bluuebunny/crossref_metadata_2025 huggingface dataset:
α-synuclein promotes neuronal dysfunction and death by disrupting the binding of ankyrin to ß-spectrin
Authors: Maor Gali , Dubreuil Ronald R. , Feany Mel B.
Published: June 2023

α-synuclein plays a key role in the pathogenesis of Parkinson’s disease and related disorders, but critical interacting partners and molecular mechanisms mediating neurotoxicity are incompletely understood. We show that α-synuclein binds directly to ß-spectrin. Using males and females in aDrosophilamodel of α-synuclein-related disorders we demonstrate that ß-spectrin is critical for α-synuclein neurotoxicity. Further, the ankyrin binding domain of ß-spectrin is required for α-synuclein binding and neurotoxicity. A key plasma membrane target of ankyrin, Na+/K+ATPase, is mislocalized when human α-synuclein is expressed inDrosophila. Accordingly, membrane potential is depolarized in α-synuclein transgenic fly brains. We examine the same pathway in human neurons and find that Parkinson’s disease patient-derived neurons with a triplication of the α-synuclein locus show disruption of the spectrin cytoskeleton, mislocalization of ankyrin and Na+/K+ATPase, and membrane potential depolarization. Our findings define a specific molecular mechanism by which elevated levels of α-synuclein in Parkinson’s disease and related α-synucleinopathies leads to neuronal dysfunction and death.

Significance Statement

The small synaptic vesicle associate protein α-synuclein plays a critical role in the pathogenesis of Parkinson’s disease and related disorders, but the disease-relevant binding partners of α-synuclein and proximate pathways critical for neurotoxicity require further definition. We show that α-synuclein binds directly to ß-spectrin, a key cytoskeletal protein required for localization of plasma membrane proteins and maintenance of neuronal viability. Binding of α-synuclein to ß-spectrin alters the organization of the spectrin-ankyrin complex, which is critical for localization and function of integral membrane proteins, including Na+/K+ATPase. These finding outline a previously undescribed mechanism of α-synuclein neurotoxicity and thus suggest potential new therapeutic approaches in Parkinson’s disease and related disorders.
Hyperaccumulation of Vanadium in animals: two sponges compete with urochordates
Authors: de Pao Mendonca Kassandra , Chaurand Perrine , Campos Andrea , Angeletti Bernard , Rovezzi Mauro , Delage Ludovic , Borchiellini Carole , Bivic André Le , Issartel Julien , Renard Emmanuelle , Levard Clément
Published: June 2023

Vanadium (V) is the second most abundant transition metal in the oceans. Nevertheless, its concentration in organisms is generally low despite its involvement in various physiological or enzymatic functions. Because exposure to high concentrations was shown to be harmful for various organisms including animals, the unexpected very high concentrations found in urochordates and annelids yielded additional studies to decipher their biological meaning.

Here we report cases of V hyperaccumulators in a distinct animal phylum (Porifera): the two homoscleromorph sponge speciesOscarella lobularisandOscarella tuberculata(up to 30 mg/g dw). These high concentrations overpass those reported previously in urochordates and annelids and are not found in the 5 other sponge species studied here. In bothOscarellaspecies, vanadium is mainly accumulated in the 100 μm surface tissues, and in particular in mesohylar cells, as vanadyl (+4) before being partly reduced to V (+3) in the deeper tissues. Genomic surveys failed to find any previously described gene implicated in vanadium metabolism, suggesting that V hyperaccumulation emerged convergently in this lineage. This feature may be of interest for developing bioremediation strategies in marine ecosystems or bioinspired processes to recycle this critical metal.

Synopsis

This study reports extremely high concentrations of vanadium in two sponges. This unusual bioaccumulation of reduced V (+3) in mesohylar cells relies on unknown molecular mechanisms.
A class of secreted mammalian peptides with potential to expand cell-cell communication
Authors: Wiggenhorn Amanda L. , Abuzaid Hind Z. , Coassolo Laetitia , Li Veronica L. , Tanzo Julia T. , Wei Wei , Lyu Xuchao , Svensson Katrin J. , Long Jonathan Z.
Published: June 2023

Peptide hormones and neuropeptides are fundamental signaling molecules that control diverse aspects of mammalian homeostasis and physiology. Here we demonstrate the endogenous presence of a sequence diverse class of orphan, blood-borne peptides that we call “capped peptides.” Capped peptides are fragments of secreted proteins and defined by the presence of two post-translational modifications – N-terminal pyroglutamylation and C-terminal amidation – which function as chemical “caps” of the intervening sequence. Capped peptides share many regulatory characteristics in common with that of other signaling peptides, including dynamic regulation in blood plasma by diverse environmental and physiologic stimuli. One capped peptide, CAP-TAC1, is a tachykinin neuropeptide-like molecule and a nanomolar agonist of multiple mammalian tachykinin receptors. A second capped peptide, CAP-GDF15, is a 12-mer peptide that reduces food intake and body weight. Capped peptides therefore define a largely unexplored class of circulating molecules with potential to regulate cell-cell communication in mammalian physiology.
22kHz Ultrasonic Vocalizations and Body Freezing May Represent Two Systems of Fear in Rodent Fear Conditioning Paradigms
Authors: Zheng Benhuiyuan , Bao Lili , Yu Delin , Yin Bin
Published: June 2023

The “two-system” framework of fear proposed by LeDoux and Pine (2016) sparked a discussion on the understanding of fear, prompting a reevaluation of rodent fear conditioning studies. We propose that 22kHz ultrasonic vocalizations (USV) may symbolize the subjective negative emotional states in rats. To evaluate this, we designed a series of fear conditioning experiments with varied parameters, comparing the expression of 22kHz USV and body freezing – a traditional fear index. These expressions were further assessed in fear generalization tests. Our findings suggest a distinct separation between body freezing and 22kHz vocalizations in fear conditioning under different conditions. The results indicate that 22kHz USV may more accurately signify the subjective state of fear, whereas body freezing may denote an automatic defensive response in rats. Consequently, we posit that the two-system fear framework may extend to rodent fear conditioning paradigms. Therefore, researchers should place greater emphasis on 22kHz vocalizations when investigating the subjective state of fear.
Practice often and always get ready: a spiking mechanistic model for voluntary motor control
Authors: Zhao Chen , Cui He
Published: June 2023

In many voluntary movement, neural activities ranging from cortex to spinal cord can be roughly described as the stages of motor intention, preparation, and execution. Recent advances in neuroscience have proposed many theories to understand how motor intention can be transformed into action following these stages, but they still lack a holistic and mechanistic theory to account for the whole process. Here, we try to formulate this question by abstracting two underlying principles: 1) the neural system is specializing the final motor command through a hierarchical network by multitudes of training supervised by the action feedback (“practice often”); 2) prediction is a general mechanism throughout the whole process by providing feedback control for each local layer (“always get ready”). Here we present a theoretical model to regularize voluntary motor control based on these two principles. The model features hierarchical organization and is composed of spiking building blocks based on the previous work in predictive coding and adaptive control theory. By simulating our manual interception paradigm, we show that the network could demonstrate motor preparation and execution, generate desired output trajectory following intention inputs, and exhibit comparable cortical and endpoint dynamics with the empirical data.
Investigating Clot-flow Interactions by Integrating Intravital Imaging with In Silico Modeling for Analysis of Flow, Transport, and Hemodynamic Forces
Authors: Teeraratkul Chayut , Tomaiuolo Maurizio , Stalker Timothy J. , Mukherjee Debanjan
Published: June 2023

As a blood clot forms, grows, deforms, and embolizes following a vascular injury, local clot-flow interactions lead to a highly dynamic flow environment. The local flow influences transport of biochemical species relevant for clotting, and determines the forces on the clot that in turn lead to clot deformation and embolization. Despite this central role, quantitative characterization of this dynamic clot-flow interaction and flow environment in the clot neighborhood remains a major challenge. Here, we propose an approach that integrates dynamic intravital imaging with computer geometric modeling and computational flow and transport modeling to develop a unifiedin silicoframework to quantify the dynamic clot-flow interactions. We outline the development of the methodology referred to as Intravital Integrated In Silico Modeling orIVISim, and then demonstrate the method on a sample set of simulations comprising clot formation following laser injury in two mouse cremaster arteriole injury model data: one wild-type mouse case, and one diYF knockout mouse case. Simulation predictions are verified against experimental observations of transport of caged fluorescent Albumin (cAlb) in both models. Through these simulations, we illustrate how theIVISimmethodology can provide insights into hemostatic processes, the role of flow and clot-flow interactions, and enable further investigations comparing and contrasting different biological model scenarios and parameter variations.
Oxygen loss compromises the survival and cognition of a coastal cephalopod
Authors: Court Mélanie , Macau Marta , Ranucci Maddalena , Repolho Tiago , Lopes Vanessa Madeira , Rosa Rui , Paula José Ricardo
Published: June 2023

The ocean is undergoing deoxygenation and the spread of hypoxic areas. Ocean deoxygenation and standing levels of hypoxia are shrinking fundamental niches, particularly in coastal areas, yet documented repercussions on species development and behavior are limited. Here, we tackled the impacts of deoxygenation (7 mg O2 L-1), mild hypoxia (nocturnal 5 mg O2 L-1), and severe hypoxia (2 mg O2 L-1) on cuttlefish (Sepia officinalis) development (hatching success, development time, mantle length) and behavior, i.e., ability to learn (associative-and socially), to camouflage, and to explore its surroundings spatially. We found that hypoxia yielded lower survival rates, smaller body sizes and inhibited predatory (increased latency to attack the prey) and anti-predator (camouflage) behaviors. Acute and chronic exposure to low oxygen produced similar effects on cognition (inability to socially learn, increased open-field activity levels, no changes in thigmotaxis). It is thus expected that, although cuttlefish can withstand oxygen limitation to a certain degree, expanding hypoxic zones will diminish current habitat suitability.
Early Alzheimer’s disease pathology in human cortex is associated with a transient phase of distinct cell states
Authors: Gazestani Vahid , Kamath Tushar , Nadaf Naeem M. , Burris SJ , Rooney Brendan , Junkkari Antti , Vanderburg Charles , Rauramaa Tuomas , Therrien Martine , Tegtmeyer Matthew , Herukka Sanna-Kaisa , Abdulraouf Abdulraouf , Marsh Samuel , Malm Tarja , Hiltunen Mikko , Nehme Ralda , Stevens Beth , Leinonen Ville , Macosko Evan Z.
Published: June 2023

Cellular perturbations underlying Alzheimer’s disease are primarily studied in human postmortem samples and model organisms. Here we generated a single-nucleus atlas from a rare cohort of cortical biopsies from living individuals with varying degrees of Alzheimer’s disease pathology. We next performed a systematic cross-disease and cross-species integrative analysis to identify a set of cell states that are specific to early AD pathology. These changes–which we refer to as the Early Cortical Amyloid Response—were prominent in neurons, wherein we identified a transient state of hyperactivity preceding loss of excitatory neurons, which correlated with the selective loss of layer 1 inhibitory neurons. Microglia overexpressing neuroinflammatory-related processes also expanded as AD pathological burden increased. Lastly, both oligodendrocytes and pyramidal neurons upregulated genes associated with amyloid beta production and processing during this early hyperactive phase. Our integrative analysis provides an organizing framework for targeting circuit dysfunction, neuroinflammation, and amyloid production early in AD pathogenesis.
Comparative Brain-Wide Mapping of Ketamine and Isoflurane-Activated Nuclei and Functional Networks
Authors: Hu Yue , Du Wenjie , Qi Jiangtao , Luo Huoqing , Zhang Zhao , Luo Mengqiang , Wang Yingwei
Published: June 2023

Ketamine (KET) and isoflurane (ISO) are two widely used general anesthetics, yet their distinct and shared neurophysiological mechanisms remain elusive. In this study, we conducted a comparative analysis of the effects of KET and ISO on c-Fos expression across the brain, utilizing hierarchical clustering and c-Fos-based functional network analysis to evaluate the responses of individual brain regions to each anesthetic. Our findings reveal that KET activates a wide range of brain regions, notably in the cortical and subcortical nuclei involved in sensory, motor, emotional, and reward processing, with the temporal association areas (TEa) as a strong hub, suggesting a top-down mechanism affecting consciousness by primarily targeting higher-order cortical networks. In contrast, ISO predominantly influences brain regions in the hypothalamus, impacting neuroendocrine control, autonomic function, and homeostasis, with the locus coeruleus (LC) as a connector hub, indicating a bottom-up mechanism in anesthetic-induced unconsciousness. KET and ISO both activate brain areas involved in sensory processing, memory and cognition, reward and motivation, as well as autonomic and homeostatic control, highlighting their shared effects on various neural pathways. In conclusion, our results highlight the distinct but overlapping effects of KET and ISO, enriching our understanding of the mechanisms underlying general anesthesia.
Subcutaneous and orally self-administered high-dose carprofen in male and female mice: pharmacokinetics, tolerability and impact on cage-side pain indicators
Authors: Glasenapp Aylina , Bankstahl Jens P. , Bähre Heike , Glage Silke , Bankstahl Marion
Published: June 2023

Surgical interventions in mice are prerequisite in various research fields and require appropriate pain relief, not only to ensure animal welfare but also to avoid influence of pain on research findings. Carprofen is a non-steroidal anti-inflammatory drug that is commonly used as an analgesic for interventions inducing mild to moderate pain in animals. Despite its frequent use also in laboratory rodents, data on pharmacokinetics and side effects, and on its potential impact on behavioral pain indicators are rare.

This study aimed to determine pharmacokinetic and tolerability profiles of high dose carprofen in male and female C57Bl/6J mice, administered via single subcutaneous injection (s.c.) and oral self-administration per drinking water (d.w.). Plasma concentrations of carprofen were measured at various time points, and side effects were evaluated using a modified Irwin test protocol, hematology and histopathology. Additionally, potential effects on behavioral pain indicators commonly used to assess post-surgical pain, such as the mouse grimace scale, wheel running activity, burrowing, nesting and grooming behavior were investigated.

Quantification of carprofen in plasma revealed maximum plasma concentrations of 133.4 ± 11.3 µg/ml after 1 hour and an elimination half-life of 8.52 hour after single s.c. injection of 20 mg/kg carprofen. Oral self-administration of carprofen (25 mg/kg/24 h) resulted in a steady-state < 24 hours over 5 days after treatment start with plasma levels of around 60 µg/ml. The carprofen-medicated water was highly accepted, and increased d.w. intake was observed in the first 24 hours after exposure for both sexes (p < 0.0001). Irwin test detected only minor side effects, and hematology and histopathology where without pathological findings that could be attributed to carprofen treatment. Except for a decrease of 49-70 % in wheel running activity in male mice, behavioral pain indicators were only very mildly affected.

This study determined carprofen plasma levels in mice lying well above an estimated therapeutic concentration for both routes of administration. Carprofen was well tolerated at recommended high doses and may provide sufficient analgesia for minor interventions as well as be applied as a tolerable component in multimodal analgesic regimens.
miniBUSCO: a faster and more accurate reimplementation of BUSCO
Authors: Huang Neng , Li Heng
Published: June 2023

Motivation

Assembly completeness evaluation of genome assembly is a critical assessment of the accuracy and reliability of genomic data. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. BUSCO is one of the most widely used tools for assessing the completeness of genome assembly by comparing the presence of a set of single-copy orthologs conserved across a wide range of taxa. However, the runtime of BUSCO can be long, particularly for some large genome assemblies. It is a challenge for researchers to quickly iterate the genome assemblies or analyze a large number of assemblies.

Results

Here, we present miniBUSCO, an efficient tool for assessing the completeness of genome assemblies. miniBUSCO utilizes the protein-to-genome aligner miniprot and the datasets of conserved orthologous genes from BUSCO. Our evaluation of the real human assembly indicates that miniBUSCO achieves a 14-fold speedup over BUSCO. Furthermore, miniBUSCO reports a more accurate completeness of 99.6% than BUSCO’s completeness of 95.7%, which is in close agreement with the annotation completeness of 99.5% for T2T-CHM13.

Availability

https://github.com/huangnengCSU/minibusco.

Contact

hli@ds.dfci.harvard.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
Improving risk communication: a pilot randomised-control trial assessing the impact of visual aids for interventional consent
Authors: Chatzopoulou Despoina , Jalal Arif Hanafi Bin , Stoyanov Danail , Marcus Hani J , Pandit Anand S
Published: June 2023

Introduction

Informed consent is a fundamental component in the work-up for surgical procedures. Our study aims to assess the impact of visual tools in the informed consent process of a common medical and neurosurgical procedure: a lumbar puncture.

Methods

Participants were healthy adults without any underlying cognitive impairment, and they were randomized to complete a questionnaire containing either the control video or intervention video. Both videos contained identical audio narration, however the intervention video included additional visual aids such as anatomical diagrams, icon arrays and Paling scales. Outcome measure included knowledge of the procedure (including recall of numerical risks), 5-point Likert scale questions, usability as measured by the System Usability Scale, acceptability as measured by the Acceptability of Intervention Measure and appropriateness as measured by the Intervention Appropriateness Measure.

Results

In total, 52 participants were randomized to the control (n = 25) or intervention (n=27) group. There was no statistical difference in numerical risk recall, understanding of the procedure or its benefits. The intervention group reported better understanding of the risks (p = 0.05), felt they could more easily better explain the risks to others (p = 0.01), and felt less overwhelmed with information (p = 0.03). The intervention group was also rated as more acceptable (p = 0.02).

Conclusion

Our pilot study tentatively demonstrates that visual risk communication adjuncts offer several advantages over traditionally obtained surgical consent without being inferior in understanding of the procedure or recall of numerical risks.
Olfactory cortex output pathways exhibit robust differences in their ability to drive learned aversion
Authors: Vieira Inês , Bryzgalov Dmitri
Published: June 2023

The olfactory (piriform) cortex contains a large diversity of neural cell types, defined by their molecular identity, morphology, functional properties and projection target specificity. How these distinct neural cell types contribute to the control of olfactory-driven behaviors remains unknown. Here, we use a behavioral task in which optogenetic activation of subpopulations of piriform neurons is associated with an unconditioned aversive stimulus. We find that piriform neurons projecting to the olfactory bulb or the medial prefrontal cortex efficiently drive a learned escape behavior. In contrast, neurons projecting to the cortical amygdala or the lateral entorhinal cortex failed to support a behavioral response. Our results suggest that different piriform neural subnetworks exhibit robust differences in their ability to relate neural activity to behavioral output.
Prevalence and Risk factors of Urinary Schistosomiasis in Kaporo Village, Karonga District, Malawi
Authors: Nyondo Christopher S. , Mthawanji Rhosheen , Chisale Master
Published: June 2023

Objective

The aim of the study was to determine the prevalence and Risk factors of urogenital schistosomiasis in Karonga district; it also sought to determine the relationship between involvement in MDA advocacy campaigns and Knowledge level of the disease.

Methods

The study enrolled 251 participants that responded to the questionnaire-guided interview and submitted urine for microscopy.

Results

Of 251 children that were enrolled 87 (34.7%) were found to haveS.haematobiumeggs. Chi-square analysis established that having a parent in rice farming (p=0.029) occupation is a key risk factor for urogenital schistosomiasis. It was also surprising to note that those schoolchildren who received Praziquantel during MDA had significantly higher prevalence (p=0.010). Furthermore, this study revealed that they is no association between a child involving in MDA advocacy compaigns and level of knowledge on schistosomiasis transmission.
A prospective, single-center, randomized phase 2 trial of etoposide in severe COVID-19
Authors: Halpin Meredith , Lerner Adam , Sagar Manish , Govender Praveen , Shah Bhavesh , Weinberg Janice , Sarosiek Shayna , Sloan J. Mark
Published: June 2023

The systemic inflammatory response seen in patients with severe COVID-19 shares many similarities with the changes observed in hemophagocytic lymphohistiocytosis (HLH); a disease characterized by excessive immune activation. Many patients with severe COVID qualify for a diagnosis of HLH. Etoposide, an inhibitor of topoisomerase II is used to control inflammation in HLH. This randomized, open-label, single center phase II trial attempted to determine whether etoposide can be used to blunt the inflammatory response in severe COVID. This trial was closed early after eight patients were randomized. This underpowered trial did not meet its primary endpoint of improvement in pulmonary status by two categories on an 8 point ordinal scale of respiratory function. There were not significant differences in secondary outcomes including overall survival at 30 days, cumulative incidence of grade 2 through 4 adverse events during hospitalization, duration of hospitalization, duration of ventilation and improvement in oxygenation or paO2/FIO2 ratio or improvement in inflammatory markers associated with cytokine storm. A high rate of grade 3 myelosuppression was noted in this critically ill population despite dose reduction, a toxicity which will limit future attempts to explore the utility of etoposide for virally-driven cytokine storm or HLH.
Association of alpha-aminoadipic acid (2-AAA) with cardiometabolic risk factors in healthy and high-risk individuals
Authors: Desine Stacy , Gabriel Curtis L. , Smith Holly M. , Antonetti Olivia R. , Wang Chuan , Calcutt M. Wade , Doran Amanda C. , Silver Heidi J. , Nair Sangeeta , Terry James G. , Carr J. Jeffrey , Linton MacRae F. , Brown Jonathan D. , Koethe John R. , Ferguson Jane F.
Published: June 2023

Plasma levels of the metabolite alpha-aminoadipic acid (2-AAA) have been associated with risk of type 2 diabetes (T2D) and atherosclerosis. However, little is known about the relationship of 2-AAA to other cardiometabolic risk markers in pre-disease states, or in the setting of comorbid disease. We measured circulating 2-AAA using two methods in 1) a sample of 261 healthy individuals (2-AAA Study), and 2) in a sample of 134 persons comprising 110 individuals with treated HIV, with or without T2D, a population at high risk of metabolic disease and cardiovascular events despite suppression of circulating virus, and 24 individuals with T2D without HIV (HATIM Study). We examined associations between plasma 2-AAA and markers of cardiometabolic health within each cohort. We observed differences in 2-AAA by sex and race in both cohorts, with higher levels observed in men compared with women, and in Asian compared with Black or white individuals (P<0.05). There was no significant difference in 2-AAA by HIV status within individuals with T2D in the HATIM Study. We confirmed associations between 2-AAA and dyslipidemia in both cohorts where high 2-AAA associated with low HDL cholesterol (P<0.001) and high triglycerides (P<0.05). As expected, within the cohort of people with HIV, 2-AAA was higher in the setting of T2D compared to pre-diabetes or normoglycemia (P<0.001). 2-AAA was positively associated with body mass index (BMI) in the 2-AAA Study, and with waist circumference and measures of visceral fat volume in HATIM (all P<0.05). Further, 2-AAA associated with increased liver fat in persons with HIV (P<0.001). Our study confirms 2-AAA as a marker of cardiometabolic risk in both healthy individuals and those at high cardiometabolic risk, reveals relationships with adiposity and hepatic steatosis, and highlights important differences by sex and race. Further studies are warranted to establish molecular mechanisms linking 2-AAA to disease in other high-risk populations.
Mortality associated with influenza and Omicron infections in France and vaccination of healthcare workers in nursing homes
Authors: Goldstein Edward
Published: June 2023

Background

During the winter of 2022-2023, high rates of all-cause mortality, not seen since April 2020, were recorded in France, with excess all-cause mortality being related to the Omicron and influenza epidemics during that period. Moreover, that period saw a significant increase in the proportion of residents in long-term care facilities among cases of death in the population. Studies have found that increased influenza vaccination coverage in healthcare workers can result in a substantial reduction (up to 20%-30% during the course of select influenza seasons in the pre-pandemic period) in all-cause mortality in residents in nursing homes.

Methods

We applied the previously developed methodology to estimate the contribution of influenza infections to all-cause mortality in France for the 2014-2015 through the 2018-2019 influenza seasons, and the contribution of both SARS-CoV-2 and influenza infections to all-cause mortality between week 33, 2022 through week 12, 2023.

Results

For the 2014-2015 through the 2018-2019 seasons, influenza was associated with an average of 15654 (95% CI (13013,18340)) deaths, while between week 33, 2022 through week 12, 2023, we estimated 7851 (5213,10463) influenza-associated deaths and 32607 (20794,44496) SARS-CoV-2 associated deaths. The number of SARS-CoV-2-associated deaths during the Omicron epidemic was significantly higher than the number of deaths with COVID-19 listed on the death certificate or the hospitalization record – for example, between weeks 33-52 in 2022, we estimated 23983 (15307,32620) SARS-CoV-2-associated deaths in France, compared with 12811 deaths with COVID-19 listed on the death certificate, and 8639 in-hospital deaths with COVID-19 during the same period. Examination of US mortality data suggests a significant contribution of Omicron infections to mortality for cardiac disease and mental/behavioral disorders with COVID-19 not listed on the death certificate.

Conclusions

Our results suggest the need for boosting influenza vaccination coverage in different population groups (including healthcare workers, particularly nurse assistants for whom influenza vaccination coverage rates in France are low), as well as for wider use of influenza antiviral medications in influenza-related respiratory hospitalizations with different diagnoses (including pneumonia). Wider detection and treatment of Omicron infections, particularly in older individuals/persons with underlying health conditions such as cardiac disease and mental/behavioral disorders, and wider use of bivalent COVID-19 boosters would be needed in the event of the recrudescence of Omicron circulation in France.
Phosphoprotein dynamics of interacting tumor and T cells by HySic
Authors: Ibáñez-Molero Sofía , Pruijs Jinne , Atmopawiro Alisha , Wang Fujia , Altelaar Maarten , Peeper Daniel S. , Stecker Kelly E.
Published: June 2023

Functional interactions between cytotoxic T cells and tumor cells are central to anti-cancer immunity. Some of the proteins involved, particularly immune checkpoints expressed by T cells, serve as promising clinical targets in immunotherapy. However, our understanding of the complexity and dynamics of the interactions between tumor cells and T cells is only rudimentary. Here we present HySic (forHybrid quantification ofSILAC (Stable Isotope Labelling by Amino acids in Cell culture)-labeled interactingcells) as an innovative method to quantify protein and phosphorylation dynamics between and within physically interacting (heterotypic) cells. We show that co-cultured HLA/antigen-matched tumor and T cells engage in physical and stable interactions, allowing for in-depth HySic analysis. This method does not require physical separation of the two cell types for subsequent MS proteome and phosphoproteome measurement using label free quantification (LFQ). We demonstrate that HySic can be used to unravel proteins contributing to functional T cell:tumor cell interactions. We validated HySic with established interactions, including those mediating IFNγ signaling. Using HySic we identified the RHO/RAC/PAK1 signaling pathway to be activated upon interaction of T cells and tumor cells. Pharmacologic inhibition of PAK1 sensitized tumor cells to T cell killing. Thus, HySic is an innovative and simple method to study short-term protein signaling dynamics in physically interacting cells, which can be easily extended to other biological systems.
Novel genomic offset metrics account for local adaptation in climate suitability forecasts and inform assisted migration
Authors: Lachmuth Susanne , Capblancq Thibaut , Prakash Anoob , Keller Stephen R. , Fitzpatrick Matthew C.
Published: June 2023

Local adaptation is increasingly being integrated into macroecological models, offering an evolutionary perspective that has been largely missing from climate change biogeography. Genomic offsets, which quantify the disruption of existing genotype-environment associations under environmental change, are an informative landscape genomic tool that allows for the incorporation of intra-specific adaptive differentiation into forecasts of climate suitability and thus management planning. Gradient forest (GF), a method originally developed to model community turnover along environmental gradients, is now the most commonly used approach in genomic offset estimation. However, major hurdles in the application of GF-derived offsets are (1) an inability to interpret the absolute magnitude of genomic offsets in a biologically meaningful way and (2) uncertainty in how genomic offsets compare to established species-level approaches like Ecological Niche Models (ENMs).

We used both ENMs and novel, genomic offset metrics derived from GF modeling of genomic variation along climatic gradients to assess the climate change vulnerability of red spruce (Picea rubens), a cool-temperate tree species endemic to eastern North America. We show how genomic offsets can be standardized relative to contemporary genomic variation across the landscape to better represent their biological significance and facilitate comparisons among studies. In three common gardens, we found a significant negative relationship between standardized genomic offsets and red spruce growth and higher explanatory power for standardized offsets than (raw) climate transfer distances.

We also derived new threshold-based metrics that we term Donor and Recipient Importance and which quantify transferability of propagules between donor and recipient localities while minimizing disruption of genotype-environment associations. This approach leverages landscape genomic information to account for local adaptation when predicting climate suitability. ENMs and our novel genomic offset metrics largely agreed in forecasting drastic northward range shifts. Combining several offset-based metrics, we show that the projected northward shift of suitable climate mainly applies to populations located in the center and northern parts of the current range, whereas southern populations might be able to persistin situowing to specific local climate adaptations. The novel metrics thus yield refined, region-specific prognoses for local persistence and show how management could be improved by considering assisted migration.
Substrate availability and dietary fibre regulate metabolism of tryptophan by human gut microbes
Authors: Sinha Anurag K. , Laursen Martin F. , Brinck Julius E. , Rybtke Morten L. , Pedersen Mikael , Roager Henrik M. , Licht Tine R.
Published: June 2023

Tryptophan is catabolized by gut microbes, resulting in a wide range of metabolites implicated in both beneficial and adverse host effects. However, it remains elusive how the gut microbial tryptophan metabolism is governed either towards indole, associated with adverse effects in chronic kidney disease, or towards indolelactic acid (ILA) and indolepropionic acid (IPA), associated with protective effects in type 2 diabetes and inflammatory bowel disease. Here, we used human fecal cultures in combination with a controlled three-species model to test competition for tryptophan, and measured the resulting metabolites bothin vitroand in gnotobiotic mice colonized with the three species. We revealed that the generation of specific tryptophan-derived metabolites was not predominantly determined by the abundance of tryptophan metabolizing bacteria, but rather by substrate-dependent regulation of specific metabolic pathways.In vitroandin vivo, indole-producingEscherichia coliand ILA- and IPA-producingClostridium sporogenescompeted for tryptophan. Importantly, the fibre degradingBacteroides thetaiotaomicronaffected this competition by cross-feeding monosaccharides toE. coli, which inhibited indole production through catabolite repression, and thereby made more tryptophan available toC. sporogenes, increasing ILA and IPA production. We thus present the first mechanistic explanation for why consumption of fermentable fibres suppress indole production but promote the generation of other tryptophan metabolites associated with health benefits. We conclude that the availability of tryptophan and dietary fibre regulates gut microbiome tryptophan metabolism pathways, and consequently influences the balance between the different tryptophan catabolites generated. This balance has implications for host-microbial cross-talk affecting human health.
Expanding the toolbox of probioticEscherichia coliNissle 1917 for synthetic biology
Authors: Ba Fang , Zhang Yufei , Ji Xiangyang , Liu Wan-Qiu , Ling Shengjie , Li Jian
Published: June 2023

Escherichia coliNissle 1917 (EcN) is a probiotic microbe that has the potential to be developed as a promising chassis for synthetic biology applications. However, the molecular tools and techniques for utilizing EcN have not been fully explored. To address this opportunity, we systematically expanded the EcN-based toolbox, enabling EcN as a powerful platform for more applications. First, two EcN cryptic plasmids and other compatible plasmids were genetically engineered to enrich the manipulable plasmid toolbox for multiple gene coexpression. Next, we developed two EcN-based enabling technologies, including the conjugation strategy for DNA transfer, and quantification of protein expression capability. Finally, we expanded the EcN-based applications by developing EcN native integrase-mediated genetic engineering capabilities and establishing anin vitrocell-free protein synthesis (CFPS) system. Overall, this study expanded the toolbox for manipulating EcN as a commonly used probiotic chassis, providing several simplified, dependable, and predictable strategies for researchers working in synthetic biology fields.

For Table of Contents Use Only
Identification of domains inPlasmodium falciparumproteins of unknown function using DALI search on Alphafold predictions
Authors: Behrens Hannah Michaela , Spielmann Tobias
Published: June 2023

Plasmodium falciparum, the causative agent of malaria, poses a significant global health challenge, yet much of its biology remains elusive. A third of the genes in theP. falciparumgenome lack annotations regarding their function, impeding our understanding of the parasite’s biology. In this study, we employed structure predictions and the DALI search algorithm to analyse proteins encoded by uncharacterized genes in the reference strain 3D7 ofP. falciparum.

By comparing Alphafold predictions to experimentally determined protein structures in the Protein Data Bank, we found similarities to known domains in 353 proteins of unknown function, shedding light on their potential functions. The lowest-scoring 5% of similarities were additionally validated using the size-independent TM-align algorithm, confirming the detected similarities in 88% of the cases. Notably, in over 70P. falciparumproteins the presence of domains resembling heptatricopeptide repeats, which are typically involvement in RNA binding and processing, was detected. This suggests this family, which is important in transcription in mitochondria and apicoplasts, is much larger inPlasmodiumparasites than previously thought. The results of this domain search provide a resource to the malaria research community that is expected to inform and enable experimental studies.
Design and assembly of the 117-kbPhaeodactylum tricornutumchloroplast genome
Authors: Walker Emma J.L. , Pampuch Mark , Chang Nelson , Cochrane Ryan R. , Karas Bogumil J.
Published: June 2023

There is a growing impetus to expand the repository of chassis available to synthetic biologists. The chloroplast genome presents a unique chassis for engineering photosynthetic eukaryotes by virtue of its compact size, lack of epigenetic regulation, and containment within the secluded lipid bilayers of the organelle. The development of the chloroplast as a synthetic biology chassis, however, has been limited by a lack of efficient techniques for whole genome cloning and engineering. Here, we demonstrate two approaches for cloning the 117 kbPhaeodactylum tricornutumchloroplast genome that have 90 to 100% efficiency when screening as few as tenSaccharomyces cerevisiaecolonies following yeast assembly. The first method directly uses PCR-amplified fragments of the genome for yeast assembly, whereas the second method relies upon the pre-cloning of eight overlapping genomic regions into individual plasmids that they can later be released from. The cloned genome can be stably maintained and propagated withinEscherichia coli, which provides an exciting opportunity for engineering a novel delivery mechanism for bringing DNA directly to the algal chloroplast. As well, one of the cloned genomes was designed to contain a singleSapI site within the yeastURA3open-reading frame, which can be used to linearize the genome and integrate designer cassettes via golden-gate cloning or further iterations of yeast assembly.
Expanded diversity of novel hemoplasmas in rare and undersampled Neotropical bats
Authors: Volokhov Dmitriy V. , Lock Lauren R. , Dyer Kristin E. , DeAnglis Isabella K. , Andrews Benjamin R. , Simonis Molly C. , Stockmaier Sebastian , Carter Gerald G. , Downs Cynthia J. , Fenton M. Brock , Simmons Nancy B. , Becker Daniel J.
Published: June 2023

Hemotropic mycoplasmas are emerging as a model system for studying bacterial pathogens in bats, but taxonomic coverage of sampled host species remains biased. We leveraged a long-term field study in Belize to uncover novel hemoplasma diversity in bats by analyzing 80 samples from 19 species, most of which are infrequently encountered. PCR targeting the partial 16S rRNA gene found 41% of bats positive for hemoplasmas. Phylogenetic analyses found two novel host shifts of hemoplasmas, four entirely new hemoplasma genotypes, and the first hemoplasma detections in four bat species. One of these novel hemoplasmas (fromNeoeptesicus furinalis) shared 97.6% identity in the partial 16S rRNA gene to a human hemoplasma (CandidatusMycoplasma haemohominis). Additional analysis of the partial 23S rRNA gene allowed us to also designate two novel hemoplasma species, inMyotis elegansandPhyllostomus discolor, with the proposed namesCandidatusMycoplasma haematomyotis sp. nov. andCandidatusMycoplasma haematophyllostomi sp. nov., respectively. Our analyses show that additional hemoplasma diversity in bats can be uncovered by targeting rare or undersampled host species.
Condensation of PRPP amidotransferase by phase separation promotesde novopurine synthesis through intermolecular intermediate channeling in yeast
Authors: Takaine Masak , Morita Rikuri , Yoshinari Yuto , Nishimura Takashi
Published: June 2023

De novopurine synthesis (DPS) is up-regulated under conditions of high purine demand to ensure the production of genetic materials and chemical energy, thereby supporting cell proliferation. However, the regulatory mechanisms governing DPS remain largely unclear. We herein show that PRPP amidotransferase (PPAT), the rate-limiting enzyme in DPS, forms dynamic and motile condensates in Saccharomyces cerevisiae cells under a purine-depleted environment. The formation of condensates requires phase separation, which is driven by target of rapamycin complex 1 (TORC1)-induced ribosome biosynthesis. The self-assembly of PPAT molecules facilitates condensate formation, with intracellular PRPP and purine nucleotides both regulating this self-assembly. Moreover, molecular dynamics simulations suggest that clustering-mediated PPAT activation occurs through intermolecular substrate channeling. Cells unable to form PPAT condensates exhibit growth defects, highlighting the physiological importance of condensation. These results suggest that PPAT condensation is an adaptive mechanism that regulates DPS in response to both TORC1 activity and cellular purine demands.
Emerging costs in a “hidden” workforce: The longitudinal psychosocial effects of caregiving during the COVID-19 pandemic among Norwegian adults
Authors: Hansen Thomas , Hynek Kamila , McMunn Anne , Nes Ragnhild Bang , Skirbekk Vegard , Vollrath Margarethe , Methi Fredrik
Published: June 2023

During COVID-19 many informal caregivers experienced increased caregiving load while access to formal and informal support systems and coping resources decreased. Little is known about the psychosocial costs of these challenges for an essential yet vulnerable and “hidden” frontline workforce. This study explores and compares changes in psychosocial well-being (psychological well-being, psychological ill-being, and loneliness) before and across up to three stages of the COVID-19 pandemic among caregivers and non-caregivers. We also examine predictors of psychosocial well-being among caregivers during the peak of the pandemic. We use longitudinal data collected online in the Norwegian Counties Public Health Survey (age 18–92) in four countries and up to four data points (n=14,881). Caregivers are those who provide care unpaid, continuous (≥ monthly across all time points) help to someone with health problems. Findings show that levels of psychosocial well-being first remained stable but later, during the peak stages of the pandemic, dropped markedly. Caregivers (13−15% of the samples) report lower psychosocial well-being than non-caregivers both before and during the pandemic. Caregivers seem especially vulnerable in terms of ill-being, and during the peak of the pandemic caregivers report higher net levels of worry (OR = 1.22, p< .01) and anxiety (OR = 1.23, p< .01) than non-caregivers. As expected, impacts are graver for caregivers who provide more intensive care and those reporting health problems or poor access to social support. Our study findings are valuable information for interventions to support caregivers during this and future pandemics.
Cortical circuitry mediating inter-areal touch signal amplification
Authors: Ryan Lauren , Sun-Yan Andrew , Laughton Maya , Peron Simon
Published: June 2023

Sensory cortical areas are often organized into topographic maps which represent the sensory epithelium1,2. Individual areas are richly interconnected3, in many cases via reciprocal projections that respect the topography of the underlying map4,5. Because topographically matched cortical patches process the same stimulus, their interaction is likely central to many neural computations6-10. Here, we ask how topographically matched subregions of primary and secondary vibrissal somatosensory cortices (vS1 and vS2) interact during whisker touch. In the mouse, whisker touch-responsive neurons are topographically organized in both vS1 and vS2. Both areas receive thalamic touch input and are topographically interconnected4. Volumetric calcium imaging in mice actively palpating an object with two whiskers revealed a sparse population of highly active, broadly tuned touch neurons responsive to both whiskers. These neurons were especially pronounced in superficial layer 2 in both areas. Despite their rarity, these neurons served as the main conduits of touch-evoked activity between vS1 and vS2 and exhibited elevated synchrony. Focal lesions of the whisker touch-responsive region in vS1 or vS2 degraded touch responses in the unlesioned area, with whisker-specific vS1 lesions degrading whisker-specific vS2 touch responses. Thus, a sparse and superficial population of broadly tuned touch neurons recurrently amplifies touch responses across vS1 and vS2.
Crystal structures of two SmIII complexes with dipicolinate [DPA]2− ligands: comparison of luminescent properties of products obtained at different pH values
Authors: Mortensen Sabina Svava , Sørensen Thomas Just
Published: June 2023

The formation of the two title compounds, Na3[Sm(DPA)3]·14H2O trisodium tris(pyridine-2,6-dicarboxylato-κ3
O
2,N,O
6)samarate(III) tetradecahydrate, Na3[Sm(C7H3NO4)3]·14H2O, and catena-poly[[[diaqua(6-carboxypyridine-2-carboxylato-κ3
O
2,N,O
6)samarium(III)]-μ-pyridine-2,6-dicarboxylato-κ4
O
2,N,O
6:O
2] tetrahydrate], {[Sm(C7H3NO4)(C7H4NO4)(H2O)2]·4H2O}
n
, depends on the pH value adjusted with NaOH solution. In both crystal structures, the coordination spheres of the SmIII cations were found to be best described by a tricapped trigonal prism (TTP), with a more regular O6N3 donor set for Na3[Sm(DPA)3]·14H2O than that of O7N2 for [Sm(DPA)(HDPA)(H2O)2]·4H2O. The supramolecular features of both crystal structures are dominated by O—H...O hydrogen bonds between water molecules and the O atoms of the dipicolinato ligands. Samples were made from solutions at pH = 2, pH = 5, pH = 7, and pH = 10, and the crystals present in each sample were ground to a powder. The powder samples were analyzed with powder X-ray diffraction and luminescence spectroscopy. The splitting of the bands in the luminescence spectra recorded on powders at 77 K was observed to vary with the pH.