bluuebunny/crossref_metadata_2025 huggingface dataset:
The centrosomal protein 83 (CEP83) regulates human pluripotent stem cell differentiation towards the kidney lineage
Authors: Mansour Fatma , Hinze Christian , Telugu Narasimha Swamy , Kresoja Jelena , Shaheed Iman B. , Mosimann Christian , Diecke Sebastian , Schmidt-Ott Kai M.
Published: June 2022

Background

During embryonic development, the mesoderm undergoes patterning into diverse lineages including axial, paraxial, and lateral plate mesoderm (LPM). Within the LPM, the so-called intermediate mesoderm (IM) forms kidney and urogenital tract progenitor cells, while remaining LPM forms cardiovascular, hematopoietic, mesothelial and additional progenitor cells. The signals that regulate these early lineage decisions are incompletely understood. Here, we found that the centrosomal protein 83 (CEP83), a centriolar component necessary for primary cilia formation and mutated in pediatric kidney disease, influences the differentiation of human induced pluripotent stem cells (hiPSCs) towards intermediate mesoderm.

Methods

We induced inactivating deletions of CEP83 in hiPSCs and applied a 7 day in vitro protocol of intermediate mesoderm kidney progenitor differentiation, based on timed application of WNT and FGF agonists. We characterized induced mesodermal cell populations using single cell and bulk transcriptomics and tested their ability to form kidney structures in subsequent organoid culture.

Results

While hiPSCs with homozygous CEP83 inactivation were normal regarding morphology and transcriptome, their induced differentiation into IM progenitor cells was perturbed. Mesodermal cells induced after 7 days of monolayer culture of CEP83-deficient hiPCS exhibited absent or elongated primary cilia, displayed decreased expression of critical IM genes (PAX8, EYA1, HOXB7) and an aberrant induction of LPM markers (e. g. FOXF1, FOXF2, FENDRR, HAND1, HAND2). Upon subsequent organoid culture, wildtype cells differentiated to form kidney tubules and glomerular-like structures, whereas CEP83-deficient cells failed to generate kidney cell types, instead upregulating cardiomyocyte, vascular, and more general LPM progenitor markers.

Conclusion

Our data suggest that CEP83 regulates the balance of intermediate mesoderm and lateral plate mesoderm formation from human pluripotent stem cells, identifying a potential link between centriolar or ciliary function and mesodermal lineage induction.
Purely STDP-based assembly dynamics: stability, learning, overlaps, drift and aging
Authors: Manz Paul , Memmesheimer Raoul-Martin
Published: June 2022

Memories may be encoded in the brain via strongly interconnected groups of neurons, called assemblies. The concept of Hebbian plasticity suggests that these assemblies are generated through synaptic plasticity, strengthening the recurrent connections within select groups of neurons that receive correlated stimulation. To remain stable in absence of such stimulation, the assemblies need to be self-reinforcing under the plasticity rule. Previous models of such assembly maintenance require additional mechanisms of fast homeostatic plasticity often with biologically implausible timescales. Here we provide a model of neuronal assembly generation and maintenance purely based on spike-timing-dependent plasticity (STDP) between excitatory neurons. It uses irregularly and stochastically spiking neurons and STDP that depresses connections of uncorrelated neurons. We find that assemblies do not grow beyond a certain size, because temporally imprecisely correlated spikes dominate the plasticity in large assemblies. Assemblies in the model can be learned or spontaneously emerge. The model allows for prominent, stable overlap structures between static assemblies. Further, assemblies can drift, particularly according to a novel, transient overlap-based mechanism. Finally the model indicates that assemblies grow in the aging brain, where connectivity decreases.

Author summary

It is widely assumed that memories are represented by ensembles of nerve cells that have strong interconnections with each other. It is to date not clear how such strongly interconnected nerve cell ensembles form, persist, change and age. Here we show that already a basic rule for activity-dependent synaptic strength plasticity can explain the learning or spontaneous formation and the stability of assemblies. In particular, it is not necessary to explicitly keep the overall total synaptic strength of a neuron nearly constant, a constraint that was incorporated in previous models in a manner inconsistent with current experimental knowledge. Furthermore, our model achieves the challenging task of stably maintaining many overlaps between assemblies and generating the experimentally observed drift of memory representations. Finally, the model predicts that if the number of synaptic connections in the brain decreases, as observed during aging, the size of the neuron ensembles underlying memories increases. This may render certain memories in the aging brain more robust and prominent but also less specific.
Obesogenic diet induces circuit-specific memory deficits in mice
Authors: Bakoyiannis Ioannis , Ducourneau Eva-Gunnel , N’diaye Matéo , Fermigier Alice , Ducroix-Crepy Céline , Bosch-Bouju Clémentine , Coutureau Etienne , Trifilieff Pierre , Ferreira Guillaume
Published: June 2022

Obesity is associated with neurocognitive dysfunction, including memory deficits. This is particularly worrisome during adolescence, which represents a crucial period for maturation of brain structures, such as the hippocampus which are crucial for cognition. In rodent models, we recently reported that memory impairments induced by obesogenic high-fat diet (HFD) intake during the periadolescent period can be reversed by chemogenetic manipulation of the ventral hippocampus (vHPC). Here, we used an intersectional viral approach in HFD-fed male mice to chemogenetically inactivate specific vHPC efferent pathways to nucleus accumbens or medial prefrontal cortex during memory tasks. We first demonstrated that HFD enhanced activation of both pathways after training and that our chemogenetic approach was effective in normalising this activation. Inactivation of the vHPC-nucleus accumbens pathway rescued HFD-induced deficits in recognition but not location memory. Conversely, inactivation of the vHPC-medial prefrontal cortex pathway restored location but not recognition memory impairments produced by HFD. Either pathway manipulation did not affect exploration, locomotion or anxiety-like behaviour. These findings suggest that HFD intake throughout adolescence impairs different types of memory through overactivation of specific hippocampal efferent pathways and that targeting these overactive pathways has therapeutic potential.
Super-enhancers require a combination of classical enhancers and novel facilitator elements to drive high levels of gene expression
Authors: Blayney Joseph , Francis Helena , Camellato Brendan , Mitchell Leslie , Stolper Rosa , Boeke Jef , Higgs Douglas , Kassouf Mira
Published: June 2022

Super-enhancers (SEs) are a class of compound regulatory elements which control expression of key cell-identity genes. It remains unclear whether they are simply clusters of independent classical enhancers or whether SEs manifest emergent properties and should therefore be considered as a distinct class of element. Here, using synthetic biology and genome editing, we engineered the well characterised erythroid α-globin SE at the endogenous α-globin locus, removing all SE constituent elements in a mouse embryonic stem cell-line, to create a “blank canvas”. This has allowed us to re-build the SE through individual and combinatorial reinsertion of its five elements (R1, R2, R3, Rm, R4), to test the importance of each constituent’s sequence and position within the locus. Each re-inserted element independently creates a region of open chromatin and binds its normal repertoire of transcription factors; however, we found a high degree of functional interdependence between the five constituents. Surprisingly, the two strongest α-globin enhancers (R1 and R2) act sub-optimally both on their own and in combination, and although the other three elements (R3, Rm and R4) exhibit no discernible enhancer activity, they each exert a major positive effect in facilitating the activity of the classical enhancers (R1 and R2). This effect depends not simply on the sequence of each element but on their positions within the cluster. We propose that these “facilitators” are a novel form of regulatory element, important for ensuring the full activity of SEs, but distinct from conventional enhancer elements.
Optimizing insect metabarcoding using replicated mock communities
Authors: Iwaszkiewicz-Eggebrecht Elzbieta , Granqvist Emma , Buczek Mateusz , Prus Monika , Roslin Tomas , Tack Ayco J.M. , Andersson Anders F. , Miraldo Andreia , Ronquist Fredrik , Łukasik Piotr
Published: June 2022

Metabarcoding (high-throughput sequencing of marker gene amplicons) has emerged as a promising and cost-effective method for characterizing insect community samples. Yet, the methodology varies greatly among studies and its performance has not been systematically evaluated to date. In particular, it is unclear how accurately metabarcoding can resolve species communities in terms of presence-absence, abundances, and biomass. Here we use mock community experiments and a simple probabilistic model to evaluate the performance of different metabarcoding protocols. Specifically, we ask four questions: (Q1) How consistent are the recovered community profiles across replicate mock communities?; (Q2) How does the choice of lysis buffer affect the recovery of the original community?; (Q3) How are community estimates affected by differing lysis times and homogenization?; and (Q4) Is it possible to obtain adequate species abundance estimates through the use of biological spike-ins? We show that estimates are quite variable across community replicates. In general, a mild lysis protocol is better at reconstructing species lists and approximate counts, while homogenization is better at retrieving biomass composition. Tiny insects are more likely to be detected in lysates, while some tough species require homogenization to be detected. Results are less consistent across biological replicates for lysates than for homogenates. Some species are associated with strong PCR amplification bias, which complicates the reconstruction of species counts. Yet, with adequate spike-in data, species abundance can be determined with roughly 40% standard error for homogenates, and with roughly 50% standard error for lysates, under ideal conditions. In the latter case, however, this often requires species-specific reference data, while spike-in data generalizes better across species for homogenates. We conclude that a non-destructive, mild lysis approach shows the highest promise for presence/absence description of the community, while also allowing future morphological or molecular work on the material. However, homogenization protocols perform better for characterizing community composition, in particular in terms of biomass.
WITHDRAWN: Nucleic acid biomarkers of immune response and cell and tissue damage in COVID-19 and MIS-C
Authors: Loy Conor J. , Sotomayor-Gonzalez Alicia , Servellita Venice , Nguyen Jenny , Lenz Joan , Bhattacharya Sanchita , Williams Meagan , Cheng Alexandre P. , Bliss Andrew , Saldhi Prachi , Brazer Noah , Streithorst Jessica , Suslovic William , Hsieh Charlotte , Bahar Burak , Wood Nathan , Foresythe Abiodun , Gliwa Amelia , Bhakta Kushmita , Perez Maria A. , Hussaini Laila , Anderson Evan J. , Chahroudi Ann , Delaney Meghan , Butte Atul J. , DeBiasi Roberta , Rostad Christina A. , De Vlaminck Iwijn , Chiu Charles Y.
Published: June 2022

Withdrawal Statement

The authors have withdrawn their manuscript owing to data from patients who had not been consented being inadvertently used in the preprint. This has been corrected in the version of the study published in Cell Reports Medicine. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Impact of Pre-Existing Chronic Viral Infection and Reactivation on the Development of Long COVID
Authors: Peluso Michael J. , Deveau Tyler-Marie , Munter Sadie E. , Ryder Dylan , Buck Amanda , Beck-Engeser Gabriele , Chan Fay , Lu Scott , Goldberg Sarah A. , Hoh Rebecca , Tai Viva , Torres Leonel , Iyer Nikita S. , Deswal Monika , Ngo Lynn H. , Buitrago Melissa , Rodriguez Antonio , Chen Jessica Y. , Yee Brandon C. , Chenna Ahmed , Winslow John W. , Petropoulos Christos J. , Deitchman Amelia N. , Hellmuth Joanna , Spinelli Matthew A. , Durstenfeld Matthew S. , Hsue Priscilla Y. , Kelly J. Daniel , Martin Jeffrey N. , Deeks Steven G. , Hunt Peter W. , Henrich Timothy J.
Published: June 2022

The presence and reactivation of chronic viral infections such as Epstein-Barr virus (EBV), cytomegalovirus (CMV) and human immunodeficiency virus (HIV) have been proposed as potential contributors to Long COVID (LC), but studies in well-characterized post-acute cohorts of individuals with COVID-19 over a longer time course consistent with current case definitions of LC are limited. In a cohort of 280 adults with prior SARS-CoV-2 infection, we observed that LC symptoms such as fatigue and neurocognitive dysfunction at a median of 4 months following initial diagnosis were independently associated with serological evidence of recent EBV reactivation (early antigen-D [EA-D] IgG positivity) or high nuclear antigen IgG levels, but not with ongoing EBV viremia. Evidence of EBV reactivation (EA-D IgG) was most strongly associated with fatigue (OR 2.12). Underlying HIV infection was also independently associated with neurocognitive LC (OR 2.5). Interestingly, participants who had serologic evidence of prior CMV infection were less likely to develop neurocognitive LC (OR 0.52) and tended to have less severe (>5 symptoms reported) LC (OR 0.44). Overall, these findings suggest differential effects of chronic viral co-infections on the likelihood of developing LC and predicted distinct syndromic patterns. Further assessment during the acute phase of COVID-19 is warranted.

The authors found that Long COVID symptoms in a post-acute cohort were associated with serological evidence of recent EBV reactivation and pre-existing HIV infection when adjusted for participant factors, sample timing, comorbid conditions and prior hospitalization, whereas underlying CMV infection was associated with a decreased risk of Long COVID.
Antenatal depressive symptoms are strongly predicted by the severity of pre-menstrual syndrome: results of partial least squares analysis
Authors: Abe Yoshiko , Sirichokchatchawan Wandee , Sangkomkamhang Ussanee , Satthapisit Sirina , Suwimonteerabutr Junpen , Maes Michael
Published: June 2022

Objective

Antenatal depression (AD) is the commonest morbidity during pregnancy. There is evidence that premenstrual syndrome (PMS) and AD share common immune-inflammatory pathways. Few studies have assessed the relation between the affective symptoms of PMS and AD. The present study aims to evaluate the association between the severity of depressive PMS and AD in early and late pregnancy.

Methods

Women in early pregnancy (<=16 weeks) were recruited and followed until late pregnancy (>=20 weeks). The Premenstrual Symptoms Screening Tool (PSST) was used to assess PMS and AD symptoms were assessed using the Edinburgh Postnatal Depression Scale (EPDS). Results: The PSST score was significantly and positively associated with the EPDS scores both in early and late pregnancy. Up to 57.6% of the variance in the early EPDS score was explained by the regression on the first factor extracted from 10 depression and anxiety PSST items (dubbed the DepAnx PSST domain), PSST item insomnia, relation dissatisfaction, and the Abuse Assessment Screen item 1 (partner abuse). Additionally, 6.3% of the variance in the PSST DepAnx domain was explained by the regression on the mental-physical neglect score of the Adverse Childhood Experiences Questionnaire. There were specific indirect effects of PSST DepAnx (p<0.001), insomnia (p=0.041), relation dissatisfaction (p=0.023) and partner abuse (p=0.007) on the late EPDS which were mediated by the early EPDS score.

Conclusion

The affective, but not psychosomatic, symptoms of PMS strongly predict depressive symptoms during pregnancy suggesting that the pathophysiology of affective PMS symptoms overlap with those of AD.
Development of a new DHFR-based destabilizing domain with enhanced basal turnover and applicability in mammalian systems
Authors: Nakahara Emi , Mullapudi Vishruth , Joachimiak Lukasz A. , Hulleman John D.
Published: June 2022

Destabilizing domains (DDs) are an attractive strategy allowing for positive post-transcriptional small molecule-regulatable control of a fusion protein’s abundance. Yet in many instances, the currently available DDs suffer from higher-than-desirable basal levels of the fusion protein. Accordingly, we redesigned the E. coli dihydrofolate reductase (ecDHFR) DD by introducing a library of ~1200 random ecDHFR mutants fused to YFP into CHO cells. Following successive rounds of FACS sorting, we identified six new ecDHFR DD clones with significantly enhanced proteasomal turnover in the absence of a stabilizing ligand, trimethoprim (TMP). One of these clones, designated as ‘C12’, contained four unique missense mutations (W74R/T113S/E120D/Q146L) and demonstrated a significant 2.9-fold reduction in basal levels compared to the conventional ecDHFR DD YFP. This domain was similarly responsive to TMP with respect to dose-response and maximal stabilization, indicating an overall enhanced dynamic range. Interestingly, both computational and wet-lab experiments identified the W74R and T113S mutations of C12 as the main contributors towards its basal destabilization. Yet, the combination of all the C12 mutations were required to maintain both its enhanced degradation and TMP stabilization. We further demonstrate the utility of C12 by fusing it to IκBα and Nrf2, two stress-responsive proteins that have previously been challenging to regulate. In both instances, C12 significantly enhanced the basal turnover of these proteins and improved the dynamic range of regulation post stabilizer addition. These advantageous features of the C12 ecDHFR DD variant highlight its potential for replacing the conventional N-terminal ecDHFR DD, and overall improving the use of destabilizing domains, not only as a chemical biology tool, but for gene therapy avenues as well.
Damaged mitochondria recruit the effector NEMO to activate NF-κB signaling
Authors: Harding Olivia , Holzbaur Erika L.F.
Published: June 2022

Failure to clear damaged mitochondria via mitophagy disrupts physiological function and may initiate damage signaling via inflammatory cascades. However, signaling mechanisms leading from impaired mitophagy to neuro-inflammation are unclear. We discovered that NF-κB essential regulator NEMO is recruited to damaged mitochondria in a Parkin- and p62/SQSTM1-dependent manner in a time-course similar to recruitment of the structurally-related mitophagy receptor, OPTN. NEMO and p62 colocalize, partitioning into distinct domains from OPTN. Either depletion of p62 or mutation of NEMO’s ubiquitin-binding domain abolishes NEMO recruitment, indicating multifactorial interactions. The active catalytic IKK component phospho-IKKβ colocalizes with NEMO on damaged mitochondria, initiating NF-κB signaling and the upregulation of inflammatory cytokines. These findings suggest that damaged mitochondria serve as an intracellular platform for innate immune signaling by promoting the formation of activated IKK complexes in a Parkin-dependent manner. We propose that mitophagy and NF-κB signaling are competing pathways regulating the response to cellular stress.
Queuine salvaging in the human parasite Entamoeba histolytica
Authors: Sarid Lotem , Sun Jingjing , Chittrakanwong Jurairat , Trebicz-Geffen Meirav , Dedon Peter C. , Ankri Serge
Published: June 2022

Queuosine (Q) is a naturally occurring modified nucleoside that occurs in the first position of transfer RNA anticodons such as Asp, Asn, His, and Tyr. As eukaryotes lack pathways to synthesize queuine, the Q nucleobase, they must obtain it from their diet or gut microbiota. Previously, we described the effects of queuine on the physiology of the eukaryotic parasite Entamoeba histolytica and characterized the enzyme EhTGT responsible for queuine incorporation into tRNA. At present, it is unknown how E. histolytica salvages Q from gut bacteria. We used liquid chromatography–mass spectrometry (LC–MS) and N-acryloyl-3-aminophenylboronic acid (APB) PAGE analysis to demonstrate that E. histolytica trophozoites can salvage queuine from Q or E. coli K12 but not from the modified E. coli QueC strain, which cannot produce queuine. We then examined the role of EhDUF2419, a protein with homology to DNA glycosylase, as queuine salvage enzyme in E. histolytica. We found that glutathione S-transferase (GST)-EhDUF2419 catalyzed the conversion of Q into queuine. Trophozoites silenced for EhDUF2419 expression are impaired in their ability to form Q-tRNA from Q or from E. coli. We also observed that Q partially protects control trophozoites from oxidative stress (OS), but not siEhDUF2419 trophozoites. Overall, our data reveal that EhDUF2419 is central for the salvaging of queuine from bacteria and for the resistance of the parasite to OS.
Abl2 mediates microtubule nucleation and repair via tubulin co-condensation
Authors: Lyu Wanqing , Duan Daisy , Wu Kuanlin , Wu Chunxiang , Xiong Yong , Koleske Anthony J.
Published: June 2022

Abl family kinases are evolutionarily conserved regulators of cell migration and morphogenesis. Genetic experiments in Drosophila suggest that Abl family kinases interact functionally with microtubules to regulate axon guidance and neuronal morphogenesis. Vertebrate Abl2 binds to microtubules and promotes their plus-end elongation both in vitro and in cells, but the molecular mechanisms by which Abl2 regulates microtubule (MT) dynamics were unclear. We report here that Abl2 regulates MT assembly via condensation and direct interactions with both the MT lattice and tubulin dimers. We find that Abl2 promotes MT nucleation, which is further facilitated by the ability of the Abl2 C-terminal half to undergo phase separation and form co-condensates with tubulin. A naturally occurring tubulin binding-deficient Abl2 splice isoform fails to promote nucleation. Abl2 binds to regions adjacent to MT damage and facilitates their repair via fresh tubulin recruitment and increases MT rescue frequency and lifetime. MT recovery after nocodazole treatment is greatly slowed in Abl2 knockout COS-7 cells compared to wild type cells. We propose a model in which Abl2 locally concentrates tubulin and recruits it to MT tips or to defects in the MT lattice to promote MT repair, rescue, and nucleation.
Retinoic acid control of pax8 during renal specification of Xenopus pronephros involves hox and meis3
Authors: Durant-Vesga Jennifer , Suzuki Nanoka , Ochi Haruki , Le Bouffant Ronan , Eschstruth Alexis , Ogino Hajime , Umbhauer Muriel , Riou Jean-François
Published: June 2022

Development of the Xenopus pronephros relies on renal precursors grouped at neurula stage into a specific region of dorso-lateral mesoderm called the kidney field. Formation of the kidney field at early neurula stage is dependent on retinoic (RA) signaling acting upstream of renal master transcriptional regulators such as pax8 or lhx1. Althoughlhx1might be a direct target of RA-mediated transcriptional activation in the kidney field, how RA controls the emergence of the kidney field remains poorly understood. In order to better understand RA control of renal specification of the kidney field, we have performed a transcriptomic profiling of genes affected by RA disruption in lateral mesoderm explants isolated prior to the emergence of the kidney field and cultured at different time points until early neurula stage. Besides genes directly involved in pronephric development (pax8, lhx1, osr2, mecom), hox (hoxa1, a3, b3, b4, c5andd1) and the hox co-factormeis3appear as a prominent group of genes encoding transcription factors (TFs) downstream of RA. Supporting the idea of a role of meis3 in the kidney field, we have observed that meis3 depletion results in a severe inhibition ofpax8expression in the kidney field. Meis3 depletion only marginally affects expression oflhx1andaldh1a2suggesting that meis3 principally acts upstream ofpax8. Further arguing for a role of meis3 and hox in the control of pax8, expression of a combination of meis3, hoxb4 and pbx1 in animal caps inducespax8expression, but not that oflhx1. The same combination of TFs is also able to transactivate a previously identifiedpax8enhancer, Pax8-CNS1. Mutagenesis of potential PBX-Hox binding motifs present in Pax8-CNS1 further allows to identify two of them that are necessary for transactivation. Finally, we have tested deletions of regulatory sequences in reporter assays with a previously characterized transgene encompassing 36.5 kb of theX. tropicalis pax8gene that allows expression of a truncated pax8-GFP fusion protein recapitulating endogenouspax8expression. This transgene includes three conservedpax8enhancers, Pax8-CNS1, Pax8-CNS2 and Pax8-CNS3. Deletion of Pax8-CNS1 alone does not affect reporter expression, but deletion of a 3.5kb region encompassing Pax8-CNS1 and Pax8-CNS2 results in a severe inhibition of reporter expression both in the otic placode and kidney field domains.
Methylation status of VTRNA2-1/nc886 is stable across human populations, monozygotic twin pairs and in majority of somatic tissues
Authors: Marttila Saara , Tamminen Hely , Rajić Sonja , Mishra Pashupati P , Lehtimäki Terho , Raitakari Olli , Kähönen Mika , Kananen Laura , Jylhävä Juulia , Hägg Sara , Delerue Thomas , Peters Annette , Waldenberger Melanie , Kleber Marcus E , März Winfried , Luoto Riitta , Raitanen Jani , Sillanpää Elina , Laakkonen Eija K , Heikkinen Aino , Ollikainen Miina , Raitoharju Emma
Published: June 2022

Aims and methods

Our aim was to characterise the methylation level of a polymorphically imprinted gene, VTRNA2-1/nc886, in human populations and somatic tissues. We utilised 48 datasets, consisting of >30 different tissues and >30 000 individuals.

Results

We show that the nc886 methylation status is associated with twin status and ethnic background, but the variation between populations is limited. Monozygotic twin pairs present concordant methylation, while ∼30% of dizygotic twin pairs present discordant methylation in the nc886 locus. The methylation levels of nc886 are uniform across somatic tissues, except in cerebellum and skeletal muscle.

Conclusion

We hypothesize that the nc886 imprint is established in the oocyte and that after implantation, the methylation status is stable, excluding a few specific tissues.
Inflammatory mediators act at renal pericytes to elicit contraction of vasa recta and reduce pericyte density along this medullary vascular network
Authors: Lilley Rebecca J. , Taylor Kirsti , Wildman Scott S.P. , Peppiatt-Wildman Claire M.
Published: June 2022

Regardless of initiating cause, renal injury promotes a potent pro-inflammatory environment in the outer medulla and a concomitant sustained decrease in medullary blood flow (MBF). This decline in MBF is believed to one of the critical events in the pathogenesis of acute kidney injury (AKI), yet the precise cellular mechanism underlying this are still to be fully elucidated. MBF is regulated by contractile pericyte cells that reside on the descending vasa recta (DVR) capillaries, which are the primary source of blood flow to the medulla. Using the rodent and murine live kidney slice models, we sought to investigate the acute effects of key medullary inflammatory mediators TNF-α, IL-1β, IL-33, IL-18, C3a and C5a on vasa recta pericytes. Live kidney slices taken from both mice and rats and exposed to TNF-α, IL-18, IL-33, and C5a demonstrated a real-time pericyte-mediated constriction of DVR. When pro-inflammatory mediators were applied in the presence of the AT1-R blocker Losartan the inflammatory-mediated constriction that had previously been observed was significantly attenuated. When live kidney slices were exposed to inflammatory mediators for 4-hours, we noted a significantly reduction in the number of NG2+ positive pericytes along vasa recta capillaries in both rodent and murine kidney slices. Data collected in this study, demonstrate that inflammatory mediators can dysregulate pericytes to constrict DVR diameter and reduce the density of pericytes along vasa recta vessels, further diminishing the regulatory capacity of the capillary network. We postulate that preliminary findings here suggest pericytes play a role in AKI.

New & Noteworthy

How medullary blood flow (MBF) becomes disproportionately dysregulated following renal injury is poorly understood yet is associated with worse prognostic outcomes following AKI. This study shows in both rats and mice that inflammatory mediators associated with AKI have acute and sustained microvascular actions at pericytes eliciting dysregulation of descending vasa recta (DVR) diameter and their loss from the DVR. This work highlights a possible pathology behind the dysregulation and reduction of MBF observed following AKI.
In search of a dynamical vocabulary: a pipeline to construct a basis of shared traits in large-scale motions of proteins
Authors: Tarenzi Thomas , Mattiotti Giovanni , Rigoli Marta , Potestio Raffaello
Published: June 2022

The paradigmatic sequence-structure-dynamics-function relation in proteins is nowadays well established in the scientific community; in particular, large effort has been spent to probe the first connection, indeed providing convincing evidence of its strength and rationalising it in a quantitative and general framework. In contrast, however, the role of dynamics as a link between structure and function has eluded a similarly clear-cut verification and description. In this work, we propose a pipeline aimed at building a basis for the quantitative characterisation of the large-scale dynamics of a set of proteins, starting from the sole knowledge of their native structures. The method hinges on a dynamics-based clusterization, which allows a straightforward comparison with structural and functional protein classifications. The resulting basis set, obtained through the application to a group of related proteins, is shown to reproduce the salient large-scale dynamical features of the dataset. Most interestingly, the basis set is shown to encode the fluctuation patterns of homologous proteins not belonging to the initial dataset, thus highlighting the general applicability of the pipeline used to build it.
Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired
Authors: LaSarre Breah , Morlen Ryan , Neumann Gina C. , Harwood Caroline S. , McKinlay James B.
Published: June 2022

Denitrification is a form of anaerobic respiration wherein nitrate (NO3-) is sequentially reduced via nitrite (NO2-), nitric oxide, and nitrous oxide (N2O) to dinitrogen gas (N2) by four reductase enzymes. Partial denitrifying bacteria possess only one, or some, of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here we tested the denitrifying capabilities of two purple nonsulfur bacteria,Rhodopseudomonas palustrisCGA0092 andRhodobacter capsulatusSB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO2-to N2and SB1003 reduced N2O to N2. For each bacterium, N2O reduction could be used for both electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in the dark. However, N2O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO3-served as a stable, non-catalyzable molecule that was sufficient to activate N2O reduction. Using a β-galactosidase reporter we found that NO3-acted, at least in part, by stimulating N2O reductase gene expression. In SB1003, NO2-, but not NO3-, activated N2O reduction but NO2-was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use.

Importance

Denitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions.
Transcriptional profiling of Hutchinson-Gilford Progeria syndrome fibroblasts reveals deficits in mesenchymal stem cell commitment to differentiation related to early events in endochondral ossification
Authors: Martin Rebeca San , Das Priyojit , Sanders Jacob T. , Hill Ashtyn , McCord Rachel Patton
Published: June 2022

Hutchinson-Gilford Progeria Syndrome results from a mutation in Lamin A, and it is characterized by the incorporation of progerin into the nuclear lamina. Progerin expression leads to alterations in genome architecture, nuclear morphology, and epigenetic states, which in turn cause altered phenotypes in all cells of the mesenchymal lineage. Here, we report a comprehensive analysis of the transcriptional status of patient derived HGPS fibroblasts, including nine cell lines not previously reported. We observe that these fibroblasts carry abnormal transcriptional signatures, centering around five main functional hubs: DNA maintenance and epigenetics, bone development and homeostasis, blood vessel maturation and development, fat deposition and lipid management, and processes related to muscle growth. Stratification of patients by age revealed that a cohort of genes related to endochondral ossification and chondrogenic commitment show altered expression patterns in children aged four to seven years old, where this differentiation program starts in earnest, related to the growth of long bones. We further report changes in lamin associated domains and 3D genome organization around a cohort of genes of interest, identified in this study.
MicroProteins miP1b/BBX30 and miP1a/BBX31 form a positive feedback loop with ABI5 to retard seedling establishment
Authors: Singh Deeksha , Datta Sourav
Published: June 2022

In plants the switch to autotrophic growth involves germination followed by post-germination seedling establishment. When environmental conditions are not favorable, the stress hormone Abscisic Acid (ABA) signals plants to postpone seedling establishment by inducing the expression of the transcription factor ABI5. The levels of ABI5 determine the efficiency of the ABA mediated post-germination developmental growth arrest. The molecular mechanisms regulating the stability and activity of ABI5 during the transition to light are less known. We found that two microProteins miP1a/ BBX31 and miP1b/BBX30 alongwith ABI5 inhibit post-germination seedling establishment in a partially interdependent manner. MicroProteins are single-domain proteins that interact with multi-domain proteins to modulate their post-translational activity. miP1a/ BBX31 and miP1b/BBX30 physically interact with ABI5 to stabilize it and promote its binding to promoters of downstream genes in light. ABI5 reciprocally induces the expression ofBBX30andBBX31by directly binding to their promoter. ABI5 and the two microProteins thereby form a positive feedback loop to promote ABA-mediated developmental arrest of seedlings. Our study highlights the functional versatility of microProteins which can act as regulators of crucial developmental transitions in plants as well as other eukaryotes.
Tunnel dynamics of quinone derivatives and its coupling to protein conformational rearrangements in respiratory complex I
Authors: Lasham Jonathan , Haapanen Outi , Zickermann Volker , Sharma Vivek
Published: June 2022

Respiratory complex I in mitochondria and bacteria catalyzes the transfer of electrons from NADH to quinone (Q). The free energy available from the reaction is used to pump protons and to establish a membrane proton electrochemical gradient, which drives ATP synthesis. Even though several high-resolution structures of complex I have been resolved, how Q reduction is linked with proton pumping, remains unknown. Here, microsecond long molecular dynamics (MD) simulations were performed on Yarrowia lipolytica complex I structures where Q molecules have been resolved in the ~30 Å long Q tunnel. MD simulations of several different redox/protonation states of Q reveal the coupling between the Q dynamics and the restructuring of conserved loops and ion pairs. Oxidized quinone stabilizes towards the N2 FeS cluster, a binding mode not previously described in Yarrowia lipolytica complex I structures. On the other hand, reduced (and protonated) species tend to diffuse towards the Q binding sites closer to the tunnel entrance. Mechanistic and physiological relevance of these results are discussed.
The cohesin modifier ESCO2 is stable during DNA replication
Authors: Jevitt Allison M. , Rankin Brooke D. , Chen Jingrong , Rankin Susannah
Published: June 2022

Cohesion between sister chromatids by the cohesin protein complex ensures accurate chromosome segregation and enables recombinational DNA repair. Sister chromatid cohesion is promoted by acetylation of the SMC3 subunit of cohesin by the ESCO2 acetyltransferase, inhibiting cohesin release from chromatin. The interaction of ESCO2 with the DNA replication machinery, in part through PCNA-interacting protein (PIP) motifs in ESCO2, is required for full cohesion establishment. Recent reports have suggested that Cul4-dependent degradation regulates the level of ESCO2 protein during late S/G2 phase of the cell cycle. To follow up on these observations, we have characterized ESCO2 stability in Xenopus egg extracts, a cell-free system that recapitulates cohesion establishment in vitro. We found that ESCO2 was stable during DNA replication in this system. Indeed, further challenging the system by inducing DNA damage signaling or increasing the number of nuclei undergoing DNA replication had no significant impact on the stability of ESCO2. In transgenic somatic cell lines, we did not see evidence of GFP-ESCO2 degradation during S phase of the cell cycle using either flow cytometry or live-cell imaging techniques. We conclude that ESCO2 is stable during DNA replication in both embryonic and somatic cells.
Antibodies to protozoan variable surface antigens induce antigenic variation
Authors: Tenaglia Albano H. , Luján Lucas A. , Ríos Diego N. , Midlej Victor , Iribarren Paula A. , Molina Cecilia R. , Berazategui M. Agustina , Torri Alessandro , Saura Alicia , Peralta Damián O. , Rodríguez-Walker Macarena , Fernández Elmer A. , Petiti Juan P. , Serradell Marianela C. , Gargantini Pablo R. , Alvarez Vanina E. , de Souza Wanderley , Luján Hugo D.
Published: June 2022

The genomes of most protozoa encode families of variant surface antigens, whose mutually exclusive changes in expression allow parasitic microorganisms to evade the host immune response1,2. It is widely assumed that antigenic variation in protozoan parasites is accomplished by the spontaneous appearance within the population of cells expressing antigenic variants that escape antibody-mediated cytotoxicity1,2. Here we show, bothin vitroand in animal infections, that antibodies to Variant-specific Surface Proteins (VSPs) of the intestinal parasiteGiardia lambliaare not cytotoxic, inducing instead VSP clustering into liquid-ordered phase membrane microdomains that trigger a massive release of microvesicles carrying the original VSP and switch in expression to different VSPs by a calcium-dependent mechanism. Surface microvesiculization and antigenic switching are also stimulated whenTrypanosoma bruceiandTetrahymena thermophilaare confronted to antibodies directed to their GPI-anchored variable surface glycoproteins. This novel mechanism of surface antigen clearance throughout its release into microvesicles coupled to the stochastic induction of new phenotypic variants not only changes the current paradigm of spontaneous antigenic switching but also provides a new framework for understanding the course of protozoan infections as a host/parasite adaptive process.
Calcium dependence of both lobes of calmodulin is involved in binding to a cytoplasmic domain of SK channels
Authors: Halling D. Brent , Philpo Ashley E. , Aldrich Richard W.
Published: June 2022

KCa2.1-3 Ca2+-activated K+-channels (SK) require calmodulin to gate in response to cellular Ca2+. A model for SK gating proposes that the N-terminal domain (N-lobe) of calmodulin is required for activation, but an immobile C-terminal domain (C-lobe) has constitutive, Ca2+-independent binding. Although structures support a domain-driven hypothesis of SK gate activation by calmodulin, only a partial understanding is possible without measuring both channel activity and protein binding. We measured SK2 (KCa2.2) activity using inside-out patch recordings. Currents from calmodulin-disrupted SK2 channels can be restored with exogenously applied calmodulin. We find that SK2 activity only approaches full activation with full-length calmodulin with both an N- and C-lobe. We measured calmodulin binding to a C-terminal SK peptide (SKp) using both composition-gradient multi-angle light scattering and tryptophan emission spectra. Isolated lobes bind to SKp with high affinity, but isolated lobes do not rescue SK2 activity. Consistent with earlier models, N-lobe binding to SKp is stronger in Ca2+, and C-lobe binding affinity is strong independent of Ca2+. However, a native tryptophan in SKp is sensitive to Ca2+binding to both the N- and C-lobes of calmodulin at Ca2+concentrations that activate SK2, demonstrating that the C-lobe interaction with SKp changes with Ca2+. Our peptide binding data and electrophysiology show that SK gating models need deeper scrutiny. We suggest that the Ca2+-dependent associations of both lobes of calmodulin to SKp are crucial events during gating. Additional investigations are necessary to complete a mechanistic gating model consistent with binding, physiology, and structure.
Viral genetic determinants of prolonged respiratory syncytial virus infection among infants in a healthy term birth cohort
Authors: Lawless Dylan , McKennan Christopher G. , Das Suman R. , Junier Thomas , Xu Zhi Ming , Anderson Larry J , Gebretsadik Tebeb , Shilts Meghan H. , Larkin Emma , Rosas-Salazar Christian , Chappell James D. , Fellay Jacques , Hartert Tina V.
Published: June 2022

1

Background

Respiratory syncytial virus (RSV) is associated with acute respiratory infection. We sought to identify RSV variants associated with prolonged infection.

Methods

Among healthy term infants we identified those with prolonged RSV infection and conducted 1) a human GWAS to test the dependence of infection risk on host genotype, 2) a viral GWAS for association with prolonged RSV infection using RSV whole-genome sequencing, 3) an analysis of all viral public sequences, 4) an assessment of immunological responses, and 5) a summary of all major functional data. Analyses were adjusted for viral/human population structure and host factors associated with infection risk.

Results

We identified p.E123K/D and p.P218T/S/L in G protein that were associated with prolonged infection (Padj= 0.01). We found no evidence of host genetic risk for infection. The RSV variant positions approximate sequences that could bind a putative viral receptor, heparan sulfate.

Conclusions

Using analysis of both viral and host genetics we identified a novel RSV variant associated with prolonged infection in healthy infants and no evidence supporting host genetic susceptibility to infection. As the capacity of RSV for chronicity and its viral reservoir are not defined, these findings are important for understanding the impact of RSV on chronic disease and endemicity.

Key points

Using a comprehensive computational analysis of viral and host genetics we identified a novel RSV variant associated with prolonged infection and no evidence supporting host genetic infection susceptibility, findings important to understanding RSV contribution to chronic disease and viral endemicity.

A comprehensive computational statistical analysis of both host and viral genetics provided compelling evidence for RSV viral persistence in healthy human infants, a finding of significant importance to understanding the impact of RSV on chronic disease and viral endemicity.
Mutational insights among the structural proteins of SARS-CoV-2: frequencies and evolutionary trends in American countries
Authors: Abavisani Mohammad , Rahimian Karim , Khayami Reza , Mollapour Sisakht Mahsa , Mahmanzar Mohammadamin , Meshkat Zahra
Published: June 2022

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a role in the mortality of more than 6 million people worldwide. This virus owns the genome, which contains four structural proteins, including spike (S), envelope (E), membrane (M), and nucleocapsid (N). The occurrence of structural mutations can induce the emergence of new variants. Depending on the mutations, the variants may display different patterns of infectivity, mortality, and sensitivity toward drugs and vaccines. In this study, we analyzed samples of amino-acid sequences (AASs) for structural proteins from the coronavirus 2019 (COVID-19) declaration as a pandemic to April 2022 among American countries. The analysis process included considering mutations’ frequencies, locations, and evolutionary trends utilizing sequence alignment to the reference sequence. In the following, the results were compared with the same analyses among the samples of the entire world. Results displayed that despite samples of North America and international countries that own the region of 508 to 635 with the highest mutation frequency among S AASs, the region with the same characteristic was concluded as 1 to 127 in South America. Besides, the most frequent mutations in S, E, M, and N proteins from North America and worldwide samples were concluded as D614G, T9I, I82T, and R203M. In comparison, R203K was the first frequent mutation in N samples in South America. Widely comparing mutations between North America and South America and between the Americas and the world can help scientists introduce better drug and vaccine development strategies.