here, we visually screened an arrayed library of 523Mycobacterium smegmatisstrains each expressing a Dendra2-FLAG-tagged recombinant protein. We identified 29 fusion proteins that showed fluorescence patterns similar to those of IMD proteins and, consistent with this co-localization, we had previously identified 20 of these using a proteomics approach. Of the nine remaining IMD candidate proteins, three were confirmed to be associated with the IMD while some others appear to be lipid droplet-associated. Taken together, our newly devised strategy is effective in verifying the IMD association of proteins found by proteomic analyses, while facilitating the discovery of additional IMD-associated proteins.

Importance

The intracellular membrane domain (IMD) is a membrane subcompartment found inMycobacterium smegmatiscells. Proteomic analysis of purified IMD identified more than 300 proteins, including enzymes involved in cell envelope biosynthesis, that likely contribute to the function of the IMD. How can we find more IMD-associated proteins that escaped proteomic detection? Here, as an alternative approach, fluorescence microscope images of 523 proteins were screened to identify IMD-associated proteins. We confirmed the IMD association of previously identified proteins and discovered three additional proteins associated with the IMD. Together, subcellular fractionation, proteomics, and fluorescence microscopy form a robust combination to more rigorously define IMD proteins, which will aid future investigations to decipher the synthesis, maintenance and functions of this membrane domain.