bluuebunny/crossref_metadata_2025 huggingface dataset:
Flexible early prospection of potential behavior in working memory
Authors: Nasrawi Rose , Boettcher Sage E.P. , van Ede Freek
Published: March 2023

For visual working memory to serve upcoming behavior, it is crucial that we prepare for the potential use of working-memory contents ahead of time. Recent studies have demonstrated how the prospection and planning for an upcoming manual action starts early after visual encoding, and occurs alongside visual retention. Here, we address whether such ‘output planning’ in visual working memory flexibly adapts to different visual-motor mappings, and occurs even when an upcoming action will only potentially become relevant for behavior. Participants performed a visual-motor working memory task in which they remembered one or two visual items for later (potential) use. We tracked planning of upcoming behavior through contralateral attenuation of beta-band activity – a canonical motor-cortical EEG signature of manual-action planning. This revealed how action encoding and subsequent planning alongside visual working memory (1) reflects anticipated task demands rather than specific visual-motor mappings, (2) occurs even for actions that will only potentially become relevant for behavior, and (3) is associated with better performance for the encoded item, at the expense of performance to other working-memory content. This reveals how the potential prospective use of visual working memory content is flexibly planned early on, with consequences for later performance.
Impulse perturbation reveals cross-modal access to sensory working memory through learned associations
Authors: Kandemir Güven , Akyürek Elkan G.
Published: March 2023

We investigated if learned associations between visual and auditory stimuli can afford full cross-modal access to working memory. Previous research using the impulse perturbation technique has shown that cross-modal access to working memory is one-sided; visual impulses reveal both auditory and visual memoranda, but auditory impulses do not seem to reveal visual memoranda (Wolff et al., 2020b). Our participants first learned to associate six auditory pure tones with six visual orientation gratings. Next, a delayed match-to-sample task for the orientations was completed, while EEG was recorded. Orientation memories were recalled either via their learned auditory counterpart, or were visually presented. We then decoded the orientation memories from the EEG responses to both auditory and visual impulses presented during the memory delay. Working memory content could always be decoded from visual impulses. Importantly, through recall of the learned associations, the auditory impulse also evoked a decodable response from the visual WM network, providing evidence for full cross-modal access. We also observed that after a brief initial dynamic period, the representational codes of the memory items generalized across time, as well as between perceptual maintenance and long-term recall conditions. Our results thus demonstrate that accessing learned associations in long-term memory provides a cross-modal pathway to working memory that seems to be based on a common coding scheme.
Commensal Bacteria Maintain a Qa-1b-restricted Unconventional CD8+T Population in Gut Epithelium
Authors: Guan Jian , Peske J. David , Valerio Michael Manoharan , Park Chansu , Robey Ellen A. , Sadegh-Nasseri Scheherazade
Published: March 2023

Intestinal intraepithelial lymphocytes (IELs) are characterized by an unusual phenotype and developmental pathway, yet their specific ligands and functions remain largely unknown. Here by analysis of QFL T cells, a population of CD8+T cells critical for monitoring the MHC I antigen processing pathway, we established that unconventional Qa-1b-restricted CD8+T cells are abundant in intestinal epithelium. We found that QFL T cells showed a Qa-1b-dependent unconventional phenotype in the spleen and small intestine of naïve wild-type mice. The splenic QFL T cells showed innate-like functionality exemplified by rapid response to cytokines or antigen, while the gut population was refractory to stimuli. Microbiota was required for the maintenance, but not the initial gut homing of QFL T cells. Moreover, monocolonization withPediococcus pentosaceus,which expresses a peptide that cross-activated QFL T cells, was sufficient to maintain QFL T cells in the intestine. Thus, microbiota is critical for shaping the Qa-1b-restricted IEL landscape.
A lack of population structure characterizes the invasiveLonicera japonicain West Virginia and across eastern North America
Authors: Barrett Craig F. , Corbett Cameron W. , Thixton-Nolan Hana L. ,   Biology 320 Class
Published: March 2023

Invasive plant species cause massive ecosystem damage globally, yet represent powerful case studies in population genetics and rapid adaptation to new habitats. The availability of digitized herbarium collections data, and the ubiquity of invasive species across the landscape make them highly accessible for studies of invasion history and population dynamics associated with their introduction, establishment, spread, and ecological interactions. Here we focus onLonicera japonica, one of the most damaging invasive vine species in North America. We leveraged digitized collections data and contemporary field collections to reconstruct the invasion history and characterize patterns of genomic variation in the eastern USA, using a straightforward method for generating nucleotide polymorphism data and a recently published, chromosome-level genome for the species. We found an overall lack of population structure among sites in northern West Virginia, USA, as well as across sites in the central and eastern USA. Heterozygosity and population differentiation were both low based onFst, analysis of molecular variance, principal components analysis, and cluster-based analyses. We also found evidence of high inbreeding coefficients and significant linkage disequilibrium, in line with the ability of this otherwise outcrossing, perennial species to propagate vegetatively. Our findings corroborate earlier studies based on allozyme data, and suggest that intentional, human-assisted spread explains the lack of population structure, as this species was planted for erosion control and as an ornamental, escaping cultivation repeatedly across the USA. Finally, we discuss how plant invasion genomics can be incorporated into experiential undergraduate education as a way to integrate teaching and research.
Uncovering and exploiting the return of voluntary motor programs after paralysis using a bi-cortical neuroprosthesis
Authors: Duguay Maude , Bonizzato Marco , Delivet-Mongrain Hugo , Fortier-Lebel Nicolas , Martinez Marina
Published: March 2023

Rehabilitative and neuroprosthetic approaches after spinal cord injury (SCI) aim to reestablish voluntary control of movement. Promoting recovery requires a mechanistic understanding of the return of volition over action, but the relationship between re-emerging cortical commands and the return of locomotion is not well established. We introduced a neuroprosthesis delivering targeted bi-cortical stimulation in a clinically relevant contusive SCI model. In healthy and SCI cats, we controlled hindlimb locomotor output by tuning stimulation timing, duration, amplitude, and site. In intact cats, we unveiled a large repertoire of motor programs. After SCI, the evoked hindlimb lifts were highly stereotyped, yet effective in modulating gait and alleviating bilateral foot drag. Results suggest that the neural substrate underpinning motor recovery had traded-off selectivity for efficacy. Longitudinal tests revealed that the return of locomotion after SCI was time-locked with recovery of the descending drive, which advocates for rehabilitation interventions directed at the cortical target.

Highlights

A bilateral cortical implant allowed for the delivery of alternate bilateral stimulation coherently with locomotion, which modulated gait trajectories.

We analyzed the effects of stimulation parameters - timing, duration, amplitude, and site of stimulation - to maximize the improvement of locomotor output after paralysis.

A varied repertoire of motor programs evoked in intact cats was reduced to one stereotyped response after spinal cord injury (SCI) consisting in flexion modulation that efficiently alleviated hindlimb dragging.

After SCI, the return of cortical gait control emerged in synchrony with locomotor recovery.
Disentangling Mixed Classes of Covariability in Large-Scale Neural Data
Authors: Pellegrino Arthur , Stein Heike , Cayco-Gajic N Alex
Published: March 2023

Recent work has argued that large-scale neural recordings are often well described by low-dimensional ‘latent’ dynamics identified using dimensionality reduction. However, the view that task-relevant variability is shared across neurons misses other types of structure underlying behavior, including stereotyped neural sequences or slowly evolving latent spaces. To address this, we introduce a new framework that simultaneously accounts for variability that is shared across neurons, trials, or time. To identify and demix these covariability classes, we develop a new unsupervised dimensionality reduction method for neural data tensors called sliceTCA. In three example datasets, including motor cortical dynamics during a classic reaching task and recent multi-region recordings from the International Brain Laboratory, we show that sliceTCA can capture more task-relevant structure in neural data using fewer components than traditional methods. Overall, our theoretical framework extends the classic view of low-dimensional population activity by incorporating additional classes of latent variables capturing higher-dimensional structure.
Monocarboxylate transporters facilitate succinate uptake into brown adipocytes
Authors: Reddy Anita , Winther Sally , Tran Nhien , Xiao Haopeng , Jakob Josefine , Garrity Ryan , Smith Arianne , Mills Evanna L. , Chouchani Edward T.
Published: March 2023

Uptake of circulating succinate by brown adipose tissue (BAT) and beige fat elevates whole body energy expenditure, counteracts obesity, and antagonizes systemic tissue inflammation in mice. The plasma membrane transporters that facilitate succinate uptake in these adipocytes remain undefined. Here we elucidate a mechanism underlying succinate import into BAT via monocarboxylate transporters (MCTs). We show that succinate transport is strongly dependent on the proportion of it present in the monocarboxylate form. MCTs facilitate monocarboxylate succinate uptake, which is promoted by alkalinization of the cytosol driven by adrenoreceptor stimulation. In brown adipocytes, we show that MCT1 primarily facilitates succinate import, however other members of the MCT family can partially compensate and fulfill this role in the absence of MCT1. In mice, we show that acute pharmacological inhibition of MCT1 and 2 decreases succinate uptake into BAT. Conversely, congenital genetic depletion of MCT1 alone has little effect on BAT succinate uptake, indicative of additional transport mechanisms with high capacityin vivo. In sum, we define a mechanism of succinate uptake in BAT that underlies its protective activity in mouse models of metabolic disease.
AVibrio choleraeviral satellite maximizes its spread and inhibits phage by remodeling hijacked phage coat proteins into small capsids
Authors: Boyd Caroline M. , Subramanian Sundharraman , Dunham Drew T. , Parent Kristin N. , Seed Kimberley D.
Published: March 2023

Phage satellites commonly remodel capsids they hijack from the phages they parasitize, but only a few mechanisms regulating the change in capsid size have been reported. Here, we investigated how a satellite fromVibrio cholerae, PLE, remodels the capsid it has been predicted to steal from the phage ICP1 (1). We identified that a PLE-encoded protein, TcaP, is both necessary and sufficient to form small capsids during ICP1 infection. Interestingly, we found that PLE is dependent on small capsids for efficient transduction of its genome, making it the first satellite to have this requirement. ICP1 isolates that escaped TcaP-mediated remodeling acquired substitutions in the coat protein, suggesting an interaction between these two proteins. With a procapsid-like-particle (PLP) assembly platform inEscherichia coli, we demonstrated that TcaP is abona fidescaffold that regulates the assembly of small capsids. Further, we studied the structure of PLE PLPs using cryogenic electron microscopy and found that TcaP is an external scaffold, that is functionally and somewhat structurally similar to the external scaffold, Sid, encoded by the unrelated satellite P4 (2). Finally, we showed that TcaP is largely conserved across PLEs. Together, these data support a model in which TcaP directs the assembly of small capsids comprised of ICP1 coat proteins, which inhibits the complete packaging of the ICP1 genome and permits more efficient packaging of replicated PLE genomes.
Predictors for estimating subcortical EEG responses to continuous speech
Authors: Kulasingham Joshua P. , Bachmann Florine L. , Eskelund Kasper , Enqvist Martin , Innes-Brown Hamish , Alickovic Emina
Published: March 2023

Perception of sounds and speech involves structures in the auditory brainstem that rapidly process ongoing auditory stimuli. The role of these structures in speech processing can be investigated by measuring their electrical activity using scalp-mounted electrodes. However, typical analysis methods involve averaging neural responses to many short repetitive stimuli that bear little relevance to daily listening environments. Recently, subcortical responses to more ecologically relevant continuous speech were detected using linear encoding models. These methods estimate the temporal response function (TRF), which is a regression model that minimises the error between the measured neural signal and a predictor derived from the stimulus. Using predictors that model the highly non-linear peripheral auditory system may improve linear TRF estimation accuracy and peak detection. Here, we compare predictors from both simple and complex peripheral auditory models for estimating brainstem TRFs on electroencephalography (EEG) data from 24 participants listening to continuous speech. We also discuss the data length required for estimating subcortical TRFs with clear peaks. Interestingly, predictors from simple models resulted in TRFs that were similar to those estimated using complex models, and were much faster to compute. This work paves the way for efficient modelling and detection of subcortical processing of continuous speech, which may lead to improved diagnosis metrics for hearing impairment and assistive hearing technology.
Silk Fibroin Particles as Carriers in the Development of All-Natural Hemoglobin-Based Oxygen Carriers (HBOCs)
Authors: Pacheco Marisa O , Lutz Henry M , Armada Jostin , Davies Nickolas , Gerzenshtein Isabelle K , Cakley Alaura S , Spiess Bruce D , Stoppel Whitney L
Published: March 2023

Oxygen therapeutics have a range of applications in transfusion medicine and disease treatment. Synthetic molecules and all-natural or semi-synthetic hemoglobin-based oxygen carriers (HBOCs) have seen success as potential circulating oxygen carriers. However, many early HBOC products were removed from the market due to side effects from excess hemoglobin in the blood stream and hemoglobin entering the tissue. To overcome these issues, research has focused on increasing the molecular diameter of hemoglobin by polymerizing hemoglobin molecules or encapsulating hemoglobin in liposomal carriers, where immune responses and circulation times remain a challenge. This work looks to leverage the properties of silk fibroin, a cytocompatible and non-thrombogenic biopolymer, known to entrap protein-based cargo, to engineer a silk fibroin-hemoglobin-based oxygen carrier (sfHBOC). Herein, an all-aqueous solvent evaporation technique was used to form silk fibroin particles with and without hemoglobin to tailor the formulation for specific particle sizes. The encapsulation efficiency and ferrous state of hemoglobin were analyzed, resulting in 60% encapsulation efficiency and a maximum of 20% ferric hemoglobin, yielding 100 µg/mL active hemoglobin in certain sfHBOC formulations. The system did not elicit a strong inflammation responsein vitro, demonstrating the potential for this particle system to serve as an injectable HBOC.

Table of Contents Figure

Table of Contents Figure:In this manuscript, we generate silk fibroin particles using an all-aqueous processing technique starting from silk fibroin polymer systems of differing molecular weights. We analyze the extent to which silk concentration and extraction time affect particle size. Further, we analyze the encapsulation of hemoglobin in the particle system and assess immune activation in macrophage-like cultures.
If not a fake, what’s in the lake?
Authors: Foxon Floe
Published: March 2023

An animal dubbed ‘Champ’ has been sighted by hundreds of eyewitnesses in a large, near-oligotrophic lake in North America. A widely-publicised photograph taken by Mansi purportedly depicting the animal was published to much fanfare. In the present study, sightings were coded and analysed using interrupted time-series models, Pearson correlation coefficients, and descriptive statistics. The number of sightings per year was statistically significantly higher after publication of the Mansi photograph compared to before, which may be evidence of expectant attention, or publicity leading to more lake-goers and therefore more animal sightings. Sightings were consistent in condition (mostly Summer, from Noon to Evening, > 1 witness, and a calm lake surface) which may be interpreted as consistency of when lake-goers visit Champlain, or as evidence of consistent behavioural characteristics of Champ animals. Sightings were highly inconsistent in reported Champ characteristics with widely varying morphology, and most sightings were missing morphological data entirely. More than a quarter of sightings were likened to logs, land mammals, birds, fish, and boats, which are all found in the lake. There were no associations between distance to sighting, estimated length, and estimated height of objects witnessed, which may suggest that eyewitnesses provide inaccurate estimates of these measurements in lake settings. If not a fake, what’s in the lake may be ordinary phenomena mistaken for Champ. Alternatively, Lake Champlain is inhabited by as-yet undiscovered multi-humped, dark-coloured serpents approximately seven meters in length, which locomote in a fast and sinuous fashion, and which enjoy pleasant Summer evenings and crowds. Deciding which explanation best accounts for the data is left as an exercise for the reader.
Tafazzin knockdown in murine mesenchymal stem cells enhances the tafazzin knockdown mediated elevation in interleukin-10 secretion from murine B lymphocytes
Authors: Zegallai Hana M. , Abu-El-Rub Ejlal , Hatch Grant M.
Published: March 2023

Barth Syndrome is a rare X-linked genetic disorder caused by mutations in theTAFAZZINgene. We recently demonstrated that tafazzin (Taz) protein deficiency in murine mesenchymal stems (MSCs) reduces immune function of activated wild type (WT) B lymphocytes. Interleukin-10 (IL-10) is a key anti-inflammatory cytokine capable of exerting immunosuppressive effects on myeloid cells. Here we examined if Taz deficiency in murine MSCs altered proliferation and IL-10 production in Taz deficient lipopolysaccharide (LPS)-activated murine B lymphocytes. Bone marrow MSCs and splenic B lymphocytes were isolated from WT or Taz knockdown (TazKD) mice. WT or Taz deficient MSCs were co-cultured with either LPS-activated WT or LPS-activated Taz deficient B lymphocytes for 24 h and B cell proliferation and IL-10 production determined. Taz deficient MSCs exhibited increased phosphatidylinositol-3-kinase (PI3K) mRNA expression compared to WT MSCs indicative of enhanced immunosuppression. Co-culture of Taz deficient MSCs with Taz deficient LPS-activated B cells resulted in a greater reduction in proliferation of B cells compared to Taz deficient MSCs co-cultured with LPS-activated WT B cells. In addition, co-culture of Taz deficient MSCs with Taz deficient LPS-activated B cells resulted in an enhanced production of IL-10 compared to Taz deficient MSCs co-cultured with LPS-activated WT B cells. Thus, Taz deficiency in murine MSCs potentiates the Taz knockdown-mediated elevation in IL-10 secretion from LPS-activated Taz knockdown B lymphocytes. These data suggest that Taz deficient MSCs may modulate the activity of other Taz deficient immune cells potentially promoting an enhanced immunosuppressive state.
Active cortical networks promote shunting fast synaptic inhibitionin vivo
Authors: Burman Richard J. , Brodersen Paul J.N. , Raimondo Joseph V. , Sen Arjune , Akerman Colin J.
Published: March 2023

Fast synaptic inhibition determines neuronal response properties in the mammalian brain and is mediated by chloride-permeable ionotropic GABA-A receptors (GABAARs). Despite their fundamental role, it is still not known how GABAARs signal in the intact brain. Here we usein vivogramicidin recordings to investigate synaptic GABAAR signaling in mouse cortical pyramidal neurons under conditions that preserve native transmembrane chloride gradients. In anaesthetized cortex, synaptic GABAARs exert classic hyperpolarizing effects. In contrast, GABAAR-mediated synaptic signaling in awake cortex is found to be predominantly shunting. This is due to more depolarized GABAAR equilibrium potentials (EGABAAR), which are shown to result from the high levels of synaptic activity that characterize awake cortical networks. The EGABAARobserved in awake cortex can facilitate the decoupling of local networks, which improves the ability of the network to discriminate stimuli. Our findings therefore suggest that GABAAR signaling adapts to optimize cortical functions.
Tyrosyl-DNA phosphodiesterase 1 (TDP1) and SPRTN protease repair histone 3 and topoisomerase 1 DNA-protein crosslinksin vivo
Authors: Anticevic Ivan , Otten Cecile , Vinkovic Luka , Jukic Luka , Popovic Marta
Published: March 2023

DNA-protein crosslinks (DPCs) are frequent and damaging DNA lesions that affect all DNA transactions, which in turn can lead to the formation of DSBs, genomic instability and cell death. At the organismal level, impaired DPC repair (DPCR) is associated with cancer, aging, and neurodegeneration. Despite the severe consequences of DPCs, little is known about the processes underlying repair pathways at the organism level. SPRTN is a protease that removes most cellular DPCs during replication, whereas tyrosyl-DNA phosphodiesterase 1 repairs one of the most abundant enzymatic DPCs, topoisomerase 1-DPC (TOP1-DPC). How these two enzymes repair DPCs at the organism level is currently unknown. We perform phylogenetic, syntenic, structural and expression analysis to compare TDP1 orthologs between human, mouse and zebrafish. Using the zebrafish animal model and human cells, we demonstrate that TDP1 and SPRTN repair endogenous, camptothecin- and formaldehyde-induced DPCs, including histone H3- and TOP1-DPCs. We show that resolution of H3-DNA crosslinks depends on upstream proteolysis by SPRTN and subsequent peptide removal by TDP1 in RPE1 cells and zebrafish embryos, whereas SPRTN and TDP1 function in different pathways in the repair of endogenous TOP1-DPCs and total DPCs. Furthermore, our results suggest that TDP2 could potentially compensate for the impairment of TDP1 functionin vivoand in human cells. Understanding the role of TDP1 in DPC repair at the cellular and organismal levels could provide an impetus for the development of new drugs and combination therapies with TOP1-DPC inducing drugs.
Chromatin opening ability of pioneer factor Pax7 depends on unique isoform and C-terminal domain
Authors: Bascunana Virginie , Pelletier Audrey , Gouhier Arthur , Bemmo Amandine , Balsalobre Aurelio , Drouin Jacques
Published: March 2023

Pioneer factors are transcription factors (TFs) that have the unique ability to recognise their target DNA sequences within closed chromatin. Whereas their interactions with cognate DNA is similar to other TFs, their ability to interact with chromatin remains poorly understood. Having previously defined the modalities of DNA interactions for the pioneer factor Pax7, we have now used natural isoforms of this pioneer as well as deletion and replacement mutants to investigate the Pax7 structural requirements for chromatin interaction and opening. We show that the GL+ natural isoform of Pax7 that has two extra amino acids within the DNA binding paired domain is unable to activate the melanotrope transcriptome and to fully activate a large subset of melanotrope-specific enhancers targeted for Pax7 pioneer action. This enhancer subset remains in the primed state rather than being fully activated, despite the GL+ isoform having similar intrinsic transcriptional activity as the GL-isoform. C-terminal deletions of Pax7 lead to the same loss of pioneer ability, with similar reduced recruitments of the cooperating TF Tpit and of the co-regulators Ash2 and BRG1. This suggests complex interrelations between the DNA binding and C-terminal domains of Pax7 that are crucial for its chromatin opening pioneer ability.
A quantum walk model of Bicoid morphogen formation and interpretation
Authors: Lone Irfan , Trindle Carl O.
Published: March 2023

The establishment and interpretation of the concentration distribution of the morphogen Bicoid (BCD) is considered crucial for the successful embryonic development of fruit flies. However, the biophysical mechanisms behind the timely formation and subsequent interpretation of the BCD morphogen by its target genes are not yet completely understood. Here a discrete-time, one-dimensional quantum walk model of BCD gradient formation is used to explain both the observed values of diffusivity and its precise interpretation. It is shown that the decoding of positional information from the BCD morphogen by its primary target gene hb, with the observed precision of ∼ 10%, takes a time period of less than a second, as expected on the basis of recent experimental observations. From this the on-rate (kon) for the binding of BCD to its target loci is obtained. Furthermore, the model is also used to explain certain key observations of recent optogenetic experiments concerning the time windows for BCD interpretation. Finally, it is argued that the presented model represents a significant step in the utilization of quantum computation-based techniques in studying the dynamics of biological systems in general and in the field of developmental biophysics in particular.
Spatially-resolved single cell transcriptomics reveal a critical role for γδ T cells in the control of skin inflammation and subcutaneous adipose wasting during chronicTrypanosoma bruceiinfection
Authors: Quintana Juan F. , Sinton Matthew C. , Chandrasegaran Praveena , Lestari Agatha Nabilla , Heslop Rhiannon , Cheaib Bachar , Ogunsola John , Ngoyi Dieudonne Mumba , Swar Nono-Raymond Kuispond , Cooper Anneli , Coffelt Seth B. , MacLeod Annette
Published: March 2023

African trypanosome parasites colonise the skin in a process important for parasite transmission. However, how the skin responses to trypanosome infection remain unresolved. Here, using a combination of spatial and single cell transcriptomics, coupled within vivogenetic models, we investigated the local immune response of the skin in a murine model of infection. First, we detected a significant expansion of IL-17A-producing γδ T cells (primarily Vγ6+) in the infected murine skin compared to naïve controls that occur mainly in the subcutaneous adipose tissue. Second, interstitial preadipocytes located in the subcutaneous adipose tissue upregulate several genes involved in inflammation and antigen presentation, including T cell activation and survival.In silicocell-cell communication suggests that adipocytes trigger γδ T cell activation locallyvia Cd40, Il6, Il10,andTnfsf18signalling, amongst others. Third, mice deficient in IL-17A-producing γδ T cells show extensive inflammation, increased frequency of skin-resident IFNγ-producing CD8+T cells and limited subcutaneous adipose tissue wasting compared to wild-type infected controls, independent of TH1 CD4+T cells and parasite burden. Based on these observations, we proposed a model whereby adipocytes as well as Vγ6+cells act concertedly in the subcutaneous adipose tissue to limit skin inflammation and tissue wasting. These studies shed light onto the mechanisms of γδ T cell-mediated immunity in the skin in the context of African trypanosome infection, as well as a potential role of immature and mature adipocytes as homeostatic regulators in the skin during chronic infection.
Spatiotemporal cell landscape of human embryonic tooth development
Authors: Shi Yueqi , Yu Yejia , Li Jutang , Sun Shoufu , Han Li , Wang Shaoyi , Guo Ke , Yang Jingang , Wei Wenjia , Qiu Jin
Published: March 2023

Understanding the cellular composition and trajectory of human tooth development is valuable for dentistry and stem cell engineering research. Previous single-cell studies have focused on mature human tooth and developing mice tooth, but cell landscape on human embryonic dental development is still lacking. We collected tooth germ tissues from aborted fetus (17-24 week) for single cell RNA sequence and spatial transcriptome. We classified all cells into seven subclusters of epithelium, seven clusters of mesenchyme and other cell types like Schwann cell precursor and pericyte. For epithelium, the Stratum intermedium branch and the ameloblast branch diverged from a same set of KRT15+-HOPX+-ALCAM+ epithelial stem cell lineage, but the spatial distribution of two branches were not clearly distinct. This trajectory received spatially adjacent regulation signals from mesenchyme and pericyte, including JAG1 and APP. The differentiation of pulp cell and pre-odontoblast showed four waves of temporally distinct gene expression, which involved regulation networks of LHX9, DLX5 and SP7 and were regulated by upstream ligands like BMP family. Taken together, we provided a reference landscape for the research on human early tooth development, covering different spatial structures and developmental periods.
Allosteric Communication in the Gating Mechanism for Controlled Protein Degradation by the Bacterial ClpP Peptidase
Authors: Dayananda Ashan , Dennison T. S. Hayden , H.Fonseka Hewafonsekage Yasan , Avestan Mohammad S. , Wang Qi , Tehver Riina , Stan George
Published: March 2023

Proteolysis is essential for the control of metabolic pathways and cell cycle. Bacterial caseinolytic proteases (Clp) use peptidase components, such as ClpP, to degrade defective substrate proteins and to regulate cellular levels of stress-response proteins. To ensure selective degradation, access to the proteolytic chamber of the double– ring ClpP tetradecamer is controlled by a critical gating mechanism of the two axial pores. Binding of conserved loops of the Clp ATPase component of the protease or small molecules, such as acyldepsipeptide (ADEP), at peripheral ClpP ring sites triggers axial pore opening through dramatic conformational transitions of flexible N–terminal loops between disordered conformations in the “closed” pore state and ordered hairpins in the “open” pore state. In this study, we probe the allosteric communication underlying these conformational changes by comparing residue-residue couplings in molecular dynamics simulations of each configuration. Both principal component and normal mode analyses highlight large-scale conformational changes in the N-terminal loop regions and smaller amplitude motions of the peptidase core. Community network analysis reveals a switch between intraand inter-protomer coupling in the open - close pore transition. Allosteric pathways that connect the ADEP binding sites to N-terminal loops are rewired in this transition, with shorter network paths in the open pore configuration supporting stronger intra- and inter-ring coupling. Structural perturbations, either through removal of ADEP molecules or point mutations, alter the allosteric network to weaken the coupling.
Chemically Tunable FOXM1-D Sensor Revealed FOXM1 Direct Influence on Cell Cycle
Authors: Phongkitkarun Kriengkrai , Chusorn Porncheera , Kamkaew Maliwan , Lam Eric W.-F. , Promptmas Chamras , Sampattavanich Somponnat
Published: March 2023

Forkhead box protein M1 (FOXM1) is a proliferation-associated transcription factor contributing to the G2/M phase transition of the cell cycle. Although the upregulation of FOXM1 has been observed in different cancer types, how the regulation of FOXM1 dynamically alters during cell cycles and potentially contributes to tumorigenesis is not well understood. We showed here the development and application of a tunable FOXM1-DHFR (FOXM1-D) sensor that enables surveillance and manipulation of the FOXM1 abundance. Using trimethoprim (TMP) to stabilize the sensor, we measured the kinetics of FOXM1-D production, degradation, and cytosolic-to-nuclear translocation in the G1 and G2 cell-cycle phases. By controlling FOXM1-D stability in different synchronized cell cycle pools, we found that the G1- and S-synchronized cells finished their first cell division faster, although the G2-synchronized cells were unaffected. Our analysis of single-cell FOXM1-D dynamics revealed that the two-round dividing cells had a lower amplitude and later peak time than those arrested in the first cell division. Destabilizing FOXM1-D in the single-round dividing cells enabled these cells to re-enter the second cell division, proving that overproduction of FOXM1 causes cell cycle arrest and prevents unscheduled proliferation.
PD1 is transcriptionally regulated by LEF1 in mature T cells
Authors: Zhao Pin , Sun Lanming , Zhao Cong , Malik Samiullah
Published: March 2023

Programmed cell death 1 (PD1) plays a vital role in cancer immune evasion. So monoclonal antibodies targeting PD-1 to boost the immune system are being developed for the treatment of cancer. But the effect of PD1/PD-L1 blocking antibody only works in a subset of patients or some tumors. It is well established that PD-1 can affect the positive selection of T cells. Mice lacking PD1 or PD-L1 had more DP T cells in the thymus. However, how it affects the T-cell repertoire is not very clear. For T cell development and maturation, TCF1 and its homolog LEF1, act as indispensable factors and TCF1 has been most studied. In our work, we found that LEF1, not TCF1, positively regulated the transcription of PD1 by generating two mice models, including ERT2-CRE-LEF1flox/floxmice and concanavalin A (ConA)-mediated T activation mice model. We investigated LEF1 and PD1 expression in mature T cells, including CD4+ T cells, CD8+ T cells, and Treg cells in these two mice models. And we also evaluated the expression of PD1 in tumor-infiltrating lymphocytes in the tumor-implantation experiments. Furthermore, the regulation of PD1 by LEF1 was verified in LEF1 knockdown cells. Our conclusions provided a novel insight into PD1 regulation in immune responses and explored potential strategies for clinical anti-PD1 treatment.
OprF impactsPseudomonas aeruginosabiofilm matrix eDNA levels in a nutrient-dependent manner
Authors: Cassin Erin K. , Araujo-Hernandez Sophia A. , Baughn Dena S. , Londono Melissa C. , Rodriguez Daniela Q. , Tseng Boo Shan
Published: March 2023

The biofilm matrix is composed of exopolysaccharides, eDNA, membrane vesicles, and proteins. While proteomic analyses have identified numerous matrix proteins, their functions in the biofilm remain understudied compared to the other biofilm components. In thePseudomonas aeruginosabiofilm, several studies have identified OprF as an abundant matrix protein and, more specifically, as a component of biofilm membrane vesicles. OprF is a major outer membrane porin ofP. aeruginosacells. However, current data describing the effects of OprF in theP. aeruginosabiofilm is limited. Here we identify a nutrient-dependent effect of OprF in static biofilms, whereby ΔoprFcells form significantly less biofilm than wild type when grown in media containing glucose or low sodium chloride concentrations. Interestingly, this biofilm defect occurs during late static biofilm formation and is not dependent on the production of PQS, which is responsible for outer membrane vesicle production. Furthermore, while biofilms lacking OprF contain approximately 60% less total biomass than those of wild type, the number of cells in these two biofilms is equivalent. We demonstrate thatP. aeruginosaΔoprFbiofilms with reduced biofilm biomass contain less eDNA than wild-type biofilms. These results suggest that the nutrient-dependent effect of OprF is involved in the maintenance of matureP. aeruginosabiofilms by retaining eDNA in the matrix.

IMPORTANCE

Many pathogens form biofilms, which are bacterial communities encased in an extracellular matrix that protects them against antibacterial treatments. The roles of several matrix components of the opportunistic pathogenPseudomonas aeruginosahave been characterized. However, the effects ofP. aeruginosamatrix proteins remain understudied and are untapped potential targets for antibiofilm treatments. Here we describe a conditional effect of the abundant matrix protein OprF on late-stageP. aeruginosabiofilms. A ΔoprFstrain formed significantly less biofilm in low sodium chloride or with glucose. Interestingly, the defective ΔoprFbiofilms did not exhibit fewer resident cells but contained significantly less extracellular DNA (eDNA) than wild type. These results suggest that OprF is involved in matrix eDNA retention in mature biofilms.
Analysis of SARS-CoV-2 mutations associated with resistance to therapeutic monoclonal antibodies that emerge after treatment
Authors: Focosi Daniele , McConnell Scott , Sullivan David J. , Casadevall Arturo
Published: March 2023

The mutation rate of the Omicron sublineage has led to baseline resistance against all previously authorized anti-Spike monoclonal antibodies (mAbs). Nevertheless, in case more antiviral mAbs will be authorized in the future, it is relevant to understand how frequently treatment-emergent resistance has emerged so far, under different combinations and in different patient subgroups. We report the results of a systematic review of the medical literature for case reports and case series for treatment-emergent immune escape, which is defined as emergence of a resistance-driving mutation in at least 20% of sequences in a given host at a given timepoint. We identified 31 publications detailing 201 cases that included different variants of concern (VOC) and found that the incidence of treatment emergent-resistance ranged from 10% to 50%. Most of the treatment-emergent resistance events occurred in immunocompromised patients. Interestingly, resistance also emerged against cocktails of two mAbs, albeit at lower frequencies. The heterogenous therapeutic management of those cases doesn’t allow inferences about the clinical outcome in patients with treatment-emergent resistance. Furthermore, we noted a temporal correlation between the introduction of mAb therapies and a subsequent increase in SARS-CoV-2 sequences across the globe carrying mutations conferring resistance to that mAb, raising concern as to whether these had originated in mAb-treated individuals. Our findings confirm that treatment-emergent immune escape to anti-Spike mAbs represents a frequent and concerning phenomenon and suggests that these are associated with mAb use in immunosuppressed hosts.
Hearing loss after exposure to vincristine and platinum-based chemotherapy among childhood cancer survivors
Authors: Strebel Sven , Mader Luzius , Jörger Philippa , Waespe Nicolas , Uhlmann Seraina , von der Weid Nicolas , Ansari Marc , Kuehni Claudia E.
Published: March 2023

Background

Vincristine poses a suspected additional risk factor for hearing loss among childhood cancer survivors (CCS) treated with platinum-based chemotherapy, yet evidence is scarce since no study reports vincristine doses. We examined the association of vincristine with hearing loss in a national cohort of CCS.

Methods

We included CCS registered in the Swiss Childhood Cancer Registry treated at age ≤ 18 years with platinum-based chemotherapy between 1990–2014. All participants in our retrospective cohort study had audiogram and treatment data from medical records. We identified CCS exposed to vincristine and calculated the total cumulative dose. We defined clinically relevant hearing loss as grade ≥ 2 using the International Society of Pediatric Oncology Boston Ototoxicity Scale at latest follow-up.

Results

Our study population included 270 CCS (43% female; median age at cancer diagnosis 6.8 years; interquartile range [IQR]: 2.1–11.7 years) with median age at audiogram 13.5 years (IQR: 9.3–17.0 years). Vincristine exposure was associated with an increased risk of hearing loss in the multivariable logistic regression analysis (odds ratio [OR] 4.8; 95% confidence interval [CI]: 1.8–12.9). We found no evidence of dose-response relationship (OR 1.0; 95% CI: 0.97–1.04) or effect modification from vincristine from other ototoxic treatments, such as type of platinum agent, cranial radiotherapy, and hematopoietic stem cell transplantation.

Conclusion

Vincristine is associated with a higher risk of hearing loss in CCS treated with platinum-based chemotherapy. We suggest future studies investigate the underlying mechanism and causality among CCS without exposure to other ototoxic cancer treatments.
Precision MRI phenotyping of muscle volume and quality at a population scale
Authors: Thanaj Marjola , Basty Nicolas , Whitcher Brandon , Sorokin Elena P. , Liu Yi , Srinivasan Ramprakash , Cule Madeleine , Thomas E. Louise , Bell Jimmy D.
Published: March 2023

Introduction

Magnetic resonance imaging (MRI) enables direct measurements of muscle volume and quality, allowing for an in-depth understanding of their associations with anthropometric traits, and health conditions. However, it is unclear which muscle volume measurements: total muscle volume, regional measurements, measurements of muscle quality: intermuscular adipose tissue (IMAT) or proton density fat fraction (PDFF), are most informative and associate with relevant health conditions such as dynapenia and frailty.

Methods

We developed a pipeline to automatically segment and extract image-derived phenotypes (IDPs) including total and regional muscle volumes and measures of muscle quality, and applied it to the neck-to-knee Dixon images in 44,520 UK Biobank participants. We further segmented paraspinal muscle from 2D quantitative MRI to quantify muscle PDFF and iron concentration. We defined dynapenia based on grip strength below sex-specific cut-off points and frailty based on five criteria. We used logistic regression to investigate the association between muscle volume and quality measurements and dynapenia and frailty.

Results

Muscle volumes were significantly higher in male compared with female participants, even after correcting for height while, IMAT, (corrected for muscle volume) and paraspinal muscle PDFF were significantly higher in female compared with male participants. From the overall cohort, 7.6% (N = 3,261) were identified with dynapenia, and 1.1% (N = 455) with frailty. Dynapenia and frailty were positively associated with age and negatively associated with physical activity levels. In dynapenia, muscle volume IDPs were most informative, particularly total muscle exhibiting odds ratios (OR) of 0.392 and 95% confidence intervals (CI) = 0.361 - 0.426, while for frailty, muscle quality was found to be most informative, in particular thigh IMAT volume indexed to height squared (OR = 1.396, 95% CI = 1.374 - 1.418), both with p-values below the Bonferroni-corrected threshold (p<8.6×10−5).

Conclusions

Our fully automated method enables the quantification of muscle volumes and quality suitable for large population-based studies. For dynapenia, muscle volumes particularly those including greater body coverage such as total muscle are the most informative, whilst, for frailty, markers of muscle quality were the most informative IDPs. These results suggest that different measurements may have varying diagnostic values for different health conditions.
Colorectal Cancer Risk and Ancestry in Colombian admixed Populations
Authors: Criollo-Rayo Angel , Bohórquez Mabel Elena , Lott Paul , Carracedo Angel , Tomlinson Ian , Castro Jorge Mario , Mateus Gilbert , Molina Daniel , Vargas Catalina Rubio , Puentes Carlos ,   CHIBCHA Consortium, Echeverry Magdalena , Carvajal Luis
Published: March 2023

Several colorectal cancer susceptibility disease loci have been discovered through Genome-wide association studies. However most of the variants were originally identified in Caucasian populations. Demographic history and admixture background may impact the association of known CRC variants due to the differences in linkage disequilibrium across different populations. We performed a genomic study in a sample of 955 cases and 968 controls from admixed populations in Colombia by genotyping ∼1 million SNPs aimed to detect the impact of genetic structure in the association of 20 known SNPs risk for colorectal cancer. The replication was reached for eleven out of 20 nominally associated SNPs; with allelic odds ratios (OR) between 1.14 and 1.41, indicating a minimal individual risk increment; on the other hand, the overall OR for co-inherited SNPs was 5.4 (95% CI: 3.052-9.731,P=1.16E-08). Most of the variants followed a recessive model with significant homozygous ORs distributed between 1.3 and 1.65. The major associated markers were: rs4939827 (18q21.1,P=7.35E-6), rs10411210 (19q13.11,P=0.001) rs10795668 (10p14,P=0.0024), rs4444235 (14q.2.2,P=0.005), rs961253 (20p12.3,P=0.006), rs16892766 (8q23.3,P=0.011) and rs1050547 (8q24.21,P=0.017). Additionally, European ancestral component was associated with colorectal cancer risk (p=6.48E-04, OR = 4.244 95% IC: 1.701-10.68). Our findings in Colombia indicates a significant contribution of the known CRC risk SNPs to the disease in the Colombian population, which in turns can be explained by the genetic European component influx during the admixture process. The unassociated SNPs indicates frequency and genetic structure differences between European and Colombian populations or due to the sample process.
Multi-Site Analysis of Biosynthetic Gene Clusters (BGCs) from the Periodontitis Oral Microbiome
Authors: Koohi-Moghadam Mohamad , Watt Rory M. , Leung W. Keung
Published: March 2023

Bacteria are key modulators of human health and disease. Biochemicals synthesized by bacterial biosynthetic gene clusters (BGCs) have been shown to play key roles in microbiome–host and microbe–microbe interactions. Whilst BGCs have been widely investigated in the human gut, very few studies have explored BGCs within oral niches. In this pilot study, we used shotgun metagenomic sequencing to profile the microbiota from three different oral sites: saliva, subgingival plaque, and supragingival plaque, within subjects with periodontitis (n = 23) versus controls (n = 16). Our aim was to identify BGCs associated with periodontitis, as well as BGCs that exhibited site (niche) selectivity. We identified 10,742 BGCs in the cohort, some of which were unique for a specific oral site. Aryl polyenes (APEs) and Bacteriocin were the most prevalent clusters, but we also found several ‘novel’ BGCs that were widely distributed across diverse bacterial phyla; other BGCs exhibited selectivity for periodontitis niches. Taken together, our findings significantly expand our metagenomic understanding of microbiota within healthy and diseased oral niches. By uncovering previously unexplored biosynthetic pathways, we provide a potential road-map for the future exploration of poorly understood host-microbe and microbe-microbe interactions in the oral cavity that may contribute to periodontitis.