bluuebunny/crossref_metadata_2025 huggingface dataset:
Accelerated Bone Healing in Calvarial and Femoral Defects with Injectable Microcarriers that Mimic the Osteogenic Niche
Authors: Haase Candice , Jaligama Sravani , Mondragon Eli , Pan Simin , McNeill Eoin P. , Co Cynthia , Tahan Daniel , Clough Bret H. , Sears Nick , Dominic Abhishai , Kameoka Jun , Gregory Carl A. , Kaunas Roland
Published: November 2021

Osteo-enhanced human mesenchymal stem cells (OEhMSCs) secrete an osteogenic cell matrix (OCM) that mimics the composition of anabolic bone tissue and strongly enhances OEhMSC retention and subsequent bone repair in vivo. Here we demonstrate a system for rapid production of gelatin methacrylate microcarriers coated with decellularized OCM (OCM-GelMA) to serve as an injectable bone graft material with high osteogenic potential comparable to a clinically utilized gold standard, bone morphogenic protein 2 (BMP-2). OEhMSCs seeded onto OCM-GelMA secreted high levels of osteogenic and angiogenic cytokines and expressed higher levels of BMP-2 relative to OEhMSCs on bare GelMA microcarriers. OEhMSCs co-administered with OCM-GelMA microcarriers resulted in enhanced healing of murine critical-sized calvarial defects, which was comparable to that achieved with a BMP-2-laden gelatin sponge control. When tested in a murine femoral defect model, OCM-GelMA co-administered with OEhMSCs also induced profound bone growth within the defect. We submit that OCM-GelMA promotes OEhMSC paracrine release to accelerate bone repair, indicating their potential as a bone graft for use in minimally invasive surgery.
Bacterial chemotaxis to saccharides is governed by a trade-off between sensing and uptake
Authors: Norris Noele , Alcolombri Uria , Keegstra Johannes M. , Yawata Yutaka , Menolascina Filippo , Frazzoli Emilio , Levine Naomi M. , Fernandez Vicente I. , Stocker Roman
Published: November 2021

To swim up gradients of nutrients, E. coli senses nutrient concentrations within its periplasm. For small nutrient molecules, periplasmic concentrations typically match extracellular concentrations. However, this is not necessarily the case for saccharides, such as maltose, which is transported into the periplasm via a specific porin. Previous observations have shown that under various conditions E. coli limits maltoporin abundance so that, for extracellular micromolar concentrations of maltose, there are predicted to be only nanomolar concentrations of free maltose in the periplasm. Thus, in the micromolar regime, the total uptake of maltose from the external environment into the cytoplasm is limited not by the abundance of cytoplasmic transport proteins but by the abundance of maltoporins. Here we present results from experiments and modeling showing that this porin-limited transport enables E. coli to sense micromolar gradients of maltose despite having a high-affinity ABC transport system that is saturated at these micromolar levels. We used microfluidic assays to study chemotaxis of E. coli in various gradients of maltose and methyl-aspartate and leveraged our experimental observations to develop a mechanistic transport-and-sensing chemotaxis model. Incorporating this model into agent-based simulations, we discover a trade-off between uptake and sensing: although high-affinity transport enables higher uptake rates at low nutrient concentrations, it severely limits dynamic sensing range. We thus propose that E. coli may limit periplasmic uptake to increase its chemotactic sensitivity, enabling it to use maltose as an environmental cue.

Statement of Significance

Bacterial chemotaxis is among the best-studied systems in biology and is paradigmatic of the mechanisms used by cells to link sensory inputs with regulated responses, thus providing insight into the ecological basis of cellular physiology. Here we present a mechanistic chemotaxis model that describes how the regulation of the transport of a sugar into and out of the cell’s periplasm affects the cell’s motile response to that sugar. Based on observations from population-level chemotaxis assays, we uncover an ecologically relevant trade-off between sensing and uptake. The general finding of this work is that, while high-affinity transport allows for higher uptake rates, it can severely limit the cell’s dynamic sensing range.
Protamine lacking piscine spermatozoa are transcriptionally active
Authors: Castro-Arnau Júlia , Chauvigné François , Gómez-Garrido Jessica , Esteve-Codina Anna , Dabad Marc , Alioto Tyler , Finn Roderick Nigel , Cerdà Joan
Published: November 2021

Transcriptional quiescence of post-meiotic spermatozoa associated with protamine-mediated chromatin condensation is widely recognized in animals. How sperm acquire the extratesticular maturational competence to move and fertilize the egg is therefore thought to occur via non-transcriptional mechanisms. Here, using transcriptional profiling during spermatozoon differentiation in a fish that does not condense chromatin with protamines, we uncover spatially distinct roles of the GnRH receptor and PDGF signaling pathways between the somatic epithelia of the extratesticular ducts and the maturing spermatozoa. In vitro induction and inhibition experiments demonstrate that the endocrine signaling pathways are conserved in different lineages of fish and activate de novo transcription of spermatozoon genes required for the acquisition of full motility. These experiments further confirmed that mitochondrial translation is important for sperm maturation in anamniotes as in amniotes, but that transcriptional quiescence of post-meiotic spermatozoa is not a pan vertebrate phenomenon. On the contrary, the data show that the identified signal transduction pathways between the soma and the sperm upregulate effector genes essential for maturational competence and male fertility.
Biochemical analysis of deacetylase activity of rice sirtuin OsSRT1, a class IV member in plants
Authors: Mitra Nilabhra , Dey Sanghamitra
Published: November 2021

The role of plant sirtuins is slowly unwinding. There are only reports of H3K9Ac deacetylation by OsSRT1. This belongs to class IV sirtuin family with a longer C-terminus. Here C-terminus is required for ligand binding and catalysis. OsSRT1 can deacetylate the lys residues at the N terminal tail of both H3 and H4. It can also target the non-histone target, OsPARP1 playing a role in DNA damage repair pathway. Changes in the extent of different histone deacetylation by OsSRT1 is also related with different abiotic stress conditions. NAM and ADP-ribose has negative effect on OsSRT1 deacetylation.

Highlights

OsSRT1 is capable of deacetylating various lysine residues of histone H3 and H4 as well as OsPARP1.

The extra long C-terminus of OsSRT1 is required for its substrate binding and thus, its catalysis.

On plant’s exposure to H2O2 and Arsenic toxicity, there is a relationship between increased expression of OsSRT1 and increased deacetylation of H3 and H4.
Natural variation in root exudation of GABA and DIMBOA impacts the maize root endosphere and rhizosphere microbiomes
Authors: Wang Peng , Lopes Lucas Dantas , Lopez-Guerrero Martha G. , van Dijk Karin , Alvarez Sophie , Riethoven Jean-Jack , Schachtman Daniel P.
Published: November 2021

Root exudates are important for shaping root-associated microbiomes. However, studies on a wider range of metabolites in exudates are required for a comprehensive understanding about their influence on microbial communities. We identified maize inbred lines that differ in exudate concentrations of DIMBOA and GABA using a semi-hydroponic system. These lines were grown in the field to determine the changes in microbial diversity and gene expression due to varying concentrations of DIMBOA and GABA in exudates using 16S rRNA amplicon sequencing and metatranscriptomics. Results showed individual and interaction effects of DIMBOA and GABA on the rhizosphere and root endosphere β-diversity, most strongly at the V10 growth stage. The main bacterial families affected by both compounds were Ktedonobacteraceae and Xanthomonadaceae. Higher concentrations of DIMBOA in exudates affected the rhizosphere metatranscriptome, enriching for KEGG pathways associated with plant disease. This study validated the use of natural variation within plant species as a powerful approach for understanding the role of root exudates on microbiome selection. We also showed that a semi-hydroponic system can be used to identify maize genotypes that differ in GABA and DIMBOA exudate concentrations under field conditions. The impact of GABA exudation on root-associated microbiomes was shown for the first time.
Single-Cell Multiomics Defines Tolerogenic Extrathymic Aire-Expressing Populations with Unique Homology to Thymic Epithelium
Authors: Wang Jiaxi , Lareau Caleb A. , Bautista Jhoanne , Gupta Alexander , Sandor Katalin , Germino Joe , Yin Yajie , Arvedson Matt , Reeder Gabriella C. , Cramer Nathan T. , Xie Fang , Ntranos Vasilis , Satpathy Ansuman T. , Anderson Mark S. , Gardner James M.
Published: November 2021

The Autoimmune Regulator (Aire) gene, well defined for its role in medullary thymic epithelial cells (mTECs) and immune self-tolerance, is also expressed in extrathymic Aire-expressing cells (eTACs) in the secondary lymphoid organs. eTACs have been shown to be hematopoietic antigen presenting cells (APCs) and potent inducers of immune tolerance (1–3). However, the precise identity and function of these cells remain unclear. Here, we use high-dimensional single-cell multiomics and functional approaches to define eTACs at the transcriptional, genomic, and proteomic level. We find that eTACs consist of two similar cell types: CCR7+ Aire-expressing migratory dendritic cells (AmDCs) and a unique Aire-hi population co-expressing Aire and RAR-related orphan receptor gamma-t (RORγt). The latter, which have significant transcriptional and genomic homology to migratory dendritic cells (migDCs) and mTECs, we term Janus cells (JCs). All eTACs, and JCs in particular, have a highly accessible chromatin structure and high levels of broad gene expression, including tissue-specific antigens, as well as remarkable transcriptional and genomic homology to thymic medullary epithelium. As in the thymus, Aire expression in eTACs is also dependent on RANK-RANK-ligand interactions. Furthermore, lineage-tracing shows that JCs are not precursors to the majority of AmDCs. Finally, self-antigen expression by eTACs is sufficient to mediate negative selection of T cells escaping thymic selection and can prevent autoimmune diabetes in non-obese diabetic mice. This transcriptional, genomic, and functional symmetry between a hematopoietic Aire-expressing population in the periphery and an epithelial Aire-expressing population in the thymus suggests that a core biological program may influence self-tolerance and self-representation across the spectrum of immune development.
Detection of Selenium/Sulphur substitution in the heterologous expression of Thioredoxin isoform 1 (Trx1) fromSaccharomyces cerevisiae
Authors: de Almeida Filho Humberto Antunes , Lery Leticia Miranda Santos , Valente Ana Paula , Netto Luis Eduardo Soares , de Almeida Fabio Ceneviva Lacerda
Published: November 2021

Thioredoxins are ubiquous proteins with 2 cysteines at the active site. The isoform 1 of Thioredoxin fromSaccharomyces cerevisae(Trx1) has six sulphur aminoacids, two cysteines and four methionines. In this work we performed the replacement of cysteines by selenocysteines by growth of a transformed celular expression vectorE. coli BL21-DE3in selenocysteine containing culture medium. The Maldi-TOF spectra of Seleno/Sulphur substituted Trx1 revealed six component peaks with 46-48 Da range between them, that is the isotopic Seleno-Sulfur difference, showing the replacement of the Cysteines and Methionines to Selenocysteines and Selenomethionines. The Maldi-TOF spectra of the peptides derived from Trypsin digestion of the purified Thioredoxin (peptide mass fingerprint) show Selenocysteine and Selenomethionine containing peptides. Therefore we are demonstrating that cystein can be replaced by selenocystein and be metabolically converted to selenomethionine during Trx1 heterologous translation. Furthermore, the Maldi-TOF spectra are showing the presence of the most abundant isotopes of selenium inserted in the peptides containing cysteine and methionine, derived from the Trx1 digestion. The one dimensional77Se–1Hheteronuclear multiple quantum coherence NMR spectroscopy (1D-HMQC) for reduced Seleno substituted Trx1 (Se-Trx1), revealed three ressonance lines for1Hβ1from Selenocysteines 30 and 33, between 1.6 and 2,0 ppm. The bidimensional HMQC spectra (2D-HMQC) of the reduced Se-Trx1 show the77Se ressonance signal in 178 ppm, coupled with1Hβ1and1Hβ2lines between 2.1 and 1.8 ppm. The 1D-HMQC for oxidized Trx1 revealed the only one broad resonance in 2.6 ppm probably relative to the1Hβ1prótons. The 2D-HMQC spectrum of oxidized protein shows a higher chemical shift of selenocysteine77Se (832 ppm) if compared to reduced state (178 ppm). Together these data are showing that the protocol ofSe – Ssubstitution developed here is a efficient method to label the active site of Thioredoxin 1 with a broad band chemical shift atom77Se. Furthermore the large spectral window of the77SeNMR detected between reduced and oxidized states of the Thioredoxin 1 shows that this atom is an excellent probe for accessing oxidative states and probably the conformational dynamics of the active site of the Se-Trx1.
Large-scale discovery of recombinases for integrating DNA into the human genome
Authors: Durrant Matthew G. , Fanton Alison , Tycko Josh , Hinks Michaela , Chandrasekaran Sita S. , Perry Nicholas T. , Schaepe Julia , Du Peter P. , Lotfy Peter , Bassik Michael C. , Bintu Lacramioara , Bhatt Ami S. , Hsu Patrick D.
Published: November 2021

Recent microbial genome sequencing efforts have revealed a vast reservoir of mobile genetic elements containing integrases that could be useful genome engineering tools. Large serine recombinases (LSRs), such as Bxb1 and PhiC31, are bacteriophage-encoded integrases that can facilitate the insertion of phage DNA into bacterial genomes. However, only a few LSRs have been previously characterized and they have limited efficiency in human cells. Here, we developed a systematic computational discovery workflow that identifies thousands of new LSRs and their cognate DNA attachment sites by. We validate this approach via experimental characterization of LSRs in human cells, leading to three classes of LSRs distinguished from one another by their efficiency and specificity. We identify landing pad LSRs that efficiently integrate into synthetically installed attachment sites orthogonal to the human genome, human genome-targeting LSRs with computationally predictable pseudosites, and multi-targeting LSRs that can unidirectionally integrate cargos at with similar efficiency and superior specificity to commonly used transposases. LSRs from each category were functionally characterized in human cells, overall achieving up to 7-fold higher plasmid recombination than Bxb1 and genome insertion efficiencies of 40-70% with cargo sizes over 7 kb. Overall, we establish a paradigm for large-scale discovery of microbial recombinases and reconstruction of their target sites directly from microbial sequencing data. This strategy provides a rich resource of over 60 experimentally characterized LSRs that can function in human cells and thousands of additional candidates for large-payload genome editing without exposed DNA double-stranded breaks.
A Retrotranslocation Assay that Predicts Defective VCP/p97-Mediated Trafficking of a Retroviral Signal Peptide
Authors: Das Poulami , Xu Wendy Kaichun , Singh Gautam Amit Kumar , Lozano Mary M. , Dudley Jaquelin P.
Published: November 2021

Studies of viral replication have provided critical insights into host processes, including protein trafficking and turnover. Mouse mammary tumor virus (MMTV) is a betaretrovirus that encodes a functional 98-amino acid signal peptide (SP). MMTV SP is generated from both Rem and envelope precursor proteins by signal peptidase cleavage in the endoplasmic reticulum (ER) membrane. We previously showed that SP functions as an HIV-1 Rev-like protein that is dependent on the AAA ATPase VCP/p97 to subvert ER-associated degradation (ERAD). SP contains a nuclear/nucleolar localization sequence (NLS/NoLS) within the N-terminal 45 amino acids. To directly determine the SP regions needed for membrane extraction and trafficking, we developed a quantitative retrotranslocation assay with biotin acceptor peptide (BAP)-tagged SP proteins. Use of alanine substitution mutants of BAP-tagged MMTV SP in retrotranslocation assays revealed that mutation of amino acids 57 and 58 (M57-58) interfered with ER membrane extraction, whereas adjacent mutations did not. The M57-58 mutant also showed reduced interaction with VCP/p97 in co-immunoprecipitation experiments. Using transfection and reporter assays to measure activity of BAP-tagged proteins, both M57-58 and an adjacent mutant (M59-61) were functionally defective compared to wild-type SP. Confocal microscopy revealed defects in SP nuclear trafficking and abnormal localization of both M57-58 and M59-61. Furthermore, purified GST-tagged M57-58 and M59-61 demonstrated reduced ability to oligomerize compared to tagged wild-type SP. These experiments suggest that SP amino acids 57-58 are critical for VCP/p97 interaction and retrotranslocation, whereas residues 57-61 are critical for oligomerization and nuclear trafficking independent of the NLS/NoLS. Our results emphasize the complex host interactions with long signal peptides.

IMPORTANCE

Endoplasmic reticulum-associated degradation (ERAD) is a form of cellular protein quality control that is manipulated by viruses, including the betaretrovirus, mouse mammary tumor virus (MMTV). MMTV-encoded signal peptide (SP) has been shown to interact with an essential ERAD factor, VCP/p97 ATPase, to mediate its extraction from the ER membrane, also known as retrotranslocation, for RNA-binding and nuclear function. In this manuscript, we developed a quantitative retrotranslocation assay that identified an SP substitution mutant, which is defective for VCP interaction as well as nuclear trafficking, oligomer formation, and function. An adjacent SP mutant was competent for retrotranslocation and VCP interaction, but shared the other defects. Our results revealed the requirement for VCP during SP trafficking and the complex cellular pathways used by long signal peptides.
Computational characterization of recombinase circuits for periodic behaviors
Authors: Landau Judith , Cuba Samaniego Christian , Giordano Giulia , Franco Elisa
Published: November 2021

In nature, recombinases are site-specific proteins capable of rearranging DNA, and they are expanding the repertoire of gene editing tools used in synthetic biology. The on/off response of recombinases, achieved by inverting the direction of a promoter, makes them suitable for Boolean logic computation; however, recombinase-based logic gate circuits are single-use due to the irreversibility of the DNA rearrangement, and it is still unclear how a dynamical circuit, such as an oscillator, could be engineered using recombinases. Preliminary work has demonstrated that recombinase-based circuits can yield periodic behaviors in a deterministic setting. However, since a few molecules of recombinase are enough to perform the inverting function, it is crucial to assess how the inherent stochasticity at low copy number affects the periodic behavior. Here, we propose six different circuit designs for recombinase-based oscillators. We model them in a stochastic setting, leveraging the Gillespie algorithm for extensive simulations, and we show that they can yield periodic behaviors. To evaluate the incoherence of oscillations, we use a metric based on the statistical properties of auto-correlation functions. The main core of our design consists of two self-inhibitory, recombinase-based modules coupled by a common promoter. Since each recombinase inverts its own promoter, the overall circuit can give rise to switching behavior characterized by a regular period. We introduce different molecular mechanisms (transcriptional regulation, degradation, sequestration) to tighten the control of recombinase levels, which slows down the response timescale of the system and thus improves the coherence of oscillations. Our results support the experimental realization of recombinase-based oscillators and, more generally, the use of recombinases to generate dynamic behaviors in synthetic biology.
Association of cochlear outer hair cell - type II spiral ganglion afferents with protection from noise-induced hearing loss
Authors: Cederholm Jennie M.E. , Parley Kristina E. , Perera Chamini J. , von Jonquieres Georg , Pinyon Jeremy L. , Julien Jean-Pierre , Ryugo David K. , Ryan Allen F. , Housley Gary D.
Published: November 2021

The medial olivocochlear (MOC) efferent feedback circuit projecting to the cochlear outer hair cells (OHCs) confers protection from noise-induced hearing loss and is generally thought to be driven by inner hair cell (IHC) - type I spiral ganglion afferent (SGN) input. Knockout of the Prph gene (PrphKO) encoding the peripherin type III intermediate filament disrupted the OHC - type II SGN innervation and virtually eliminated MOC – mediated contralateral suppression from noise delivered to the opposite ear, measured as a reduction in cubic distortion product otoacoustic emissions. Electrical stimulation of the MOC pathway elicited contralateral suppression indistinguishable between wildtype (WT) and PrphKO mice, indicating that the loss of contralateral suppression was not due to disruption of the efferent arm of the circuit; IHC – type I SGN input was also normal, based on auditory brainstem responses. High-intensity, broadband noise (108 dB SPL, 1 hour) produced permanent hearing loss in PrphKO mice, but not in WT littermates. These findings associate OHC-type II input with MOC efferent - based otoprotection at loud sound levels.
The TFIIH Complex is Required to Establish and Maintain Mitotic Chromosome Structure
Authors: Haase Julian , Chen Richard , Bonner Mary Kate , Jenkins Lisa M. Miller , Kelly Alexander E.
Published: November 2021

Condensins compact chromosomes to promote their equal segregation during mitosis, but the mechanism of condensin engagement with and action on chromatin is incompletely understood. Here, we show that the general transcription factor TFIIH complex is continuously required to establish and maintain a compacted chromosome structure in transcriptionally silent Xenopus egg extracts. Inhibiting the DNA-dependent ATPase activity of the TFIIH complex subunit XPB rapidly and reversibly induces a complete loss of chromosome structure and prevents the enrichment of condensins I and II, but not topoisomerase II, on chromatin. In addition, inhibiting TFIIH prevents condensation of both mouse and Xenopus nuclei in Xenopus egg extracts, which suggests a fundamental mechanism of TFIIH action. Reducing nucleosome density through partial histone depletion restores chromosome structure and condensin enrichment in the absence of TFIIH activity. We propose that the TFIIH complex promotes mitotic chromosome condensation by dynamically altering chromatin structure to facilitate condensin loading and condensin-dependent loop extrusion.
Regulation of PP2A, PP4, and PP6 holoenzyme assembly by carboxyl-terminal methylation
Authors: Lyons Scott P. , Greiner Elora C. , Cressey Lauren E. , Adamo Mark E. , Kettenbach Arminja N.
Published: November 2021

The family of Phosphoprotein Phosphatases (PPPs) is responsible for most cellular serine and threonine dephosphorylation. PPPs achieve substrate specificity and selectivity by forming multimeric holoenzymes. PPP holoenzyme assembly is tightly controlled, and changes in the cellular repertoire of PPPs are linked to human disease, including cancer and neurodegeneration. For PP2A, PP4, and PP6, holoenzyme formation is in part regulated by carboxyl (C)-terminal methyl-esterification (often referred to as “methylation”). Here, we use mass spectrometry-based proteomics, methylation-ablating mutations, and genome editing to elucidate the role of C-terminal methylation on PP2A, PP4, and PP6 holoenzyme assembly. We find that the catalytic subunits of PP2A, PP4, and PP6 are frequently methylated in cancer cells and that deletion of the C-terminal leucine faithfully recapitulates loss of methylation. We observe that loss of PP2A methylation consistently reduced B55, B56, and B72 regulatory subunit binding in cancer and non-transformed cell lines. However, Striatin subunit binding is only affected in non-transformed cells. For PP4, we find that PP4R1 and PP4R3β bind in a methylation-dependent manner. Intriguingly, loss of methylation does not affect PP6 holoenzymes. Our analyses demonstrate in an unbiased, comprehensive, and isoform-specific manner the crucial regulatory function of endogenous PPP methylation in transformed and non-transformed cell lines
COVID-19 vaccinations: perceptions and behaviours in people with primary ciliary dyskinesia
Authors: Pedersen Eva SL , Mallet Christina M , Lam Yin Ting , Bellu Sara , Cizeau Isabelle , Copeland Fiona , Fernandez Trini Lopez , Manion Michelle , Harris Amanda , Lucas Jane S , Santamaria Francesca ,   COVID-PCD patient advisory group, Goutaki Myrofora , Kuehni Claudia E
Published: November 2021

Primary ciliary dyskinesia (PCD) is a rare genetic disease that causes recurrent respiratory infections. People with PCD may be at high risk of severe COVID-19 and vaccination against SARS-CoV-2 is therefore important. We studied vaccination willingness, speed of vaccination uptake, side effects, and changes in social contact behavior after vaccination in people with PCD. We used data from COVID-PCD, an international participatory cohort study. A questionnaire was e-mailed to participants in May 2021 that asked about COVID-19 vaccinations. 423 participants from 31 countries replied (median age: 30 years; 261 (62%) female). Vaccination uptake and willingness was high with 273 of 287 adults (96%) being vaccinated or willing to be in June 2021; only 4% were hesitant. The most common reasons for hesitancy were fear of side effects (reported by 88%). Mild side effects were common but no participant reported severe side effects. Half of participants changed their social contact behaviour after vaccination by seeing friends and family more often. The high vaccination willingness in the study population might reflect the extraordinary effort taken by PCD support groups to inform people about COVID-19 vaccination. Clear and specific public information and involvement of representatives is important for high vaccine uptake.
Sources of variation in the spectral slope of the sleep EEG
Authors: Kozhemiako N , Mylonas D , Pan JQ , Prerau MJ , Redline S , Purcell SM
Published: November 2021

Building on previous work linking changes in the electroencephalogram (EEG) spectral slope to arousal level, Lendner et al. (2021) reported that wake, non rapid eye movement (NREM) sleep and rapid eye movement (REM) sleep exhibit progressively steeper 30-45 Hz slopes, interpreted in terms of increasing cortical inhibition. Here we sought to replicate Lendner et al.’s scalp EEG findings (based on 20 individuals) in a larger sample of 11,630 individuals from multiple cohorts in the National Sleep Research Resource (NSRR). In a final analytic sample of N = 10,255 distinct recordings, there was unambiguous statistical support for the hypothesis that, within individuals, the mean spectral slope grows steeper going from wake to NREM to REM sleep. We found that the choice of mastoid referencing scheme modulated the extent to which electromyogenic or electrocardiographic artifacts were likely to bias 30-45 Hz slope estimates, as well as other sources of technical, device-specific bias. Nonetheless, within individuals, slope estimates were relatively stable over time. Both cross-sectionally and longitudinal, slopes tended to become shallower with increasing age, particularly for REM sleep; males tended to show flatter slopes than females across all states. Although conceptually distinct, spectral slope did not predict sleep state substantially better than other summaries of the high frequency EEG power spectrum (>20 Hz, in this context) including beta band power, however. Finally, to more fully describe sources of variation in the spectral slope and its relationship to other sleep parameters, we quantified state-dependent differences in the variances (both within and between individuals) of spectral slope, power and interhemispheric coherence, as well as their covariances. In contrast to the common conception of the REM EEG as relatively wake-like (i.e. ‘paradoxical’ sleep), REM and wake were the most divergent states for multiple metrics, with NREM exhibiting intermediate profiles. Under a simplified modelling framework, changes in spectral slope could not, by themselves, fully account for the observed differences between states, if assuming a strict power law model. Although the spectral slope is an appealing, theoretically inspired parameterization of the sleep EEG, here we underscore some practical considerations that should be borne in mind when applying it in diverse datasets. Future work will be needed to fully characterize state-dependent changes in the aperiodic portions of the EEG power spectra, which appear to be consistent with, albeit not fully explained by, changes in the spectral slope.
Parametric control of flexible timing through low-dimensional neural manifolds
Authors: Beiran Manuel , Meirhaeghe Nicolas , Sohn Hansem , Jazayeri Mehrdad , Ostojic Srdjan
Published: November 2021

Biological brains possess an unparalleled ability to adapt behavioral responses to changing stimuli and environments. How neural processes enable this capacity is a fundamental open question. Previous works have identified two candidate mechanisms: a low-dimensional organization of neural activity and a modulation by contextual inputs. We hypothesized that combining the two might facilitate generalization and adaptation in complex tasks. We tested this hypothesis in the framework of flexible timing tasks where dynamics play a key role. Examining trained recurrent neural networks, we found that confining the dynamics to a low-dimensional subspace allowed tonic inputs to parametrically control the overall input-output transform, enabling generalization to novel inputs and adaptation to changing conditions. Reverse-engineering and theoretical analyses demonstrated that this parametric control relies on a mechanism where tonic inputs modulate the dynamics along non-linear manifolds in activity space while preserving their geometry. Comparisons with data from behaving monkeys confirmed the behavioral and neural signatures of this mechanism.
Natural variation in gene expression and Zika virus susceptibility revealed by villages of neural progenitor cells
Authors: Wells Michael F. , Nemesh James , Ghosh Sulagna , Mitchell Jana M. , Mello Curtis J. , Meyer Daniel , Raghunathan Kavya , Tegtmeyer Matthew , Hawes Derek , Neumann Anna , Worringer Kathleen A. , Raymond Joseph J. , Kommineni Sravya , Chan Karrie , Ho Daniel , Peterson Brant K. , Piccioni Federica , Nehme Ralda , Eggan Kevin , McCarroll Steven A.
Published: November 2021

Variation in the human genome contributes to abundant diversity in human traits and vulnerabilities, but the underlying molecular and cellular mechanisms are not yet known, and will need scalable approaches to accelerate their recognition. Here, we advanced and applied an experimental platform that analyzes genetic, molecular, and phenotypic heterogeneity across cells from very many human donors cultured in a single, shared in vitro environment, with algorithms (Dropulation and Census-seq) for assigning phenotypes to individual donors. We used natural genetic variation and synthetic (CRISPR-Cas9) genetic perturbations to analyze the vulnerability of neural progenitor cells to infection with Zika virus. These analyses identified a common variant in the antiviral IFITM3 gene that regulated IFITM3 expression and explained most inter-individual variation in NPCs’ susceptibility to Zika virus infectivity. These and other approaches could provide scalable ways to recognize the impact of genes and genetic variation on cellular phenotypes.

HIGHLIGHTS

Measuring cellular phenotypes in iPSCs and hPSC-derived NPCs from many donors

Effects of donor sex, cell source, genetic and other variables on hPSC RNA expression

Natural genetic variation and synthetic perturbation screens both identify IFITM3 in NPC susceptibility to Zika virus

A common genetic variant in IFITM3 explains most inter-individual variation in NPC susceptibility to Zika virus
mTOR Inhibition Overcomes RSK3-mediated Resistance to BET Inhibitors in Small Cell Lung Cancer
Authors: Kumari Anju , Gesumaria Lisa , Liu Yan-Jin , Hughitt V. Keith , Zhang Xiaohu , Ceribelli Michele , Wilson Kelli M. , Klumpp-Thomas Carleen , Chen Lu , McKnight Crystal , Itkin Zina , Thomas Craig J. , Mock Beverly A. , Schrump David S. , Chen Haobin
Published: November 2021

Purpose

SCLC is a recalcitrant malignancy with limited treatment options. BET inhibitors have shown promising preclinical activity in SCLC, but their broad sensitivity spectrum limits their clinical prospects in this malignancy. Drug combination could be a solution.

Experimental design

We performed high-throughput drug combination screens in SCLC cell lines to identify potential therapeutics synergizing with BET inhibitors. Validation was performed in SCLC cell lines and patient-derived xenograft models. Genome-wide RNA sequencing of xenograft tumors was performed to determine the mechanism underlying the synergy of the drug combination.

Results

Inhibitors of the PI-3K-AKT-mTOR pathway were the top candidates from the screens. Among the therapeutics targeting this pathway, mTOR inhibitors showed the highest degree of synergy with BET inhibitors in vitro. Furthermore, the combination of these two classes of drugs showed superior antitumor efficacy and tolerability in vivo. Using both in vitro and in vivo SCLC models, we demonstrate that BET inhibitors activate the intrinsic apoptotic cascade, and mTOR inhibitors further enhance these apoptotic effects. Mechanistically, BET inhibitors activate the TSC2-mTOR-p70S6K1 signaling cascade by upregulating RSK3, an upstream kinase of TSC2. Activation of p70S6K1 leads to BAD phosphorylation and cell survival. mTOR inhibition blocks this survival signaling cascade and potentiates the antitumor effects of BET inhibitors.

Conclusions

Our results demonstrate that RSK3 upregulation is a novel resistance mechanism of BET inhibitors in SCLC, and mTOR inhibition can overcome this resistance and enhance apoptosis. These findings provide a rationale to evaluate the combination of mTOR and BET inhibitors in patients with SCLC.
Gene recruitments and dismissals in argonaut octopus genome provide insights to pelagic lifestyle adaptation and shell-like eggcase reacquisition
Authors: Yoshida Masa-aki , Hirota Kazuki , Imoto Junichi , Okuno Miki , Tanaka Hiroyuki , Kajitani Rei , Toyoda Atsushi , Itoh Takehiko , Ikeo Kazuho , Sasaki Takenori , Setiamarga Davin H. E.
Published: November 2021

The paper nautilus,Argonauta argo, also known as the greater argonaut, is a species of octopods distinctly characterized by its pelagic lifestyle and by the presence of a spiral-shaped shell-like eggcase in females. The eggcase functions by protecting the eggs laid inside it, and by building and keeping air intakes for buoyancy. To reveal the genomic background of the species’ adaptation to pelagic lifestyle and the acquisition of its shell-like eggcase, we sequenced the draft genome sequence of the species. The genome size was 1.1 Gb, which is the smallest among the cephalopods known to date, with the top 215 scaffolds (average length 5,064,479 bp) covering 81% (1.09 Gb) of the total assembly. A total of 26,433 protein-coding genes were predicted from 16,802 assembled scaffolds. From these, we identified nearly intact HOX, Parahox, Wnt clusters and some gene clusters probably related to the pelagic lifestyle, such asreflectin, tyrosinase, andopsin. For example,opsinmight have undergone an extensive duplication in order to adapt to the pelagic lifestyle, as opposed to other octopuses, which are mostly the benthic. Our gene models also discovered several genes homologous to those related to calcified shell formation in Conchiferan Mollusks, such as Pif-like, SOD, and TRX. Interestingly, comparative genomics analysis revealed that the homologous genes for such genes were also found in the genome of the octopus, which does not have a shell, as well as the basal cephalopodsNautilus. Therefore, the draft genome sequence ofA. argowe presented here had not only helped us to gain further insights into the genetic background of the dynamic recruitment and dismissal of genes for the formation of an important, converging extended phenotypic structure such as the shell and the shell-like eggcase, but also the evolution of lifestyles in Cephalopods and the octopods, from benthic to pelagic.
Mice infected with Mycobacterium tuberculosis are resistant to secondary infection with SARS-CoV-2
Authors: Mejia Oscar Rosas , Gloag Erin S. , Li Jianying , Ruane-Foster Marisa , Claeys Tiffany A. , Farkas Daniela , Farkas Laszlo , Xin Gang , Robinson Richard T.
Published: November 2021

Mycobacterium tuberculosis (Mtb) and SARS-CoV-2 (CoV2) are the leading causes of death due to infectious disease. Although Mtb and CoV2 both cause serious and sometimes fatal respiratory infections, the effect of Mtb infection and its associated immune response on secondary infection with CoV2 is unknown. To address this question we applied two mouse models of COVID19, using mice which were chronically infected with Mtb. In both model systems, Mtb-infected mice were resistant to secondary CoV2 infection and its pathological consequences, and CoV2 infection did not affect Mtb burdens. Single cell RNA sequencing of coinfected and monoinfected lungs demonstrated the resistance of Mtb-infected mice is associated with expansion of T and B cell subsets upon viral challenge. Collectively, these data demonstrate that Mtb infection conditions the lung environment in a manner that is not conducive to CoV2 survival.

AUTHOR SUMMARY

Mycobacterium tuberculosis (Mtb) and SARS-CoV-2 (CoV2) are distinct organisms which both cause lung disease. We report the surprising observation that Mtb-infected mice are resistant to secondary infection with CoV2, with no impact on Mtb burden and resistance associating with lung T and B cell expansion.
Stage-specific control of oligodendrocyte survival and morphogenesis by TDP-43
Authors: Heo Dongeun , Ling Jonathan P. , Molina-Castro Gian C. , Langseth Abraham J. , Waisman Ari , Nave Klaus-Armin , Möbius Wiebke , Wong Philip C. , Bergles Dwight E.
Published: November 2021

Generation of oligodendrocytes in the adult brain enables both adaptive changes in neural circuits and regeneration of myelin sheaths destroyed by injury, disease, and normal aging. This transformation of oligodendrocyte precursor cells (OPCs) into myelinating oligodendrocytes requires processing of distinct mRNAs at different stages of cell maturation. Although mislocalization and aggregation of the RNA binding protein TDP-43 occur in both neurons and glia in neurodegenerative diseases, the consequences of TDP-43 loss within different stages of the oligodendrocyte lineage are not well understood. By performing stage-specific genetic inactivation ofTardbp in vivo, we show that oligodendrocyte lineage cells are differentially sensitive to loss of TDP-43. While OPCs depend on TDP-43 for survival, with conditional deletion resulting in cascading cell loss followed by rapid regeneration to restore their density, oligodendrocytes become less sensitive to TDP-43 depletion as they mature. Deletion of TDP-43 early in the maturation process led to eventual oligodendrocyte degeneration, seizures and premature lethality, while oligodendrocytes that experienced late deletion survived and mice exhibited a normal lifespan. At both stages, TDP-43 deficient oligodendrocytes formed fewer and thinner myelin sheaths and extended new processes that inappropriately wrapped neuronal somata and blood vessels. Transcriptional analysis revealed that in the absence of TDP-43, key proteins involved in oligodendrocyte maturation and myelination were misspliced leading to aberrant incorporation of cryptic exons. Inducible deletion of TDP-43 from oligodendrocytes in the adult CNS induced the same progressive morphological changes and mice acquired profound hindlimb weakness, suggesting that loss of TDP-43 function in oligodendrocytes may contribute to neuronal dysfunction in neurodegenerative disease.
LuxT is a Global Regulator of Low-Cell Density Behaviors Including Type III Secretion, Siderophore Production, and Aerolysin Production inVibrio harveyi
Authors: Eickhoff Michaela J. , Fei Chenyi , Cong Jian-Ping , Bassler Bonnie L.
Published: November 2021

Quorum sensing (QS) is a chemical communication process in which bacteria produce, release, and detect extracellular signaling molecules called autoinducers. Via combined transcriptional and post-transcriptional regulatory mechanisms, QS allows bacteria to collectively alter gene expression on a population-wide scale. Recently, the TetR-family transcriptional regulator LuxT was shown to controlV. harveyi qrr1, encoding the Qrr1 small RNA that functions at the core of the QS regulatory cascade. Here, we use RNA-Sequencing to reveal that, beyond control ofqrr1, LuxT is a global regulator of 414V. harveyigenes including those involved in type III secretion, siderophore production, and aerolysin toxin biosynthesis. Importantly, LuxT directly repressesswrZ,encoding a GntR-family transcriptional regulator, and LuxT control of type III secretion, siderophore, and aerolysin genes occurs by two mechanisms, one that is SwrZ-dependent and one that is SwrZ-independent. All of these target genes specify QS-controlled behaviors that are enacted whenV. harveyiis at low cell density. Thus, LuxT and SwrZ function in parallel with QS to drive particular low cell density behaviors. Phylogenetic analyses reveal thatluxTis highly conserved amongVibrionaceae,butswrZis less well conserved. In a test case, we find that inAliivibrio fischeri,LuxT also repressesswrZ. SwrZ is a repressor ofA. fischerisiderophore production genes. Thus, LuxT repression ofswrZdrives activation ofA. fischerisiderophore gene expression. Our results indicate that LuxT is a major regulator amongVibrionaceae,and, in the species that also possessswrZ, LuxT functions with SwrZ to control gene expression.

Importance

Bacteria precisely tune gene expression patterns to successfully react to changes that occur in the environment. Defining the mechanisms that enable bacteria to thrive in diverse and fluctuating habitats, including in host organisms, is crucial for a deep understanding of the microbial world and also for development of effective applications to promote or to combat particular bacteria. In this study, we show that a regulator called LuxT controls over 400 genes in the marine bacteriumVibrio harveyiand, moreover, that LuxT is highly conserved amongVibrionaceaespecies, ubiquitous marine bacteria that often cause disease. We characterize the mechanisms by which LuxT controls genes involved in virulence and nutrient acquisition. We show that LuxT functions in parallel with a set of regulators of the bacterial cell-to-cell communication process called quorum sensing to promoteV. harveyibehaviors at low cell density.
Potent antibody immunity to SARS-CoV-2 variants elicited by a third dose of inactivated vaccine
Authors: Ju Bin , Zhou Bing , Song Shuo , Fan Qing , Ge Xiangyang , Wang Haiyan , Cheng Lin , Guo Huimin , Shu Dan , Liu Lei , Zhang Zheng
Published: November 2021

SARS-CoV-2 variants are still prevalent worldwide and continue to pose a challenge to the effectiveness of current vaccines. It remains unknown whether a third dose of inactivated vaccine elicits immune potential against SARS-CoV-2 variants. Here, we showed a significant decline in plasma neutralization against SARS-CoV-2 at seven months after a second dose of the inactivated vaccine in a large-scale cohort. However, we also found that a third vaccination with an inactivated vaccine largely increased plasma neutralization against variants including Beta, Delta, and Lambda. More importantly, the high-affinity anti-RBD memory B cells were also generated by the third vaccination, suggesting a more potent and longer protection. These findings highlighted the importance and effectiveness of a third dose of inactivated vaccine in conferring higher protection against the emerging variants in populations.
Money cannot buy happiness: improving governance in the banking sector through spirituality
Authors: Robina-Ramírez Rafael , Medina-Merodio José Amelio , Estriégana Rosa , Jimenez-Naranjo Hector V.
Published: November 2021

Purpose

A model is proposed to develop happiness in the banking sector based on an improvement in the spirituality of employees.

Design/methodology/approach

Following the Schwartz’s model for behavioural transformation, a new path has been proposed based on the development of the transcendent vision of work. The data obtained were analysed using the partial least squares-structural equation modeling (SEM) method.

Findings

Contrary to the widespread idea that happiness is orientated towards the enjoyment of goods, bank employees prefer to develop spiritual values and resources that allow them to respond adequately to massive layoffs and pressures at work.

Research limitations/implications

The bank employees’ schedules made it difficult to organise group sessions. Multiple sessions prevented us all from interacting.

Practical implications

It is established a training strategy for the pursuit of happiness, to propose an engine for actions orientated towards happiness and to introduce transcendence and spirituality as requirements for finding happiness during daily work.

Social implications

There is a need to return to traditional values and principles in daily work. This will have a positive effect on communities and society.

Originality/value

A new concept has been coined: spiritual resources. This new variable can help to combat adversity by exploring the meaning of transcendence at work.
I want to work there: how public relations agencies communicate organizational culture and identity on Instagram
Authors: Watkins Brandi , Smith Stephanie A.
Published: November 2021

Purpose

This study examined Instagram content shared by public relations (PR) agencies, through the sensitizing framework of organizational identity theory, to determine what messages related to organizational identity, culture and image were communicated to external audiences. This study highlights the various ways that Instagram can be used for strategic organizational communication.

Design/methodology/approach

A qualitative, thematic analysis of Instagram content was conducted. The constant comparative analysis was guided by organizational identity theory, which provided an individual-level perspective for interpreting organizational messages within the posts.

Findings

PR agencies use hashtags, employee sharing and communicating about agency outreach efforts and accolades to communicate organizational identity. PR agencies communicate aspects of its culture through employee engagement and development, employee cohesiveness and through communicating a commitment to diversity, philanthropy and community service. PR agencies influenced its organizational image by communicating content related to promotion and support of creative efforts, having a public Instagram account and retelling the history of the agency.

Originality/value

This study extends our understanding of corporate self-presentation strategies on social media.