bluuebunny/crossref_metadata_2025 huggingface dataset:
Ultra-fast deep-learned pediatric CNS tumor classification during surgery
Authors: Vermeulen C. , Pagès-Gallego M. , Kester L. , Kranendonk M.E.G. , Wesseling P. , van der Lugt J. , van Baarsen K. , Hoving E.W. , Tops B.B.J. , de Ridder J.
Published: January 2023

The primary treatment of CNS tumors starts with a neurosurgical resection in order to obtain tumor tissue for diagnosis and to reduce tumor load and mass effect. The neurosurgeon has to decide between radical resection versus a more conservative strategy to prevent surgical morbidity. The prognostic impact of a radical resection varies between tumor types. However due to a lack of pre-operative tissue-based diagnostics, limited knowledge of the precise tumor type is available at the time of surgery. Current standard practice includes preoperative imaging and intraoperative histological analysis, but these are not always conclusive. After surgery, histopathological and molecular tests are performed to diagnose the precise tumor type. The results may indicate that an additional surgery is needed or that the initial surgery could have been less radical. Using rapid Nanopore sequencing, a sparse methylation profile can be directly obtained during surgery, making it ideally suited to enable intraoperative diagnostics. We developed a state-of-the-art neural-network approach called Sturgeon, to deliver trained models that are lightweight and universally applicable across patients and sequencing depths. We demonstrate our method to be accurate and fast enough to provide a correct diagnosis with as little as 20 to 40 minutes of sequencing data in 45 out of 49 pediatric samples, and inconclusive results in the other four. In four intraoperative cases we achieved a turnaround time of 60-90 minutes from sample biopsy to result; well in time to impact surgical decision making. We conclude that machine-learned diagnosis based on intraoperative sequencing can assist neurosurgical decision making, allowing neurological comorbidity to be avoided or preventing additional surgeries.
General practitioners ending their practice and impact on patients’ health, health care use and mortality. A protocol for national registry cohort studies in Norway, 2006 to 2021
Authors: Vinjerui Kristin Hestmann , Anthun Kjartan Sarheim , Asheim Andreas , Carlsen Fredrik , Mjølstad Bente Prytz , Nilsen Sara Marie , Pape Kristine , Håkon Bjørngaard Johan
Published: January 2023

Introduction

Continuous general practitioner (GP) and patient relations associate with positive health outcomes. Termination of GP-practice is unavoidable, while consequences of final breaks in relations are less explored. We will study how an ended GP-relation affects patient’s health care utilization and mortality, compared to patients with a continuous GP-relation.

Methods and analysis

Linking personal-level national registries data on GP-affiliation, sociodemographic characteristics, health care use and mortality, from 2008 to 2021, we will identify patients of GPs terminating practice, and match these GP-patient pairs on age, sex (both), immigrant status and education (patient), and number of patients and practice period (GPs), to GP-patient pairs with a continuous relationship in other municipalities, and compare acute and elective primary and specialist health care use mortality, before and after ended GP-practice, using Poisson regression with high-dimensional fixed effects. We will address expected modifying factors, such as patients with complex health care needs, quality of termination and GP-availability in the municipalities.

Ethics and dissemination

This study protocol is part of the approved project Improved Decisions with Causal Inference in Health Services Research, 2016/2158/REK Midt (the Regional Committees for Medical and Health Research Ethics) and does not require consent. We will publish in peer-reviewed journals, accessible in NTNU Open, and present at scientific conferences. To reach a broader audience, we will summarize articles in the project’s web page, regular and social media, and disseminate to relevant stakeholders.

Strengths and limitations of this study

This study adds to research on GP-patient relation continuity and associations, exploring termination of relations and designing a natural experiment in register data, facilitating causal inference.

The study includes the entire Norwegian population and their general practitioners (GPs) from 2008 to 2021, linking several mandatory, high-quality, healthcare, and demographic registers on a personal level.

The register data include exact time points (xxx or months? xxx) for the intervention, termination of GP-relation, and the outcomes, health care utilization and death.

By matching GP-patient pairs in practice period and distinct municipalities, we minimize time-varying confounders and dilution of effects.

As in all observational studies, our results may be influenced by residual confounding
Fetal spina bifida associates with dysregulation in nutrient-sensitive placental gene networks: findings from a matched case-control study
Authors: White Marina , Arif-Pardy Jayden , Van Mieghem Tim , Connor Kristin L
Published: January 2023

To improve outcomes of fetuses with spina bifida (SB), better knowledge is needed on the molecular drivers of SB and its comorbidities. We have recently shown in historical data that SB often associates with reduced fetal growth. We here use placental transcriptome sequencing and a novel nutrient-focused analysis pipeline to determine whether this association is due to placental dysfunction. We show that fetuses with SB have dysregulation in placental gene networks that play a role in nutrient transport, branching angiogenesis, and immune/inflammatory processes. Several of these networks are sensitive to multiple micronutrients, other than the well-known folic acid, and this deserves further investigation. An improved understanding of placental phenotype in fetuses with SB may help identify novel mechanisms associated with SB and its comorbidities, and reveal new targets to improve fetal outcomes in this population.
The development of a guidance document for interprofessional collaborative advance care planning in dementia care
Authors: Khemai C. , Janssen D.J.A. , Van Dongen J. , Biesmans J.M.A. , Bolt S.R. , Schols J.M.G.A. , Meijers J.M.M.
Published: January 2023

Advance care planning (ACP) is an essential part of palliative dementia care and should embrace a collaborative approach involving persons with dementia, family members and various healthcare professionals (HCPs). This study aimed to develop a guidance document for IPC in ACP in dementia care for HCPs from nursing homes, using a mixed-method design and taking an appreciative inquiry approach comprising semi-structured focus groups and interviews with HCPs. The study participants (N=18) included certified nurses, registered nurses, a quality nurse, nurse specialists, team leaders, physicians specialized in old age medicine, psychologists, and a teacher/researcher (mean age 43.8 years; 79% female). The data analysis indicated six elements to include in the guidance document. The first three elements concerned common awareness of collaborative ACP in dementia care, role clarification for various professions, and actively working towards shared goals in collaborative ACP in dementia care. The last three themes focused on the dynamic processes in collaborative ACP in dementia care: interprofessional communication, coordination, monitoring and evaluation. This study provides a guidance document that HCPs could use in practice to identify the elements they can address to improve collaborative ACP in dementia care.
Antibody escape, the risk of serotype formation, and rapid immune waning: modeling the implications of SARS-CoV-2 immune evasion
Authors: Albright Catherine , Van Egeren Debra , Thakur Aditya , Chakravarty Arijit , White Laura F. , Stoddard Madison
Published: January 2023

As the COVID-19 pandemic progresses, widespread community transmission of SARS-CoV-2 has ushered in a volatile era of viral immune evasion rather than the much-heralded stability of “endemicity” or “herd immunity.” At this point, an array of viral variants has rendered essentially all monoclonal antibody therapeutics obsolete and strongly undermined the impact of vaccinal immunity on SARS-CoV-2 transmission. In this work, we demonstrate that antigenic drift resulting in evasion of pre-existing immunity is highly evolutionarily favored and likely to cause waves of short-term transmission. In the long-term, invading variants that induce weak cross-immunity against pre-existing strains may co-circulate with those pre-existing strains. This would result in the formation of serotypes that increase disease burden, complicate SARS-CoV-2 control and raise the potential for increases in viral virulence. Less durable immunity does not drive positive selection as a trait, but such strains may transmit at high levels if they establish. Overall, our results draw attention to the importance of inter-strain cross-immunity as a driver of transmission trends and the importance of early immune evasion data to predict the trajectory of the pandemic.
One marine protected area is not enough: The trophic ecology of the broadnose sevengill shark (Notorynchus cepedianus) in the Southwest Atlantic
Authors: Funes Manuela , De Wysiecki Agustín M. , Bovcon Nelson D. , Jaureguizar Andrés J. , Irigoyen Alejo J.
Published: January 2023

The broadnose sevengill shark (Notorynchus cepedianus) has been categorized as Vulnerable by the IUCN and shows a declining population trend in the Southwest Atlantic. Bycatch and poaching are the major threats in the region.

Although some ecological requirements have been described, there are still several information gaps regarding its ecology. Important aspects of its trophic ecology, like main prey items or key feeding grounds, remain uncertain and are essential to design effective conservation strategies.

We applied stable isotope and stomach content analyses to describe the trophic ecology of sevengill shark within a marine protected area of Peninsula Valdés in Patagonia, Argentina.

The stomach content analysis determined the southern elephant seal,Mirounga leonina, as the most frequently regurgitated prey item (70%F) during abundance peaks of both species in Península Valdes. The stable isotope analysis indicated that the overall contribution of the elephant seal to the diet of the sevengill shark was around 30% and that this percentage varied with the size of individuals.

Present results strengthen the current understanding of the trophic ecology of the sevengill shark. This study confirmed the use of the marine protected area as an essential foraging ground and identified its main prey items. Also, it reinforced the critical need to expand conservation tools beyond this particular coastal protection.
Functional effects of haemoglobin can be rescued by haptoglobin in anin vitromodel of subarachnoid haemorrhage
Authors: Warming Hannah , Deinhardt Katrin , Garland Patrick , More John , Bulters Diederik , Galea Ian , Vargas-Caballero Mariana
Published: January 2023

During subarachnoid haemorrhage, a blood clot forms in the subarachnoid space releasing extracellular haemoglobin (Hb), which causes oxidative damage and cell death in surrounding tissues. High rates of disability and cognitive decline in SAH survivors is attributed to loss of neurons and functional connections during secondary brain injury. Haptoglobin sequesters Hb for clearance, but this scavenging system is overwhelmed after a haemorrhage. Whilst exogenous haptoglobin application can attenuate cytotoxicity of Hb andin vivo, andin vivothe functional effects of sub-lethal Hb concentrations on surviving neurons and whether cellular function can be protected with haptoglobin treatment remain unclear. Here we use cultured neurons to investigate neuronal health and function across a range of Hb concentrations to establish the thresholds for cellular damage and investigate synaptic function. Hb impairs ATP concentrations and cytoskeletal structure. At clinically relevant but sublethal Hb concentrations, synaptic AMPAR-driven currents are reduced, accompanied by a reduction in GluA1 subunit expression. Haptoglobin co-application can prevent these deficits by scavenging free Hb to reduce it to sub-threshold concentrations and does not need to be present at stoichiometric amounts to achieve efficacy. Haptoglobin itself does not impair measures of neuronal health and function at any concentration tested. Our data highlight a role for Hb in modifying synaptic function after SAH, which may link to impaired cognition or plasticity, and support the development of haptoglobin as a therapy for subarachnoid haemorrhage.
Structural basis for triacylglyceride extraction from mycobacterial inner membrane by MFS transporter Rv1410
Authors: Remm Sille , De Vecchis Dario , Schöppe Jendrik , Hutter Cedric A.J. , Gonda Imre , Hohl Michael , Newstead Simon , Schäfer Lars V. , Seeger Markus A.
Published: January 2023

Mycobacterium tuberculosisis protected from antibiotic therapy by a multi-layered hydrophobic cell envelope. Major facilitator superfamily (MFS) transporter Rv1410 and the periplasmic lipoprotein LprG are involved in transport of triacylglycerides (TAGs) that seal the mycomembrane. Here, we report a 2.7 Å structure of a mycobacterial Rv1410 homologue, which adopts an outward-facing conformation and exhibits unusual transmembrane helix 11 and 12 extensions that protrude ∼20 Å into the periplasm. A small, very hydrophobic cavity suitable for lipid transport is constricted by a unique and functionally important ion-lock likely involved in proton coupling. Combining mutational analyses and MD simulations, we propose that TAGs are extracted from the core of the inner membrane into the central cavity via lateral clefts present in the inward-facing conformation. The periplasmic helix extensions are crucial for lifting TAGs away from the membrane plane and channeling them into the lipid binding pocket of LprG.
Aluminium alters excitability by inhibiting calcium, sodium and potassium currents in bovine chromaffin cells
Authors: Baraibar Andrés M. , de Pascual Ricardo , Jiménez Carretero Victoria , Hernández Juárez Natalia , Aguirregabiria Alonso Itxaso Edurne , Hernández-Guijo Jesús M.
Published: January 2023

Aluminium (Al3+) has long been related to neurotoxicity and neurological diseases. This study aims to describe the specific actions of this metal on cellular excitability and neurotransmitter release. Al3+reduced intracellular calcium concentrations around 25% and decreased catecholamine secretion in a dose-dependent manner, with an IC50of 89.1 μM. Al3+blocked calcium currents in a time- and concentration-dependent manner with an IC50of 560 μM. This blockade was irreversible, since it did not recover after wash-out. Moreover, Al3+produced a bigger blockade on N-, P- and Q-type calcium channels subtypes (69.5%) than on L-type channels subtypes (50.5%). Sodium currents were also inhibited by Al3+in a time- and concentration-dependent manner, 24.3% blockade at the closest concentration to the IC50(419 μM). This inhibition was reversible. Voltage-dependent potassium currents were non-significantly affected by Al3+. Nonetheless, calcium/voltage-dependent potassium currents were inhibited in a concentration-dependent manner, with an IC50of 447 μM. This inhibition was related to the depression of calcium influx through voltage-dependent calcium channels subtypes coupled to BK channels. In summary, the blockade of these ionic conductances altered cellular excitability that reduced the action potentials firing and so, the neurotransmitter release and the synaptic transmission. These findings prove that aluminium has neurotoxic properties because it alters neuronal excitability by inhibiting the sodium currents responsible for the generation and propagation of impulse nerve, the potassium current responsible for the termination of action potentials, and the calcium current responsible for the neurotransmitters release.
Ultrasensitive detection of circulating LINE-1 ORF1p as a specific multi-cancer biomarker
Authors: Taylor Martin S. , Wu Connie , Fridy Peter C. , Zhang Stephanie J. , Senussi Yasmeen , Wolters Justina C. , Cheng Wen-Chih , Heaps John , Miller Bryant D. , Mori Kei , Cohen Limor , Jiang Hua , Molloy Kelly R. , Chait Brian T. , Goggins Michael , Bhan Irun , Franses Joseph W. , Yang Xiaoyu , Taplin Mary-Ellen , Wang Xinan , Christiani David C. , Johnson Bruce E. , Meyerson Matthew , Uppaluri Ravindra , Egloff Ann Marie , Denault Elyssa N. , Spring Laura M. , Wang Tian-Li , Shih Ie-Ming , Jung Euihye , Arora Kshitij S. , Zukerberg Lawrence R. , Yilmaz Osman H. , Chi Gary , Norden Bryanna L. , Song Yuhui , Nieman Linda , Parikh Aparna R. , Strickland Matthew , Corcoran Ryan B. , Mustelin Tomas , Eng George , Yilmaz Ömer H. , Matulonis Ursula A. , Skates Steven J. , Rueda Bo R. , Drapkin Ronny , Klempner Samuel J. , Deshpande Vikram , Ting David T. , Rout Michael P. , LaCava John , Walt David R. , Burns Kathleen H.
Published: January 2023

Improved biomarkers are needed for early cancer detection, risk stratification, treatment selection, and monitoring treatment response. While proteins can be useful blood-based biomarkers, many have limited sensitivity or specificity for these applications. Long INterspersed Element-1 (LINE-1, L1) open reading frame 1 protein (ORF1p) is a transposable element protein overexpressed in carcinomas and high-risk precursors during carcinogenesis with negligible detectable expression in corresponding normal tissues, suggesting ORF1p could be a highly specific cancer biomarker. To explore the potential of ORF1p as a blood-based biomarker, we engineered ultrasensitive digital immunoassays that detect mid-attomolar (10-17M) ORF1p concentrations in patient plasma samples across multiple cancers with high specificity. Plasma ORF1p shows promise for early detection of ovarian cancer, improves diagnostic performance in a multi-analyte panel, and provides early therapeutic response monitoring in gastric and esophageal cancers. Together, these observations nominate ORF1p as a multi-cancer biomarker with potential utility for disease detection and monitoring.

Statement of Significance

LINE-1 ORF1p transposon protein is pervasively expressed in many cancers and a highly specific biomarker of multiple common, lethal carcinomas and their high-risk precursors in tissue and blood. Ultrasensitive ORF1p assays from as little as 25 μL plasma are novel, rapid, cost-effective tools in cancer detection and monitoring.
Spatiotemporal dynamics of self-generated imagery reveal a reverse cortical hierarchy from cue-induced imagery
Authors: Hu Yiheng , Yu Qing
Published: January 2023

Visual imagery, the ability to generate visual experience in the absence of direct external stimulation, allows for the construction of rich internal experience in our mental world. Most imagery studies to date have focused on cue-induced imagery, namely the to-be-imagined contents were triggered by external cues. It has remained unclear how internal experience derives volitionally in the absence of any external cues, and whether this kind of self-generated imagery relies on an analogous cortical network as cue-induced imagery. Here, leveraging a novel self-generated imagery paradigm, we systematically examined the spatiotemporal dynamics of self-generated imagery, by having participants volitionally imagining one of the orientations from a learned pool; and of cue-induced imagery, by having participants imagining line orientations based on associative cues acquired previously. Using electroencephalography (EEG) and functional magnetic resonance imaging (fMRI), in combination with multivariate encoding and decoding approaches, our results revealed largely overlapping neural signatures of cue-induced and self-generated imagery in both EEG and fMRI; yet, these neural signatures displayed substantially differential sensitivities to the two types of imagery: self-generated imagery was supported by an enhanced involvement of anterior cortex in generating and maintaining imagined contents, as evidenced by enhanced neural representations of orientations in sustained potentials in central channels in EEG, and in posterior frontal cortex in fMRI. By contrast, cue-induced imagery was supported by enhanced neural representations of orientations in alpha-band activity in posterior channels in EEG, and in early visual cortex in fMRI. These results jointly support a reverse cortical hierarchy in generating and maintaining imagery contents in self-generated versus externally-cued imagery.
Extensive hybridisation between multiple differently adapted species may aid persistence in a changing climate
Authors: Satokangas I , Nouhaud P , Seifert B , Punttila P , Schultz R , Jones MM , Sirén J. , Helanterä H , Kulmuni J
Published: January 2023

Hybridisation and gene flow can have both deleterious and adaptive consequences for natural populations and species. To better understand the extent and consequences of hybridisation in nature, information on naturally hybridising non-model organisms is required, including characterising the structure and extent of natural hybrid zones. Here we study natural populations of five keystone mound-building wood ant (Formica rufagroup) species across Finland. No genomic studies across the species group exist and the extent of hybridisation and genomic differentiation in sympatry is unknown. Combining genome-wide and morphological data, we show thatFormica rufa,F. aquilonia,F. lugubris, andF. pratensisform distinct gene pools in Finland. We demonstrate more extensive hybridisation than previously thought between all five species and reveal a mosaic hybrid zone betweenF. aquilonia,F. rufaandF. polyctena. We show that hybrids between these climatically differently adapted species occupy warmer habitats than the cold-adapted parentF. aquilonia. This suggests hybrids occupy a different microclimatic niche compared to the locally abundant parent. We propose that wood ant hybridisation may increase with a warming climate, and warm winters, in particular, may provide a competitive advantage for the hybrids overF. aquiloniain the future. In summary, our results demonstrate how extensive hybridisation may help persistence in a changing climate. Additionally, they provide an example on how mosaic hybrid zones can have significant ecological and evolutionary consequences because of their large extent and independent hybrid populations that face both ecological and intrinsic selection pressures.
E2EDA: Protein domain assembly based on end-to-end deep learning
Authors: Zhu Hai-Tao , Xia Yu-Hao , Zhang Guijun
Published: January 2023

With the development of deep learning, almost all single-domain proteins can be predicted at experimental resolution. However, the structure prediction of multi-domain proteins remains a challenge. Achieving end-to-end protein domain assembly and further improving the accuracy of the full-chain modelling by accurately predicting inter-domain orientation while improving the assembly efficiency will provide significant insights into structure-based drug discovery. In addition, the available GPU memory limits the size of a full-chain protein which can be predicted. Based on the divide-and-conquer strategy, the single-domain structure is predicted by the state-of-the-art prediction method, such as AlphaFold2, and then assembled into a full-chain model through the domain assembly method, which can effectively reduce the demand for hardware resources. In this work, we propose an End-To-End Domain Assembly method based on deep learning, named E2EDA. We first develop an EffificientNetV2-based deep learning model (RMNet), which is specialised for predicting inter-domain orientations. The RMNet uses an attention mechanism to predict inter-domain rigid motion by fusing sequence features, multiple template features and single-domain features. Then, the predicted rigid motions are converted into inter-domain spatial transformations to assemble full-chain models of multi-domain proteins directly without time-consuming simulation processes. Finally, a scoring strategy, RMscore, is designed to select the best model from multiple assembled models to improve assembly accuracy. The experimental results show that the average TM-score of the model assembled by E2EDA on the benchmark set (356) is 0.84, which is better than other domain assembly methods SADA (0.80), DEMO (0.74) and AIDA (0.63). Meanwhile, on our constructed human protein dataset from AlphaFold DB, the model reassembled by E2EDA is 6.8% higher than the full-chain model predicted by AlphaFold2, indicating that E2EDA can capture more accurate inter-domain orientations to improve the quality of the model predicted by AlphaFold2. Furthermore, the average running time of E2EDA on the benchmark is reduced by 74.6% compared with the domain assembly simulation method SADA, which indicates that E2EDA can effectively improve assembly efficiency through an end-to-end manner.The online server is athttp://zhanglab-bioinf.com/E2EDA/.
hb or not hb - when and why accounting for background mortality in toxicological survival models matters?
Authors: Plantade Julie , Baudrot Virgile , Charles Sandrine
Published: January 2023

Decisions in Environmental Risk Assessment (ERA) about impacts of chemical compounds on different species are based on critical effect indicators such as the 50% lethal concentration (LC50). Regulatory documents recommend concentration-response (or concentration-effect) model fitting on standard toxicity test data to getLC50values. However, toxicokinetic-toxicodynamic (TKTD) models proved their efficiency to better exploit toxicity test data, at Tier-2 but also at Tier-1, delivering time-independent indicators. In particular,LC50values can be obtained from the reduced General Unified Threshold model of Survival (GUTS-RED) with both variants, Stochastic Death and Individual Tolerance, that include parameterhb, the background mortality. Estimatinghbduring the fitting process or not depends on studies and fitting habits, while it may strongly influence the other GUTS-RED parameters, and consequently theLC50estimate. We hypothesized that estimatinghbfrom all data in all replicates over time should provide more preciseLC50estimates. We then explored how estimatinghbimpacted: (i) GUTS-RED model parameters; (ii) goodness-of-fit criteria (fitting plot, posterior predictive check, parameter correlation); (iii)LC50accuracy and precision. We finally show that estimatinghbdoes not impact theLC50precision while providing more accurate and precise GUTS parameter estimates. Hence, estimatinghbwould lead to a more protective ERA.

Graphical abstract

Specifications table
Zinc Alters the Supramolecular Organization of Nucleic Acid Complexes with Full-Length TIA1
Authors: Yang Yizhuo , Fritzsching Keith J. , He Sasha , McDermott Ann E.
Published: January 2023

T-Cell Intracellular Antigen-1 (TIA1) is a 43 kDa multi-domain RNA-binding protein involved in stress granule formation during eukaryotic stress response, and has been implicated in neurodegenerative diseases including Welander distal myopathy and amyotrophic lateral sclerosis. TIA1 contains three RNA recognition motifs (RRMs), which are capable of binding nucleic acids and a C-terminal Q/N-rich prion-related domain (PRD) which has been variously described as intrinsically disordered or prion inducing and is believed to play a role in promoting liquid-liquid phase separation connected with the assembly of stress granule formation. Motivated by the fact that our prior work shows RRMs 2 and 3 are well-ordered in an oligomeric full-length form, while RRM1 and the PRD appear to phase separate, the present work addresses whether the oligomeric form is functional and competent for binding, and probes the consequences of nucleic acid binding for oligomerization and protein conformation change. New SSNMR data show that ssDNA binds to full-length oligomeric TIA1 primarily at the RRM2 domain, but also weakly at the RRM3 domain, and Zn2+binds primarily to RRM3. Binding of Zn2+and DNA was reversible for the full-length wild type oligomeric form, and did not lead to formation of amyloid fibrils, despite the presence of the C-terminal prion-related domain. While TIA1:DNA complexes appear as long “daisy chained” structures, the addition of Zn2+caused the structures to collapse. We surmise that this points to a regulatory role for Zn2+. By occupying various “half” binding sites on RRM3 Zn2+may shift the nucleic acid binding off RRM3 and onto RRM2. More importantly, the use of different half sites on different monomers may introduce a mesh of crosslinks in the supramolecular complex rendering it compact and markedly reducing the access to the nucleic acids (including transcripts) from solution.
The characterisation of phytoene synthase-1 and 2, and 1-D-deoxy-xylulose 5-phosphate synthase genes from red chilli pepper (Capsicum annuum)
Authors: Berry Harriet M. , Zhou Nan , Rickett Daniel V. , Baxter Charles J. , Enfissi Eugenia M. A. , Fraser Paul D.
Published: January 2023

The red colouration of ripe chilli pepper fruit is due to the presence of the carotenoid capsanthin. 1-D-deoxy-xylulose 5-phosphate synthase (DXS) and phytoene synthase(s) (PSY) are influential biosynthetic steps in the carotenoid pathway. A panel of chilli accessions for varying fruit colour intensity revealed the correlation of carotenoid content withPSYandDXStranscript levels. ThePSYandDXSgenes were sequenced from high and low carotenoid genotypes to deduce potential allelic variation.PSY-1 and -2 showed tissue specific expression, withPSY-1and 2 expressed in chromoplast and chloroplast containing tissues, respectively. Protein modelling, phylogenetic analysis and transcription factor analysis was conducted to understand how the allelic variation identified could affect carotenoid biosynthesis and regulation, and subsequently colour intensity phenotype. A candidate mutation located in the transit peptide of the PSY-1 protein sequence was identified in the low colour intensity genotype. Within the promoter region of theDXSgene present in the high colour intensity genotype sequence variation was determined in the glyceraldehyde 3-phosphate binding motif (GAPF) of the promoter region. These data can be exploited to develop tools and resources for the breeding of high colour intensity chilli pepper fruit.

Key policy highlights

Using the molecular findings disclosed in this article the potential exists to develop molecular markers for the breeding varieties of chilli peppers with improved aesthetic consumer preference and nutritional attributes.
Resting-state fMRI signals contain spectral signatures of local hemodynamic response timing
Authors: Bailes Sydney M. , Gomez Daniel E. P. , Setzer Beverly , Lewis Laura D.
Published: January 2023

Functional magnetic resonance imaging (fMRI) has proven to be a powerful tool for noninvasively measuring human brain activity; yet, thus far, fMRI has been relatively limited in its temporal resolution. A key challenge is understanding the relationship between neural activity and the blood-oxygenation-level-dependent (BOLD) signal obtained from fMRI, generally modeled by the hemodynamic response function (HRF). The timing of the HRF varies across the brain and individuals, confounding our ability to make inferences about the timing of the underlying neural processes. Here we show that resting-state fMRI signals contain information about HRF temporal dynamics that can be leveraged to understand and characterize variations in HRF timing across both cortical and subcortical regions. We found that the frequency spectrum of resting-state fMRI signals significantly differs between voxels with fast versus slow HRFs in human visual cortex. These spectral differences extended to subcortex as well, revealing significantly faster hemodynamic timing in the lateral geniculate nucleus of the thalamus. Ultimately, our results demonstrate that the temporal properties of the HRF impact the spectral content of resting-state fMRI signals and enable voxel-wise characterization of relative hemodynamic response timing. Furthermore, our results show that caution should be used in studies of resting-state fMRI spectral properties, as differences can arise from purely vascular origins. This finding provides new insight into the temporal properties of fMRI signals across voxels, which is crucial for accurate fMRI analyses, and enhances the ability of fast fMRI to identify and track fast neural dynamics.
PI(3,5)P2Controls the Signaling Activity of Class I PI3K
Authors: Sun Jiachen , Zalejski Julian , Song Seohyeon , Sharma Ashutosh , Wang Wei , Hu Yusi , Lo Wen-Ting , Koch Philipp Alexander , Singh Jagriti , Singaram Indira , An Baoshu , Zhao Jean J. , Gong Liang-Wei , Haucke Volker , Gao Ruixuan , Cho Wonhwa
Published: January 2023

3-Phosphoinositides are ubiquitous cellular lipids that play pivotal regulatory roles in health and disease. Among 3-phosphoinositides, phosphatidylinositol-3,5-bisphosphate (PI(3,5)P2) remains the least understood species in terms of its spatiotemporal dynamics and physiological function due to the lack of a specific sensor that allows spatiotemporally resolved quantitative imaging of PI(3,5)P2. Using a newly developed ratiometric PI(3,5)P2sensor engineered from the C-terminal SH2 domain of Class I phosphoinositide 3-kinases (PI3K)-p85α subunit we demonstrate that a unique pool of PI(3,5)P2is generated on lysosomes and late endosomes in response to growth factor stimulation. This PI(3,5)P2, the formation of which is mediated sequentially by Class II PI3KC2β and PIKfyve, plays a crucial role in terminating the activity of growth factor-stimulated Class I PI3K, one of the most frequently mutated proteins in cancer, via specific interaction with its regulatory p85 subunit. A small molecule inhibitor of p85α-PI(3,5)P2binding specifically blocks the feedback inhibition of Class I PI3K by PI(3,5)P2and thus serves as a PI3K activator that promotes neurite growth. Furthermore, cancer-causing mutations of the Class I PI3K-p85 subunit inhibit p85-PI(3,5)P2interaction and thereby induce sustained activation of Class I PI3K. Our results unravel a hitherto unknown spatiotemporally specific regulatory function of PI(3,5)P2that links Class I and II PI3Ks and modulates the magnitude of PI3K-mediated growth factor signaling. These results also suggest new therapeutic possibilities for treating cancer patients with p85 mutations and promoting wound healing and tissue regeneration.
Structural asymmetry in biotic interactions as a tool to understand and predict ecological persistence
Authors: Allen-Perkins Alfonso , García-Callejas David , Bartomeus Ignasi , Godoy Oscar
Published: January 2023

A universal feature of ecological systems is that species do not interact with others with the same sign and strength. Yet, the consequences of this asymmetry in biotic interactions for the short- and long-term persistence of individual species and entire communities remains unclear. Here, we develop a set of metrics to evaluate how asymmetric interactions among species translate to asymmetries in their individual vulnerability to extinction under changing environmental conditions. These metrics, which solve previous limitations of how to independently quantify the size from the shape of the so-called feasibility domain, provide rigorous advances to understand simultaneously why some species and communities present more opportunities to persist than others. We further demonstrate that our shape-related metrics are useful to predict short-term changes in species’ relative abundances during seven years in a Mediterranean grassland. Our approach is designed to be applied to any ecological system regardless of the number of species and type of interactions. With it, we show that is possible to obtain both mechanistic and predictive information on ecological persistence for individual species and entire communities, paving the way for a stronger integration of theoretical and empirical research.
Reticulocytes in donor RBC units enhance RBC alloimmunization
Authors: Thomas Tiffany A. , Qiu Annie , Kim Christopher Y. , Gordy Dominique E. , Miller Anabel , Tredicine Maria , Dzieciatkowska Monika , Zotti Flavia Dei , Hod Eldad A. , D’Alessandro Angelo , Zimring James C. , Spitalnik Steven L. , Hudson Krystalyn E.
Published: January 2023

Although red blood cell (RBC) transfusions save lives, some patients develop clinically-significant alloantibodies against donor blood group antigens, which then have adverse effects in multiple clinical settings. Few effective measures exist to prevent RBC alloimmunization and/or eliminate alloantibodies in sensitized patients. Donor-related factors may influence alloimmunization; thus, there is an unmet clinical need to identify which RBC units are immunogenic. Repeat volunteer blood donors and donors on iron supplements have elevated reticulocyte counts compared to healthy non-donors. Early reticulocytes retain mitochondria and other components, which may act as danger signals in immune responses. Herein, we tested whether reticulocytes in donor RBC units could enhance RBC alloimmunization. Using a murine model, we demonstrate that transfusing donor RBC units with increased reticulocyte frequencies dose-dependently increase RBC alloimmunization rates and alloantibody levels. Transfusing reticulocyte-rich RBC units was associated with increased RBC clearance from the circulation and a robust proinflammatory cytokine response. As compared to previously reported post-transfusion RBC consumption patterns, erythrophagocytosis from reticulocyte-rich units was increasingly performed by splenic B cells. These data suggest that reticulocytes in a donated RBC unit impact the quality of blood transfused, are targeted to a distinct compartment, and may be an underappreciated risk factor for RBC alloimmunization.
Chemokine positioning determines mutually exclusive roles for their receptors in extravasation of pathogenic human T cells
Authors: Parween Farhat , Singh Satya P. , Zhang Hongwei H , Kathuria Nausheen , Otaizo-Carrasquero Francisco A. , Shamsaddini Amirhossein , Gardina Paul J. , Ganesan Sundar , Kabat Juraj , Lorenzi Hernan A. , Myers Timothy G. , Farber Joshua M.
Published: January 2023

Pro-inflammatory T cells co-express multiple chemokine receptors, but the distinct functions of individual receptors on these cells are largely unknown. Human Th17 cells uniformly express the chemokine receptor CCR6, and we discovered that the subgroup of CD4+CCR6+cells that co-express CCR2 possess a pathogenic Th17 signature, can produce inflammatory cytokines independent of TCR activation, and are unusually efficient at transendothelial migration (TEM). The ligand for CCR6, CCL20, was capable of binding to activated endothelial cells (ECs) and inducing firm arrest of CCR6+CCR2+cells under conditions of flow - but CCR6 could not mediate TEM. By contrast, CCL2 and other ligands for CCR2, despite being secreted from both luminal and basal sides of ECs, failed to bind to the EC surfaces - and CCR2 could not mediate arrest. Nonetheless, CCR2 was required for TEM. To understand if CCR2’s inability to mediate arrest was due solely to an absence of EC-bound ligands, we generated a CCL2-CXCL9 chimeric chemokine that could bind to the EC surface. Although display of CCL2 on the ECs did indeed lead to CCR2-mediated arrest of CCR6+CCR2+cells, activating CCR2 with surface-bound CCL2 blocked TEM. We conclude that mediating arrest and TEM are mutually exclusive activities of chemokine receptors and/or their ligands that depend, respectively, on chemokines that bind to the EC luminal surfaces versus non-binding chemokines that form transendothelial gradients under conditions of flow. Our findings provide fundamental insights into mechanisms of lymphocyte extravasation and may lead to novel strategies to block or enhance their migration into tissue.
Ageing impairs the regenerative capacity of regulatory T cells in central nervous system remyelination
Authors: de la Fuente Alerie Guzman , Dittmer Marie , Heesbeen Elise , de la Vega Gallardo Nira , White Jessica , Young Andrew , McColgan Tiree , Dashwood Amy , Mayne Katie , Cabeza-Fernández Sonia , Falconer John , Rodriguez-Baena Francisco Javier , McMurran Christopher E. , Innayatullah Mohammed , Rawji Khalil S. , Franklin Robin J.M. , Dooley James , Liston Adrian , Ingram Rebecca , Tiwari Vijay K. , Penalva Rosana , Dombrowski Yvonne , Fitzgerald Denise C.
Published: January 2023

Myelin regeneration (remyelination) is essential to prevent neurodegeneration in demyelinating diseases such as Multiple Sclerosis, however, its efficiency declines with age. Regulatory T cells (Treg) recently emerged as critical players in tissue regeneration, including remyelination. However, the effect of ageing on Treg-mediated regenerative processes is poorly understood. Here, we show that expansion of aged Treg does not rescue age-associated remyelination impairment due to an intrinsically diminished capacity of aged Treg to promote oligodendrocyte differentiation and myelination. This decline in regenerative Treg functions can be rescued by a young environment. We identified Melanoma Cell Adhesion Molecule 1 (MCAM1) and Integrin alpha 2 (ITGA2) as novel candidates of Treg-mediated oligodendrocyte differentiation that decrease with age. Our findings demonstrate that ageing limits the neuroregenerative capacity of Treg, likely limiting their remyelinating therapeutic potential in aged patients, and describe two novel mechanisms implicated in Treg-driven remyelination that may be targetable to overcome this limitation.
Gigantic Macroraptorial Sperm Whale Tooth (cf.Livyatan) from the Miocene of Orange County, California
Authors: Watmore Kristin I. , Prothero Donald R.
Published: January 2023

A fossil tooth from the middle-upper Miocene Monterey or Capistrano Formation in the Orange County Cooper Center Paleontology Collection shows that a gargantuan sperm whale once inhabited the Miocene seas of southern California. Though difficult to diagnose to genus level based on a single, incomplete tooth, comparisons with known Miocene physeteroid whales provide key insight into the affinities of this fossil. Even though the tip is broken, the entire tooth is over 250 mm long and 86 mm in diameter. It has enamel only on the tip of the broken crown and there is no enamel coating over the rest of the tooth. Instead, the tooth consists mostly of layers of cementum over a core of ossified dentin. It is slightly smaller than the largest teeth of the largest known physeteroid, the South American MioceneLivyatan melvillei, a genus that has not been found outside of the Southern Hemisphere besides one record from northern Europe. It is also just slightly smaller than similar gigantic teeth reported from South Africa and Australia from the middle-late Miocene through the early Pliocene. We compared it to other Miocene members of the family such asHoplocetus,Scaldicetus, andZygophyseter, but none have teeth as large as this one. It is bigger than all known specimens of all other North American Miocene physeteroid whales, including another whale from the Monterey Formation,Albicetus oxymycterus. This fossil suggests that giant physeteroid whales closely related toLivyatanlived in the North Pacific. It represents a substantial geographic range extension for giant physeteroid whales, previously known only from the Miocene of the Southern Hemisphere and northern Europe.
Rapid and Highly Efficient Morphogenic Gene-Mediated Hexaploid Wheat Transformation
Authors: Johnson Kari , Chu Uyen Cao , Anthony Geny , Wu Emily , Che Ping , Jones Todd J.
Published: January 2023

The successful employment of morphogenic regulator genes,Zm-Baby Boom(ZmBbm) andZm-Wuschel2(ZmWus2), forAgrobacterium-mediated transformation of maize (Zea maysL.) and sorghum (Sorghum bicolorL.) has been reported to improve transformation by inducing rapid somatic embryo formation. Here, we report two morphogenic gene-mediated wheat transformation methods, either with or without morphogenic and marker gene excision. These methods yield independent-transformation efficiency up to 58% and 75%, respectively. In both cases, the tissue culture duration for generating transgenic plants was significantly reduced from 80 to nearly 50 days. In addition, the transformation process was significantly simplified to make the procedure less labor-intensive, higher-throughput and more cost-effective, by eliminating the requirement for embryonic axis excision, bypassing the necessity for prolonged dual-selection steps for callus formation, and obviating the prerequisite of cytokinin for shoot regeneration. Furthermore, we have demonstrated the flexibility of the methods and generated high-quality transgenic events across multiple genotypes using herbicide (phosphinothricin, ethametsulfuron)- and antibiotic (G418)-based selections.
Distinct nonlinear spectrotemporal integration in primary and secondary auditory cortices
Authors: Kline Amber M. , Aponte Destinee A. , Kato Hiroyuki K.
Published: January 2023

Animals sense sounds through hierarchical neural pathways that ultimately reach higher-order cortices to extract complex acoustic features, such as vocalizations. Elucidating how spectrotemporal integration varies along the hierarchy from primary to higher-order auditory cortices is a crucial step in understanding this elaborate sensory computation. Here we used two-photon calcium imaging and two-tone stimuli with various frequency-timing combinations to compare spectrotemporal integration between primary (A1) and secondary (A2) auditory cortices in mice. Individual neurons showed mixed supralinear and sublinear integration in a frequency-timing combination-specific manner, and we found unique integration patterns in these two areas. Temporally asymmetric spectrotemporal integration in A1 neurons enabled their discrimination of frequency-modulated sweep directions. In contrast, temporally symmetric and coincidence-preferring integration in A2 neurons made them ideal spectral integrators of concurrent multifrequency sounds. Moreover, the ensemble neural activity in A2 was sensitive to two-tone timings, and coincident two-tones evoked distinct ensemble activity patterns from the linear sum of component tones. Together, these results demonstrate distinct roles of A1 and A2 in encoding complex acoustic features, potentially suggesting parallel rather than sequential information extraction between these regions.
Remapping in a recurrent neural network model of navigation and context inference
Authors: Low Isabel I.C. , Giocomo Lisa M. , Williams Alex H.
Published: January 2023

Neurons in navigational brain regions provide information about position, orientation, and speed relative to environmental landmarks. These cells also change their firing patterns (“remap”) in response to changing contextual factors such as environmental cues, task conditions, and behavioral state, which influence neural activity throughout the brain. How can navigational circuits preserve their local computations while responding to global context changes? To investigate this question, we trained recurrent neural network models to track position in simple environments while at the same time reporting transiently-cued context changes. We show that these combined task constraints (navigation and context inference) produce activity patterns that are qualitatively similar to population-wide remapping in the entorhinal cortex, a navigational brain region. Furthermore, the models identify a solution that generalizes to more complex navigation and inference tasks. We thus provide a simple, general, and experimentally-grounded model of remapping as one neural circuit performing both navigation and context inference.