bluuebunny/crossref_metadata_2025 huggingface dataset:
Four Individually Identified Paired Dopamine Neurons Signal Taste Punishment in LarvalDrosophila
Authors: Weber Denise , Vogt Katrin , Miroschnikow Anton , Pankratz Michael , Thum Andreas S.
Published: July 2023

Dopaminergic neurons (DANs) carry out multiple tasks in the brain, including the transmission of information related to rewards and punishments across various animal species. They are responsible for evaluating sensory input, storing resulting associations as memory, and continuously updating them based on their relevance and reliability. Accurate comprehension of the dopaminergic system’s operation necessitates an understanding of the specific functions mediated by individual DANs. To this end, our research employsDrosophilalarvae, which possess approximately 12,000 neurons in their brains, of which only around 1% (approximately 120) are DANs.

The presynaptic projections to the mushroom body (MB) - a brain region pivotal for associative olfactory learning in insects - are limited to only eight larval dopaminergic neurons. These DANs are further subdivided into two clusters: the primary protocerebral anterior medial cluster (pPAM) comprises four cells, and the dorsolateral 1 cluster (DL1) comprises the remaining four cells. Our findings confirm previous research that demonstrates that the pPAM DANs innervating the MB’s medial lobe encode for a gustatory sugar reward signal. Furthermore, we have identified four DANs in the DL1 cluster - DAN-c1, DAN-d1, DAN-f1, and DAN-g1 - each of which innervates distinct compartments of the MB peduncle, lateral appendix, and vertical lobe. Optogenetic activation of DAN-f1 and DAN-g1 alone suffices to substitute for punishment. Furthermore, optogenetic inhibition, calcium imaging results and electron microscopy-based reconstruction of all sensory input circuits to the four DL1 DANs demonstrate that each DAN encodes a different aspect of punishment, with DAN-g1 being of central importance for the salt dependent teaching signal.

To summarize, our investigation has revealed the existence of a cellular division of labor among larval DANs concerning the transmission of dopaminergic reward (pPAM cluster) and punishment signals (DL1 cluster). Individual DANs in each cluster encode for distinct but partially overlapping aspects of the teaching signal. The striking resemblance in the organizing principle of larval DANs with that of its adult counterpart and the mammalian basal ganglion suggests that there may be a limited number of efficient neural circuit solutions available to address more complex cognitive challenges in nature.
Functional analysis of Cdc20 reveals a critical role of CRY box in mitotic checkpoint signaling
Authors: Zhang Yuqing , Young Rose , Garvanska Dimitriya H , Song Chunlin , Zhai Yujing , Wang Ying , Jiang Hongfei , Fang Jing , Nilsson Jakob , Alfieri Claudio , Zhang Gang
Published: July 2023

Accurate chromosome segregation is coordinated by the spindle assembly checkpoint (SAC) through its effector the mitotic checkpoint complex (MCC), to inhibit the anaphase-promoting complex or cyclosome (APC/C). Cdc20 is an essential mitotic regulator since it promotes mitotic exit through activating the APC/C and monitors kinetochore-microtubule attachment through activating the SAC. The proper functioning of Cdc20 requires multiple interactions with APC/C and MCC subunits. To functionally assess each of these interactions within cells requires efficient depletion of endogenous Cdc20, which is highly difficult to achieve by RNAi. Here we generated Cdc20 RNAi sensitive cell lines by CRISPR/Cas9 which display a penetrant metaphase arrest phenotype by a single RNAi treatment. In this null background, we accurately measured the contribution of each known motif of Cdc20 on APC/C and SAC activation. The CRY box, a previously identified degron was found to be critical for the SAC by promoting the MCC formation and stabilizing the interaction between the MCC and APC/C. These data reveal additional regulatory components within the SAC and establish a novel method to interrogate Cdc20 function.
Coordination of rhythmic RNA synthesis and degradation orchestrates 24-hour and 12-hour RNA expression patterns in mouse fibroblasts
Authors: Unruh Benjamin A. , Weidemann Douglas E. , Kojima Shihoko
Published: July 2023

Circadian RNA expression is essential to ultimately regulate a plethora of downstream rhythmic biochemical, physiological, and behavioral processes. Both transcriptional and post transcriptional mechanisms are considered important to drive rhythmic RNA expression, however, the extent to which each regulatory process contributes to the rhythmic RNA expression remains controversial. To systematically address this, we monitored RNA dynamics using metabolic RNA labeling technology during a circadian cycle in mouse fibroblasts. We find that rhythmic RNA synthesis is the primary contributor of 24 hr RNA rhythms, while rhythmic degradation is more important for 12 hr RNA rhythms. These rhythms were predominantly regulated byBmal1and/or the core clock mechanism, and interplay between rhythmic synthesis and degradation has a significant impact in shaping rhythmic RNA expression patterns. Interestingly, core clock RNAs are regulated by multiple rhythmic processes and have the highest amplitude of synthesis and degradation, presumably critical to sustain robust rhythmicity of cell-autonomous circadian rhythms. Our study yields invaluable insights into the temporal dynamics of both 24 hr and 12 hr RNA rhythms in mouse fibroblasts.
Sexual coordination in a whole-brain map of prairie vole pair bonding
Authors: Gustison Morgan L. , Muñoz-Castañeda Rodrigo , Osten Pavel , Phelps Steven M.
Published: July 2023

Sexual bonds are central to the social lives of many species, including humans, and monogamous prairie voles have become the predominant model for investigating such attachments. We developed an automated whole-brain mapping pipeline to identify brain circuits underlying pair-bonding behavior. We identified bonding-related c-Fos induction in 68 brain regions clustered in seven major brain-wide neuronal circuits. These circuits include known regulators of bonding, such as the bed nucleus of the stria terminalis, paraventricular hypothalamus, ventral pallidum, and prefrontal cortex. They also include brain regions previously unknown to shape bonding, such as ventromedial hypothalamus, medial preoptic area and the medial amygdala, but that play essential roles in bonding-relevant processes, such as sexual behavior, social reward and territorial aggression. Contrary to some hypotheses, we found that circuits active during mating and bonding were largely sexually monomorphic. Moreover, c-Fos induction across regions was strikingly consistent between members of a pair, with activity best predicted by rates of ejaculation. A novel cluster of regions centered in the amygdala remained coordinated after bonds had formed, suggesting novel substrates for bond maintenance. Our tools and results provide an unprecedented resource for elucidating the networks that translate sexual experience into an enduring bond.
Diversity and biotechnological potential of filamentous fungi isolated from sediments of Basque estuaries
Authors: Otamendi A. , Agirrezabala Z. , Perez-Cruz C. , Liébana R. , Berregi I. , Alonso-Sáez L. , Dueñas M.T. , Lanzén A. , Etxebeste O.
Published: July 2023

Marine environments harbor a vast diversity of microorganisms, which have developed multiple strategies to adapt to stress conditions such as high salt concentrations and nutrient scarcity and, thus, are a source of natural products and high-value enzymes, as they have the ability to degrade complex polymeric substrates. These features make marine microorganisms a valuable source for the development of new biotechnological tools. Here, we focused on the isolation of filamentous fungi, using sediment samples collected from estuaries of the Basque Country in the Bay of Biscay. The phenotype of these isolates was characterized based on the potential to grow on complex marine polysaccharides or to secrete pigments to the culture medium. Based on this screening, the genomes of two isolates of the order Hypocreales,Marquandomyces marquandiiandAlbophoma yamanashiensis, were sequenced and are described here for the first time. The analysis of their CAZYme (carbohydrate-active enzyme) and secondary metabolite gene-cluster repertoires suggest that these estuarine isolates could be used as a source of novel enzymatic activities and secondary metabolites.

One-sentence summary

Isolation and characterization of filamentous fungi from sediments of Basque estuaries and an assessment of their biotechnological potential.

Importance

Marine microbes are considered an unlimited source of molecules for biotechnology in fields such as pharmaceutics, biomedicine, cosmetics, nutraceutics, food, feed or agriculture. Thus, it is believed that blue biotechnology will make a significant contribution to the sustainability of global economy. However, the study of marine fungi lags behind that of marine bacteria and it is considered that the potential impact of fungi at the biotechnological level is underestimated. In this work, filamentous fungi from sediment samples of estuaries of the Basque Country have been isolated and the genomes of the Sordariomycete fungiMarquandomyces marquandiiandAlbophoma yamanashiensissequenced and analyzed. Their characterization will contribute to the inventory of the genomic diversity within filamentous fungi and the identification of species and activities with biotechnological potential.
Investigating Brain Alterations in the Dp1Tyb Mouse Model of Down Syndrome
Authors: Serrano Maria Elisa , Kim Eugene , Siow Bernard , Ma Da , Rojo Loreto , Simmons Camilla , Hayward Darryl , Gibbins Dorota , Singh Nisha , Strydom Andre , Fisher Elizabeth M. C. , Tybulewicz Victor L. J. , Cash Diana
Published: July 2023

Down syndrome (DS) is one of the most common birth defects and the most prevalent genetic form of intellectual disability. DS arises from trisomy of chromosome 21, but its molecular and pathological consequences are not fully understood. In this study, we compared Dp1Tyb mice, a DS model, against their wild-type (WT) littermates of both sexes to investigate the impact of DS-related genetic abnormalities on the brain phenotype.

We performedin vivowhole brain magnetic resonance imaging (MRI) and hippocampal1H magnetic resonance spectroscopy (MRS) on the animals at 3 months of age. Subsequently,ex vivoMRI scans and histological analyses were conducted post-mortem. Our findings unveiled distinct neuroanatomical and biochemical alterations in the Dp1Tyb brains.

Dp1Tyb brains exhibited a smaller surface area and a rounder shape compared to WT brains. Regional volumetric analysis revealed significant changes in 26 out of 72 examined brain regions, including the medial prefrontal cortex and dorsal hippocampus. These alterations were consistently observed in bothin vivoandex vivoimaging data. Additionally, high-resolutionex vivoimaging enabled us to investigate cerebellar layers and hippocampal subregions, revealing selective areas of decrease and remodelling in these structures.

An analysis of hippocampal metabolites revealed an elevation in glutamine and the glutamine/glutamate ratio in the Dp1Tyb mice compared to controls, suggesting a possible imbalance in the excitation/inhibition ratio. This was accompanied by the decreased levels of taurine. Histological analysis revealed fewer neurons in the hippocampal CA3 and DG layers, along with an increase in astrocytes and microglia. These findings recapitulate multiple neuroanatomical and biochemical features associated with DS, enriching our understanding of the potential connection between chromosome 21 trisomy and the resultant phenotype.
EEG-fMRI in awake rat and whole-brain simulations show decreased brain responsiveness to sensory stimulations during absence seizures
Authors: Stenroos Petteri , Guillemain Isabelle , Tesler Federico , Montigon Olivier , Collomb Nora , Stupar Vasile , Destexhe Alain , Coizet Véronique , David Olivier , Barbier Emmanuel L.
Published: July 2023

In patients suffering absence epilepsy, recurring seizures can significantly decrease their quality of life and lead to yet untreatable comorbidities. Absence seizures are characterized by spike-and- wave discharges on the electroencephalogram associated with a transient alteration of consciousness. However, it is still unknown how the brain responds to external stimuli during and outside of seizures.

This study aimed to investigate responsiveness to visual and somatosensory stimulation in GAERS, a well-established rat model for absence epilepsy. Animals were imaged under non-curarized awake state using a quiet, zero-echo-time, functional magnetic resonance imaging (fMRI) sequence. Sensory stimulations were applied during interictal and ictal periods. Whole brain hemodynamic responses were compared between these two states. Additionally, a mean-field simulation model was used to explain the changes of neural responsiveness to visual stimulation between states.

During a seizure, whole-brain responses to both sensory stimulations were suppressed and spatially hindered. In the cortex, hemodynamic responses were negatively polarized during seizures, despite the application of a stimulus. The mean-field simulation revealed restricted propagation of activity due to stimulation and agreed well with fMRI findings. Results suggest that sensory processing is hindered or even suppressed by the occurrence of an absence seizure, potentially contributing to decreased responsiveness during this absence epileptic process.
Tillering structures the genetic variability of wheat vegetative growth and its plasticity under water deficit
Authors: Leveau Stéphane , Parent Boris , Giunta Francesco , Luchaire Nathalie , Cabrera-Bosquet Llorenç , Beauchêne Katia , Jezequel Stéphane , Motzo Rosella , Martre Pierre
Published: July 2023

Leaf expansion under drought drives the trade-off between water saving for later grain production and canopy photosynthesis. Fine-tuning leaf expansion could therefore become a target of genetic progress for drought-prone environments. However, its components (branching, leaf production and elongation) may have their own genetic variability and plasticity under drought, making hard to calibrate crop simulation models and specify breeding targets. In this study, we focused on the genetic diversity of bread wheat and durum wheat to determine the links and trade-offs between the underlying processes of leaf growth under drought and how it translates to leaf expansion at the whole plant and canopy level. For that, we used non-destructive imaging both in the field and controlled condition platforms to determine the dynamics of the components of shoot expansion and analyze their relative contribution to the genetic variability of whole-plant shoot expansion under drought. Results show that leaf expansion measured at plant level in controlled environment was associated with that measured at canopy level in the field, indicating that controlled phenotyping platforms can capture the genetic variability of growth in the field. Both whole-plant and canopy expansion were associated with tillering rate. In addition, the sensitivity of shoot growth and tillering to soil water deficit were correlated, indicating that both tillering ability and sensitivity to water deficit drive the genetic variability of shoot expansion. Overall, dissecting leaf expansion dynamics allowed determining the links between shoot expansion traits under drought, and provides key targets in phenotyping, modelling and breeding for drought environments.
Acquisition of drug resistance in basal cell nevus syndrome tumors through basal to squamous cell carcinoma transition
Authors: Jussila Anna R. , Haensel Daniel , Gaddam Sadhana , Oro Anthony E.
Published: July 2023

While basal cell carcinomas (BCCs) arise from ectopic hedgehog pathway activation and can be treated with pathway inhibitors, sporadic BCCs display high resistance rates while tumors arising in Gorlin syndrome patients with germline Patched (PTCH1) mutations are uniformly suppressed by inhibitor therapy. In rare cases, Gorlin syndrome patients on long-term inhibitor therapy will develop individual resistant tumor clones that rapidly progress, but the basis of this resistance remains unstudied. Here we report a case of an SMOi-resistant tumor arising in a Gorlin patient on suppressive SMOifor nearly a decade. Using a combination of multi-omics and spatial transcriptomics, we define the tumor populations at the cellular and tissue level to conclude that Gorlin tumors can develop resistance to SMOithrough the previously described basal to squamous cell carcinoma transition (BST). Intriguingly, through spatial whole exome genomic analysis, we nominate PCYT2, ETNK1, and the phosphatidylethanolamine biosynthetic pathway as novel genetic suppressors of BST resistance. These observations provide a general framework for studying tumor evolution and provide important clinical insight into mechanisms of resistance to SMOifor not only Gorlin syndrome but sporadic BCCs as well.
Cytokinins control secondary cell wall formation in the inflorescence stem of Arabidopsis
Authors: Didi Vojtech , Arnaud Dominique , Pacinková Anna , Jupa Radek , Cegan Radim , Melnikava Alesia , Vasickova Jana , Benitez Mariana , Unda Faride , Dobisova Tereza , Riber Willi , Dostalova Zuzana , Mansfield Shawn D. , Novak Ondrej , Strnad Miroslav , Hobza Roman , Gloser Vít , Budinska Eva , Hejatko Jan
Published: July 2023

Spatiotemporal control over developmental programs is vital to all organisms. Here we show that cytokinin (signaling) deficiency leads to early secondary cell wall (SCW) formation in Arabidopsis inflorescence stem that associates with precocious upregulation of a SCW transcriptional cascade controlled by NAC TFs (NSTs). We demonstrate that cytokinin signaling through the AHK2/3 and the ARR1/10/12 suppresses the expression of severalNSTsand SCW formation in the apical portions of stems. Exogenous cytokinin application reconstituted both proper development and apical-basal gradient ofNST1andNST3in a cytokinin biosynthesis-deficient mutant. We show thatAHK2andAHK3required functionalNST1orNST3to control SCW initiation in the interfascicular fibers, further evidencing that cytokinins act upstream ofNSTs transcription factors. The premature onset of a rigid SCW biosynthesis and altered expression ofNST1/3andVND6/7due to cytokinin deficiency led to the formation of smaller tracheary elements (TEs) and impaired hydraulic conductivity. We conclude that cytokinins downregulateNSTsto inhibit premature SCW formation in the apical part of the inflorescence stem, facilitating thus the development of fully functional TEs and interfascicular fibers.

Summary statement

Cytokinins attenuate premature secondary cell wall (SCW) formation via downregulating the expression of NAC TFs, the master switches of SCW transcriptional cascade, thus affecting the tracheary elements size and conductivity.
Megakaryocyte maturation involves activation of the adaptive unfolded protein response
Authors: Faiz M. , Kalev-Zylinska M.L , Dunstan-Harrison C. , Singleton D.C , Hay M.P. , Ledgerwood E.C.
Published: July 2023

Endoplasmic reticulum stress triggers the unfolded protein response (UPR) to promote cell survival or apoptosis. Transient endoplasmic reticulum stress activation has been reported to trigger megakaryocyte production, and UPR activation has been reported as a feature of megakaryocytic cancers. However, the role of UPR signaling in megakaryocyte biology is not fully understood. We studied the involvement of UPR in human megakaryocytic differentiation using PMA (phorbol 12-myristate 13-acetate)-induced maturation of megakaryoblastic cell lines and thrombopoietin-induced differentiation of human peripheral blood-derived progenitors. Our results demonstrate that an adaptive UPR is a feature of megakaryocytic differentiation, and that this response is not associated with ER stress-induced apoptosis. Differentiation did not alter the response to the canonical endoplasmic reticulum stressors DTT or thapsigargin. However, thapsigargin, but not DTT, inhibited differentiation, consistent with the involvement of Ca2+signaling in megakaryocyte differentiation.
Drug screening in human physiologic medium identifies uric acid as an inhibitor of rigosertib efficacy
Authors: Rawat Vipin , DeLear Patrick , Prashanth Prarthana , Ozgurses Mete Emir , Tebeje Anteneh , Burns Philippa A. , Conger Kelly O. , Solís Christopher , Hasnain Yasir , Novikova Anna , Endress Jennifer E. , González-Sánchez Paloma , Dong Wentao , Stephanopoulos Greg , DeNicola Gina M. , Harris Isaac S. , Sept David , Mason Frank M. , Coloff Jonathan L.
Published: July 2023

The non-physiological nutrient levels found in traditional culture media have been shown to affect numerous aspects of cancer cell physiology, including how cells respond to certain therapeutic agents. Here, we comprehensively evaluated how physiological nutrient levels impact therapeutic response by performing drug screening in human plasma-like medium (HPLM). We observed dramatic nutrient-dependent changes in sensitivity to a variety of FDA-approved and clinically trialed compounds, including rigosertib, an experimental cancer therapeutic that has recently failed in phase 3 clinical trials. Mechanistically, we found that the ability of rigosertib to destabilize microtubules is strongly inhibited by the purine metabolism waste product uric acid, which is uniquely abundant in humans relative to traditionalin vitroandin vivocancer models. Structural modelling studies suggest that uric acid interacts with the tubulin-rigosertib complex and may act as an uncompetitive inhibitor of rigosertib. These results offer a possible explanation for the failure of rigosertib in clinical trials and demonstrate the utility of physiological media to achievein vitroresults that better represent human therapeutic responses.
Life and death in Trypillia times: Interdisciplinary analyses of the exceptional human remains from the settlement of Kosenivka, Ukraine (3700–3600 BCE)
Authors: Fuchs Katharina , Hofmann Robert , Shatilo Liudmyla , Schlütz Frank , Storch Susanne , Chabanyuk Vladislav , Kirleis Wiebke , Müller Johannes
Published: July 2023

We present an interdisciplinary analysis of finds from the Trypillia settlement of Kosenivka, Ukraine (ca. 3700–3600 BCE, Trypillia C1), that links information on human, faunal, and botanical remains with archaeological data to provide exceptionally detailed insights into life and death at a Trypillia mega-site. We obtained osteological, palaeopathological, and histotaphonomic data from human bone fragments; performed carbon and nitrogen stable isotopic analysis of human and animal bone to calculate food webs with the software FRUITS; and modelled newly generated radiocarbon dates to refine the site’s chronology. The biological profile of seven identified individuals, some of whom suffered from disease symptoms common in the Chalcolithic, represents a demographic cross-section of the population. The analysis of perimortem cranial trauma suffered by two individuals suggest cases of interpersonal conflict. Food web calculations demonstrate the large contribution of cereals to the protein component of the human diet, which is supported by dental observations, and we suggest that livestock were a major manure producer for crop cultivation.

The most probable scenario for the formation of the Kosenivka find assemblage is a deathly fire event. This makes the site a rare example where the archaeological and osteological results can be used to reconstruct a minimum number of house inhabitants. Following a literature review, we contextualise our analysis by discussing the general lack of human remains from Early and Middle Trypillia sites. The individuals from Kosenivka form part of the less than 0.05% of the total estimated Trypillia population that is represented skeletally; its members were deposited within settlements in the Middle Trypillia stage (until C1), preceding the shift to extramural burials in its late phase (C2).

Our detailed results indicate the huge explanatory potential that has yet to be unlocked in the rare and often poorly preserved bioarchaeological archives of the Cucuteni–Trypillia phenomenon.
BRCA1 and BRCA2 germline mutations driven signaling pathway alterations are sufficient to initiate breast tumorigenesis by the PIK3CAH1047Roncogene
Authors: Bhat-Nakshatri Poornima , Khatpe Aditi , Chen Duojiao , Batic Katie , Mang Henry , Herodotou Christopher , McGuire Patrick C. , Xuei Xiaoling , Gao Hongyu , Liu Yunlong , Sandusky George , Storniolo Anna Maria , Nakshatri Harikrishna
Published: July 2023

Single cell transcriptomics studies have begun to identify breast epithelial cell and stromal cell specific transcriptome differences between BRCA1/2 mutation carriers and non-carriers. We generated a single cell transcriptome atlas of breast tissues from BRCA1, BRCA2 mutation carriers and compared this single cell atlas of mutation carriers with our previously described single cell breast atlas of healthy non-carriers. We observed that BRCA1 but not BRCA2 mutations altered the ratio between basal, luminal progenitor and mature luminal cells in breast tissues. A unique subcluster of cells within luminal progenitors is underrepresented in case of BRCA1 and BRCA2 mutation carriers compared to non-carriers. Both BRCA1 and BRCA2 mutations specifically altered transcriptomes in epithelial cells which are an integral part of NF-κB, LARP1, and MYC signaling. Reduction of MYC signaling and translational machinery in BRCA1/2 mutant epithelial cells is reminiscent of embryonic diapause-like adaptation that occurs in drug tolerant populations of cells. Signaling pathway alterations in epithelial cells unique to BRCA1 mutations included STAT3, BRD4, SMARCA4, HIF2A/EPAS1, and Inhibin-A signaling. BRCA2 mutations were associated with upregulation of IL-6, PDK1, FOXO3, and TNFSF11 signaling. These signaling pathway alterations are sufficient to alter sensitivity of BRCA1/BRCA2-mutant breast epithelial cells to transformation as epithelial cells from BRCA1 mutation carriers overexpressing hTERT + PIK3CAH1047Rgenerated adenocarcinomas, whereas similarly modified mutant BRCA2 cells generated basal carcinomas in NSG mice. Thus, our studies provide a high-resolution transcriptome atlas of breast epithelial cells of BRCA1 and BRCA2 mutation carriers and reveal their susceptibility to PIK3CA mutation-driven transformation.

Statement of Significance

This study provides a single cell atlas of breast tissues of BRCA1/2 mutation carriers and demonstrates that aberrant signaling due to BRCA1/2 mutations sufficient to initiate breast cancer by mutant PIK3CA.
A Proxitome–RNA–capture Approach Reveals that Processing Bodies Repress Co–Regulated Hubs
Authors: Liu Chen , Mentzelopoulou Andriani , Hatzianestis Ioannis H. , Tzagkarakis Epameinondas , Scaltsoyiannes Vassilis , Ma Xuemin , Michalopoulou Vassiliki A. , Romero–Campero Francisco J. , Romero–Losada Ana B. , Sarris Panagiotis F. , Marhavy Peter , Bölter Bettina , Kanterakis Alexandros , Gutierrez–Beltran Emilio , Moschou Panagiotis N.
Published: July 2023

Cellular condensates are usually ribonucleoprotein assemblies with liquid– or solid–like properties. Because they lack a delineating membrane, the compositional determination of condensates is laborious. Here we set up a pipeline for proximity–biotinylation–dependent capture of RNA to investigate the RNA composition of the condensate in Arabidopsis known as the processing bodies (PBs). Using this pipeline together within situprotein–protein interaction and RNA detection,in silico, and high–resolution imaging approaches, we studied PBs under normal and heat stress conditions. The composition of PBs in RNAs is much more dynamic than that of the total transcriptome. RNAs involved in cell wall development and regeneration, hormonal signaling, secondary metabolism/defense, and RNA metabolism were enriched in PBs. RNA binding proteins and liquid–to–solid phase transitions modulated specificity of RNA recruitment in PBs. Surprisingly, RNAs were sometimes recruited together with their encoded proteins. In PBs RNAs follow distinct fates, with small liquid-like PBs modulating RNA decay while larger ones storage. The size and properties of PBs are regulated by the actin polymerization cAMP receptor (SCAR)–WASP family verprolin homologous (WAVE) complex. SCAR/WAVE modulates signaling by shuttling RNAs between PBs and the translational machinery adjusting the ethylene signaling pathway. Heat stress leads to the storage of immunity–related RNAs in PBs by reducing PBs dynamics, suggesting why processes such as immunity malfunction under heat stress. In summary, we provide a method to identify RNAs in condensates which allowed us to reveal a mechanism for RNA fate regulation.
Self-targeting spacers reveal new functions of CRISPR systems
Authors: Tangarife Cardona Miguel Angel , Arboleda Rivera Juan Camilo
Published: July 2023

The CRISPR systems enable bacteria and archaea to defend from bacteriophages or mobile genetic elements by inserting portions of the DNA of these elements into its own genome in sequences known as spacers that will later trigger the complementarity-based degradation of invading sequences. The presence of self-targeting spacers is widespread in prokaryotes; however, its functional role is still unclear. In this study, we analyzed self-targeting spacers of CRISPR systems and found a high presence of membrane proteins, aminoacyl-tRNA synthetases and ATP-binding proteins. This is a novel report that supports other research linking CRISPR systems to membrane proteins and could explain the reported relationships between antibiotic resistance and presence of CRISPR systems.
A zebrafish model for studying mechanisms of newborn hyperbilirubinemia and bilirubin induced neurological damage
Authors: Guzelkaya Metehan , Onal Ebru , Gelinci Emine , Kumral Abdullah , Cakan-Akdogan Gulcin
Published: July 2023

Unresolved neonatal hyperbilirubinemia may lead to accumulation of excess bilirubin in the body, and bilirubin in the neural tissues may induce toxicity. Bilirubin induced neurological damage (BIND) can result in acute or chronic bilirubin encephalopathy, causing temporary or lasting neurological dysfunction or severe damage resulting in infant death. Although serum bilirubin levels are used as an indication of severity, known and unknown individual differences affect the severity of the symptoms. The mechanisms of BIND have not been fully understood yet. Here, a zebrafish newborn hyperbilirubinemia model is developed and characterized. Direct exposure to excess bilirubin induced dose and time dependent toxicity linked to the accumulation of bilirubin in the body and brain. Introduced bilirubin was processed by liver which increased the tolerance of larvae. BIND in larvae was demonstrated by morphometric measurements, histopathological analyses and functional tests. The larvae that survived hyperbilirubinemia displayed mild or severe morphologies associated with defects in eye movements, body posture and swimming problems. Interestingly, the plethora of mild to severe clinical symptoms were reproduced in the zebrafish model.

Summary statement

This alternative newborn hyperbilirubinemia model in zebrafish, reports detailed analyses of bilirubin toxicity, recovery, and bilirubin induced neurological damage in varying degrees. Various clinical symptoms of BIND is successfully reproduced.
LipidSIM: inferring mechanistic lipid biosynthesis perturbations from lipidomics with a flexible, low-parameter, systematic Markov Modeling framework
Authors: Liang Chenguang , Murray Sue , Li Yang , Lee Richard , Low Audrey , Sasaki Shruti , Chiang Austin W.T. , Lin Wen-Jen , Mathews Joel , Barnes Will , Lewis Nathan E.
Published: July 2023

Lipid metabolism is a complex and dynamic system involving numerous enzymes at the junction of multiple metabolic pathways. Disruption of these pathways leads to systematic dyslipidemia, a hallmark of many pathological developments, such as nonalcoholic steatohepatitis and diabetes. Recent advances in computational tools can provide insights into the dysregulation of lipid biosynthesis, but limitations remain due to the complexity of lipidomic data, limited knowledge of interactions among involved enzymes, and technical challenges in standardizing across different lipid types. In this study, we present a low-parameter, biologically interpretable framework named Lipid Synthesis Investigative Markov model (LipidSIM), which models and predicts the source of perturbations in lipid biosynthesis from lipidomic data. LipidSIM achieves this by accounting for the interdependency between the lipid species via the lipid biosynthesis network and generates testable hypotheses regarding changes in lipid biosynthetic reactions. This feature allows the integration of lipidomics with other omics types, such as transcriptomics, to elucidate the direct driving mechanisms of altered lipidomes due to treatments or disease progression. To demonstrate the value of LipidSIM, we first applied it to hepatic lipidomics followingKeap1knockdown and found changes in mRNA expression of the lipid pathways were consistent with the LipidSIM-predicted fluxes. Second, we used it to study lipidomic changes following intraperitoneal injection of CCl4to induce fast NAFLD/NASH development and the progression of fibrosis and hepatic cancer. Finally, to show the power of LipidSIM for classifying samples with dyslipidemia, we used aDgat2-knockdown study dataset. Thus, we show that as it demands noa prioriknowledge of enzyme kinetics, LipidSIM is a valuable and intuitive framework for extracting biological insights from complex lipidomic data.
TRPV1 controls innate immunity duringCitrobacter rodentiumenteric infection
Authors: Cremin Michael , Tay Emmy , Ramirez Valerie T. , Murray Kaitlin , Nichols Rene K. , Brust-Mascher Ingrid , Reardon Colin
Published: July 2023

Mucosal immunity is critical to host protection from enteric pathogens and must be carefully controlled to prevent immunopathology. Regulation of immune responses can occur through a diverse range of mechanisms including bi-directional communication with the neurons. Among which include specialized sensory neurons that detect noxious stimuli due to the expression of transient receptor potential vanilloid receptor 1 (TRPV1) ion channel and have a significant role in the coordination of host-protective responses to enteric bacterial pathogens. Here we have used the mouse-adapted attaching and effacing pathogenCitrobacter rodentiumto assess the specific role of the TRPV1 channel in coordinating the host response. TRPV1 knockout (TRPV1-/-) mice had a significantly higherC. rodentiumburden in the distal colon and fecal pellets compared to wild-type (WT) mice. Increased bacterial burden was correlated with significantly increased colonic crypt hyperplasia and proliferating intestinal epithelial cells in TRPV1-/-mice compared to WT. Despite the increasedC. rodentiumburden and histopathology, the recruitment of colonic T cells producing IFNγ, IL-17, or IL-22 was similar between TRPV1-/-and WT mice. In evaluating the innate immune response, we identified that colonic neutrophil recruitment inC. rodentiuminfected TRPV1-/-mice was significantly reduced compared to WT mice; however, this was independent of neutrophil development and maturation within the bone marrow compartment. TRPV1-/-mice were found to have significantly decreased expression of the neutrophil-specific chemokineCxcl6and the adhesion moleculesIcam1in the distal colon compared to WT mice. Corroborating these findings, a significant reduction in ICAM-1 and VCAM-1, but not MAdCAM-1 protein on the surface of colonic blood endothelial cells fromC. rodentiuminfected TRPV1-/-mice compared to WT was observed. These findings demonstrate the critical role of TRPV1 in regulating the host protective responses to enteric bacterial pathogens, and mucosal immune responses.

Author Summary

Neuroimmune communications are vital in regulating the immune response to invading pathogens. Here, we show that during a gastrointestinal infection, pain-sensing neuronal fibers can modulate the immune response to recruit phagocytic neutrophils via upregulation of cell adhesion molecules on local blood endothelial cells. This research elucidates a novel impact of the pain-sensing ion channel, TRPV1, on host-pathogen interactions in the gastrointestinal tract as well as a potential methodology for modulating the immune response during enteric infections.
Phosphate starvation decouples cell differentiation from DNA replication control in the dimorphic bacteriumCaulobacter crescentus
Authors: Hallgren Joel , Koonce Kira , Felletti Michele , Mortier Julien , Turco Eloisa , Jonas Kristina
Published: July 2023

Upon nutrient depletion, bacteria stop proliferating and undergo physiological and morphological changes to ensure their survival. Yet, how these processes are coordinated in response to distinct starvation conditions is poorly understood. Here we compare the cellular responses ofCaulobacter crescentusto carbon (C), nitrogen (N) and phosphorus (P) starvation conditions. We find that DNA replication initiation and abundance of the replication initiator DnaA are, under all three starvation conditions, regulated by a common mechanism involving the inhibition of DnaA translation. By contrast, cell differentiation from a motile swarmer cell to a sessile stalked cell is regulated differently under the three starvation conditions. During C and N starvation, production of the signaling molecules (p)ppGpp is required to arrest cell development in the motile swarmer stage. By contrast, our data suggest that low (p)ppGpp levels under P starvation allow P-starved swarmer cells to differentiate into sessile stalked cells. Further, we show that limited DnaA abundance, and consequently absence of DNA replication initiation, is the main reason that prevents P-starved stalked cells from completing the cell cycle. Together, our findings demonstrate thatC. crescentusdecouples cell differentiation from DNA replication initiation under certain starvation conditions, two otherwise intimately coupled processes. We hypothesize that arresting the developmental program either as motile swarmer cells or as sessile stalked cells improves the chances of survival ofC. crescentusduring the different starvation conditions.

Author Summary

Bacteria frequently encounter periods of nutrient limitation. To ensure their survival, they dynamically modulate their own proliferation and cellular behaviors in response to nutrient availability. In manyAlphaproteobacteria, progression through the cell cycle is tightly coupled to morphological transitions generating distinct cell types. Here, we show how starvation for either of the major nutrients carbon, nitrogen, or phosphorus affects this coupling between key cell cycle events and cell differentiation in the model bacteriumCaulobacter crescentus. All three starvation conditions prevent cell proliferation by blocking DNA replication initiation. However, while carbon and nitrogen exhaustion cause cells to arrest the cell cycle as non-replicating motile cells, phosphorus starvation leads to accumulation of non-replicating sessile stalked cells. Our data demonstrate that starvation-dependent differences in (p)ppGpp signaling account for these different starvation responses. Together, our work provides insights into the mechanisms that allow bacteria to modulate their developmental program in response to changing environmental conditions.
Integrating Mental Health and Psycho-Social Support (MHPSS) into infectious disease outbreak and epidemic response: an umbrella review and operational framework
Authors: Alkasaby Muhammad , Philip Sharad , Douba Zain , Tu Hanna , Eaton Julian , Mohammed Muftau , Essar Mohammad Yasir , Kamal Manar Ahmed , Adeel Riaz Mehr Muhammad , Moussallem Marianne , Bosu William K , Walker Ian
Published: July 2023

Introduction

Infectious disease outbreaks have a substantial impact on people’s psychosocial well-being. Yet, mental health and psychosocial support (MHPSS) interventions are not systemically integrated into outbreak and epidemic response. Our review aims to synthesise evidence on the effectiveness of MHPSS interventions in outbreaks and propose a framework for systematically integrating MHPSS into outbreak response.

Methods

We conducted an umbrella review in accordance with the Joanna Briggs Institute (JBI) methodology for umbrella reviews.

Results

We identified 23 systematic literature reviews, 6 of which involved meta-analysis, and only 30% (n=7) were of high quality. Most of the available literature was produced during COVID-19 and focused on clinical case management and medical staff well- being, with scarce evidence on the well-being of other outbreak responders and MHPSS in other outbreak response pillars.

Conclusion

Despite the low quality of the majority of the existing evidence, MHPSS interventions have the potential to improve the psychological well- being of those affected by and those responding to outbreaks. They also can improve the outcomes of the outbreak response activities such as contact tracing, infection prevention and control, and clinical case management. Our proposed framework would facilitate integrating MHPSS into outbreak response and hence mitigate the mental health impact of outbreaks.

Review registration

PROSPERO CRD42022297138.
Macrophages heterogeneity and significance during human fetal pancreatic development
Authors: Migliorini Adriana , Ge Sabrina , Atkins Michael H. , Sambathkumar Rangarajan , Sing Angel , Chua Conan , Gehring Adam J. , Keller Gordon M. , Notta Faiyaz , Nostro Maria Cristina
Published: July 2023

Organogenesis is a complex process that relies on a dynamic interplay between extrinsic factors originating from the microenvironment and intrinsic factors specific to the tissue. For the endocrine cells of the islet of Langerhans, the local microenvironment consists of various cell types including pancreatic acinar and ductal cells as well as neuronal, immune, endothelial, and stromal cells. Interestingly, hematopoietic cells have been detected in human pancreas as early as 6 post-conception weeks (PCW)1,2, but whether they play a role during islet formation in humans remains largely unknown. To shed light on this question, we performed single nuclei RNA sequencing of the human fetal pancreas during the early weeks of the second trimester, specifically focusing on the molecular interaction between the hematopoietic niche and the pancreatic epithelium. Our analysis identified a wide range of hematopoietic cells as well as two distinct subsets of macrophages that are unique to the fetal pancreas and absent in neonatal or adult pancreatic tissues. Leveraging this discovery, we developed a co-culture system of hESC-derived endocrine-macrophage organoids to model their interactionin vitro. Remarkably, we found that macrophages promoted the differentiation and viability of developing endocrine cellsin vitroand enhanced tissue engraftment in immunocompromised mice, supporting a role for these cells in future tissue engineering strategies for diabetes.
Mitochondrial perturbation in the intestine causes microbiota-dependent injury and gene signatures discriminative of inflammatory disease
Authors: Urbauer Elisabeth , Aguanno Doriane , Mindermann Nora , Omer Hélène , Metwaly Amira , Krammel Tina , Faro Tim , Remke Marianne , Reitmeier Sandra , Bärthel Stefanie , Kersting Johannes , Huang Zihua , Xian Feng , Schmidt Manuela , Saur Dieter , Huber Samuel , Stecher Bärbel , List Markus , Gómez-Varela David , Steiger Katja , Allez Matthieu , Rath Eva , Haller Dirk
Published: July 2023

Mitochondrial dysfunction is associated with inflammatory bowel diseases (IBD). To understand how microbial-metabolic circuits contribute to intestinal tissue injury, we disrupt mitochondrial function in the epithelium by deleting heat shock protein 60 (Hsp60Δ/ΔIEC). While metabolic perturbation causes self-resolving tissue injury, regeneration is disrupted in the absence of aryl hydrocarbon receptor (Hsp60Δ/ΔIEC;AhR-/-) or IL-10 (Hsp60Δ/ΔIEC;Il10-/-) leading to IBD-like pathology. Injury is absent in the distal colon of germ-free (GF) Hsp60Δ/ΔIECmice, highlighting bacterial control of metabolic injury. Selective colonization of GF Hsp60Δ/ΔIECmice with the synthetic community OMM12confirms consistent expansion of metabolically-flexibleBacteroidesspp. across all models and mono-colonization withB. caecimurisrecapitulates injury. Transcriptional profiling of metabolically-impaired epithelium identifies gene signatures, includingIdo1,Nos2, andDuox2, distinguishing active from inactive tissue inflammation in 343 resected samples from Crohn’s disease patients. In conclusion, mitochondrial perturbation of the epithelium causes microbiota-dependent tissue injury and discriminative inflammatory gene profiles relevant for IBD.

Abstract Figure

Graphical Abstract:

Control of metabolic injury by microbial signals.

Mitochondrial perturbation of the intestinal epithelium induces tissue injury

Loss of IL-10 and AhR-related host mechanisms accelerate injury and inflammation

Mitochondrial dysfunction induces dysbiosis and expansion ofBacteroidesspp.

Metabolic injury gene signature discriminates inflamedvs.non-inflamed IBD samples
Deep learning insights into the architecture of the mammalian egg-sperm fusion synapse
Authors: Elofsson Arne , Han Ling , Bianchi Enrica , Wright Gavin J. , Jovine Luca
Published: July 2023

A crucial event in sexual reproduction is when haploid sperm and egg fuse to form a new diploid organism at fertilization. In mammals, direct interaction between egg JUNO and sperm IZUMO1 mediates gamete membrane adhesion, yet their role in fusion remains enigmatic. We used AlphaFold to predict the structure of other extracellular proteins essential for fertilization to determine if they could form a complex that may mediate fusion. We first identified TMEM81, whose gene is expressed by mouse and human spermatids, as a protein having structural homologies with both IZUMO1 and another sperm molecule essential for gamete fusion, SPACA6. Using a set of proteins known to be important for fertilization and TMEM81, we then systematically searched for predicted binary interactions using an unguided approach and identified a pentameric complex involving sperm IZUMO1, SPACA6, TMEM81 and egg JUNO, CD9. This complex is structurally consistent with both the expected topology on opposing gamete membranes and the location of predicted N-glycans not modeled by AlphaFold-Multimer, suggesting that its components could organize into a synapse-like assembly at the point of fusion. Finally, the structural modeling approach described here could be more generally useful to gain insights into transient protein complexes difficult to detect experimentally.

Impact statement

Structural modeling with AlphaFold-Multimer was used to investigate extracellular protein interactions involved in mammalian egg-sperm recognition, suggesting a putative pentameric complex that includes TMEM81, a sperm protein not previously involved in gamete recognition.