bluuebunny/crossref_metadata_2025_split huggingface dataset:
Experimental evolution under combined thermal-nutritional stress inDrosophila melanogasterresults in evolved shifts in larval thermotolerance and thermal plasticity
Authors: Choy Yeuk Man Movis , Kutz Teresa , Cockerell Fiona E. , Lombardi Emily , Hangartner Sandra , Mirth Christen K. , Sgrò Carla M. 
Published: June 2024

AbstractAnimals are facing increasing thermal and nutritional stress under climate change. Genetic adaptation is necessary to buffer long-term stress. However, it’s unclear whether adaptation to combined stress can occur without compromising viability and thermal plasticity. We tested thermotolerance and thermal plasticity in larvalDrosophila melanogasterselected under different temperatures (18°C, 25°C, 28°C) and diets (standard, diluted, low protein:carbohydrate). Basal cold tolerance was affected by both low protein concentration and temperature; larvae evolved higher basal cold tolerance on diluted and low protein:carbohydrate diets at 18°C and 28°C. Hardening increased cold tolerance for most lines, except those selected at 18°C and 28°C on low protein:carbohydrate diets and 25°C on standard diets. Basal heat tolerance was affected by selection temperature, with higher tolerance in 25°C selection lines. An interaction between selection temperature, selection diet and hardening treatment affected plasticity in heat tolerance, with most selection lines showing reduced heat tolerance upon hardening, except for lines selected at 25°C on low protein diets and at 28°C on standard diets. Our results indicate that adaptation to combined stress allows basal cold tolerance and plasticity in cold tolerance to evolve independently, but not heat tolerance, highlighting the increased vulnerability of ectotherms to long-term climate change.
Impact of cryopreservation on immune cell metabolism as measured by SCENITH
Authors: Luscombe Curtis , Jones Eben , Gregorova Michaela , Jones Nicholas , Rivino Laura 
Published: June 2024

AbstractThe dynamic functioning of immune cells is regulated by cellular metabolic processes, and there is growing interest in the study of immunometabolic correlates of dysfunctional immune responses. SCENITH is a novel flow cytometry-based technique that allows forex vivometabolic profiling of immune cells within heterogeneous samples. Cryopreservation of clinical samples is frequently undertaken to facilitate high throughput processing, but is thought to lead to cellular metabolic dysfunction. We aimed to investigate the impact of cryopreservation on immune cell metabolism, harnessing SCENITH’s unique ability to describe the divergent bioenergetic characteristics of distinct immune cell subsets.We demonstrate that T cells undergoing activation with a CD3/CD28 stimulus are less readily metabolically reprogrammed following cryopreservation. Additionally, we find that cryopreservation introduces a time-dependent metabolic artefact that favours glycolysis and impairs oxidative phosphorylation, suggesting that cryopreservation results in mitochondrial dysfunction. Despite this artefact, SCENITH was still able to reveal the distinct bioenergetic profiles of contrasting immune cells populations following cryopreservation – for example, non-classical monocytes have a higher mitochondrial dependence than classical monocytes, and T cell CD69 expression is associated with an upregulation of glycolytic capacity.Whilst we believe that SCENITH can provide valuable information about immune cell metabolism even in cryopreserved samples, our findings have important implications for the design of future studies. Investigators should carefully consider how to process and store clinical samples to ensure that cryopreservation does not confound analyses, particularly where longitudinal sampling is required.
Inferring metabolite states from spatial transcriptomes using multiple graph neural network
Authors: Luo Jiaxu , Ai Daosheng , Sun Wenzhi 
Published: June 2024

AbstractMetabolism serves as the pivotal interface connecting genotype and phenotype. While various methods are available for predicting metabolite levels from transcriptomic data, their efficacy remains poor. We developed an efficient and adaptable algorithm known as Multiple Graph-based Flux Estimation Analysis (MGFEA). By leveraging single-cell and spatial transcriptomic data, MGFEA enables the inference of metabolite levels. Furthermore, MGFEA can further improve the accuracy of these inferences through exploiting additional metabolome data.
Immunological correlates of protection mediated by a whole organismCryptococcus neoformansvaccine deficient in chitosan
Authors: Specht Charles A. , Wang Ruiying , Oliveira Lorena V. N. , Hester Maureen M. , Gomez Christina , Mou Zhongming , Carlson Diana , Lee Chrono K. , Hole Camaron R. , Lam Woei C. , Upadhya Rajendra , Lodge Jennifer K. , Levitz Stuart M. 
Published: June 2024

AbstractThe global burden of infections due to the pathogenic fungusCryptococcusis substantial in persons with low CD4+T cell counts. Previously, we deleted three chitin deacetylase genes fromC. neoformansto create a chitosan-deficient, avirulent strain, designatedcda1Δ2Δ3Δwhich, when used as a vaccine, protected mice from challenge with virulentC. neoformansstrain KN99. Here, we explored the immunological basis for protection. Vaccine-mediated protection was maintained in mice lacking B cells or CD8+T cells. In contrast, protection was lost in mice lacking α/β T cells or CD4+T cells. Moreover, CD4+T cells from vaccinated mice conferred protection upon adoptive transfer to naive mice. Importantly, while monoclonal antibody-mediated depletion of CD4+T cells just prior to vaccination resulted in complete loss of protection, significant protection was retained in mice depleted of CD4+T cells after vaccination, but prior to challenge. Vaccine-mediated protection was lost in mice genetically deficient in IFNγ, TNFα, or IL-23p19. A robust influx of leukocytes and IFNγ- and TNFα-expressing CD4+T cells was seen in the lungs of vaccinated and challenged mice. Finally, a higher level of IFNγ production by lung cells stimulated ex vivo correlated with lower fungal burden in the lungs. Thus, while B cells and CD8+T cells are dispensable, IFNγ and CD4+T cells have overlapping roles in generating protective immunity prior tocda1Δ2Δ3Δvaccination. However, once vaccinated, protection becomes less dependent on CD4+T cells, suggesting a strategy for vaccinating HIV+persons prior to loss of CD4+T cells.ImportanceThe fungusCryptococcus neoformansis responsible for >100,000 deaths annually, mostly in persons with impaired CD4+T cell function such as AIDS. There are no approved human vaccines. We previously created a genetically engineered avirulent strain ofC. neoformans, designatedcda1Δ2Δ3Δ. When used as a vaccine,cda1Δ2Δ3Δprotects mice against a subsequent challenge with a virulentC. neoformansstrain. Here, we defined components of the immune system responsible for vaccine-mediated protection. We found that while B cells and CD8+T cells were dispensible, protection was lost in mice genetically deficient in CD4+T cells, and the cytokines IFNγ, TNFα, or IL-23. A robust influx of cytokine-producing CD4+T cells was seen in the lungs of vaccinated mice following infection. Importantly, protection was retained in mice depleted of CD4+T cells following vaccination, suggesting a strategy to protect persons who are at risk for future CD4+T cell dysfunction.
Automated and high throughput measurement of leaf stomatal traits in canola
Authors: Yao Lingtian , von Caemmerer Susanne , Danila Florence R 
Published: June 2024

AbstractBackgroundAutomating stomatal trait measurement has gained popularity because of their inherent importance for field phenotyping application as stomata are critical for both carbon capture and water use efficiency in plants. Such tool has been reported for rice, wheat, tomato, barley and oil palm. However, none exist yet for canola, which is an important economic and agronomic crop globally.ResultsWe developed a new toolkit called Stomatal Comprehensive Automated Neural Network or SCAN by combining the use of high-resolution portable digital microscopy with machine learning based on You Only Look Once algorithm (YOLOv8). Digital micrographs of leaf surfaces enter the SCAN pipeline, which includes stomata detection, stomata segmentation and stomatal pore segmentation models, to measure stomatal density, stomatal size and stomatal pore area, respectively. In addition to SCAN’s ability to measure leaf stomatal traits in canola at 89 to 94% accuracy, we also showed that SCAN can be used to predict stomatal density even in species not included in the training set such as Arabidopsis, tobacco, rice, wheat, maize and proso millet. SCAN was designed for the biological science community with the premise that users are not required to possess advanced programming capabilities to manage dependency prerequisites, execute the models, and integrate the analysis. This was achieved by packaging the models into a desktop application system that can be accessed offline.ConclusionOverall, SCAN provides a non-destructive, real-time, portable, and high-throughput measurement of leaf stomatal traits in canola. The minimised hardware requirement and user-friendly desktop application system make SCAN suitable for field phenotyping application.
Benchmarking and quality control for nanopore sequencing and feasibility of rapid genomics in New Zealand: validation phase at a single quaternary hospital
Authors: Nyaga Denis M. , Tsai Peter , Gebbie Clare , Phua Hui Hui , Yap Patrick , Stabej Polona Le Quesne , Farrow Sophie , Rong Jing , Toldi Gergely , Thorstensen Eric , Stark Zornitza , Lunke Sebastian , Gamet Kimberley , Dyk Jodi Van , Greenslade Mark , O’Sullivan Justin M. 
Published: June 2024

AbstractApproximately 200 critically ill infants and children in New Zealand are in high-dependency neonatal/paediatric acute care at any given time, many with suspected genetic conditions, necessitating a scalable distributed solution for rapid genomic testing. We adopt the existing acute care genomics protocol of an accredited laboratory and established an expandable acute care clinical pipeline based around the Oxford Nanopore Technologies PromethION 2 solo system connected to a Bayesian AI-based clinical decision support tool (Fabric GEM™ software). In the establishment phase, we performed benchmarking using Global Alliance for Genomics and Health (GA4GH) benchmarking tools and Genome in a Bottle samples HG002-HG007. We evaluated single nucleotide variants (SNVs) and small insertions-deletions (indels) calls and achieved SNV precision and recall of 0.997 ± 0.0006 and 0.992 ± 0.001, respectively. Small indel identification approached a precision of 0.922 ± 0.019 and recall of 0.838 ± 0.043. Rarefaction analyses demonstrated that SNV identification plateaus at ∼20X coverage, while small indels plateaus at ∼40X coverage. Large genomic variations from Coriell Copy Number Variation Reference Panel 1 (CNVPANEL01) were reliably detected with ∼2M long reads. Finally, we present results obtained from ten trio samples that were processed through the pipeline validation phase, averaging a 5-day turnaround time, conducted in parallel with a clinically accredited short-read rapid genomic testing pipeline.
Preterm birth and paternal mental health during the perinatal period: A systematic review protocol
Authors: Philpott Lloyd Frank , Torsy Tim , D’haenens Florence , Van denhaute Ellen , Tency Inge 
Published: June 2024

AbstractIntroductionDespite the evidence that fatherhood has a long-term positive and protective effect on men’s health, there is also evidence that fatherhood in the perinatal period can be complex and demanding. The challenging nature of fatherhood during the perinatal period can be further compounded by the experience of preterm birth. Preterm birth, defined as a birth occurring before 37 weeks of gestation, has been identified as a risk factor for maternal stress, anxiety, depression and post-traumatic stress. It can be hypothesised that preterm birth is also a risk factor for fathers mental health; however, as no attempt has been made to systematically review studies that have examined preterm births and father’s mental health during the perinatal period it is currently not known how common or signficant the impact of a preterm birth is on father’s mental health during this life stage.AimThe aim of the systematic review will be to critically appraise the empirical evidence that examined preterm birth and father’s mental health during the perinatal period.DesignSystematic reviewMethodsThe review will be guided by the PRISMA reporting process. Electronic databases Medline, CINAHL, the Cochrane Library, PsycARTICLES, PsycINFO, Psychology and Behavioural Sciences Collections will be searched to identify studies that meet the inclusion criteria. Studies that researched preterm birth during the perinatal period will be included if fathers mental health was the principal focus of the research, if fathers mental health was in the title and/or aim of the study or if fathers mental health was an outcome or dependent variable. Data will be extracted and presented in narrative form including tables and figures.Trial registrationTrial registration: the protocol for this systematic review has been registered in PROSPERO [CRD42024536317].https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=536317
HIV-1 infection promotes neuroinflammation and neuron pathogenesis in novel microglia-containing cerebral organoids
Authors: Narasipura Srinivas D. , Zayas Janet P. , Ash Michelle K. , Reyes Anjelica , Shull Tanner , Gambut Stephanie , Schneider Jeffrey R. , Lorenzo-Redondo Ramon , Al-Harthi Lena , Mamede João I. 
Published: June 2024

AbstractCerebral organoids (COs) are a valuable tool to study the intricate interplay between glial cells and neurons in brain development and disease, including HIV-associated neuroinflammation. We developed a novel approach to generate microglia containing COs (CO-iMs) by co-culturing hematopoietic progenitors and induced pluripotent stem cells. This approach allowed for the differentiation of microglia within the organoids concomitantly to the neuronal progenitors. CO- iMs exhibited higher efficiency in generation of CD45+/CD11b+/Iba-1+microglia cells compared to conventional COs with physiologically relevant proportion of microglia (∼7%). CO-iMs exhibited substantially higher expression of microglial homeostatic and sensome markers as well as markers for the complement cascade. CO-iMs showed susceptibility to HIV infection resulting in a significant increase in several pro-inflammatory cytokines/chemokines and compromised neuronal function, which were abrogated by addition of antiretrovirals. Thus, CO-iM is a robust model to decipher neuropathogenesis, neurological disorders, and viral infections of brain cells in a 3D culture system.
Wide-scale Geographical Analysis of Genetic Ancestry in the South African Coloured Population
Authors: Lankheet Imke , Hammarén Rickard , Caballero Lucía Ximena Alva , Larena Maximilian , Malmström Helena , Jolly Cecile , Soodyall Himla , de Jongh Michael , Schlebusch Carina 
Published: June 2024

AbstractThe South African Coloured (SAC) population, a prominent admixed population in South Africa, reflects centuries of migration, admixture, and historical segregation. Descendants of local Khoe-San and Bantu-speaking populations, European settlers, and enslaved individuals from Africa and Asia, SAC individuals embody diverse ancestries. This study investigates the genetic makeup of SAC individuals, utilizing autosomal genotypes, mitochondrial DNA and Y-chromosome data. We analyze new genotype data for 125 SAC individuals from seven locations. Our analysis, based on a dataset comprising 356 SAC individuals from 22 geographic locations, revealed significant regional variations in ancestry. Khoe-San ancestry predominates in 14 locations, highlighting its lasting influence. Inland regions exhibit higher proportions of Khoe-San ancestry, eastern regions show more Bantu-speaker/West African ancestry, and western/coastal areas, particularly around Cape Town, display increased Asian ancestry. These patterns reflect historical migrations and settlement patterns. Additionally, sex-biased admixture ratios show male-biased admixture from East Africans and Europeans, and female-biased admixture from Khoe-San populations, which is supported by mitochondrial and Y-chromosome data. This research underscores the importance of studying the SAC population to understand South Africa’s historical migrations, providing insights into the complex genetic heritage of South Africans.
A sensorimotor-association axis of thalamocortical connection development
Authors: Sydnor Valerie J. , Bagautdinova Joëlle , Larsen Bart , Arcaro Michael J. , Barch Deanna M. , Bassett Dani S. , Alexander-Bloch Aaron F. , Cook Philip A. , Covitz Sydney , Franco Alexandre R. , Gur Raquel E. , Gur Ruben C. , Mackey Allyson P. , Mehta Kahini , Meisler Steven L. , Milham Michael P. , Moore Tyler M. , Müller Eli J. , Roalf David R. , Salo Taylor , Schubiner Gabriel , Seidlitz Jakob , Shinohara Russell T. , Shine James M. , Yeh Fang-Cheng , Cieslak Matthew , Satterthwaite Theodore D. 
Published: June 2024

AbstractHuman cortical development follows a sensorimotor-to-association sequence during childhood and adolescence1–6. The brain’s capacity to enact this sequence over decades indicates that it relies on intrinsic mechanisms to regulate inter-regional differences in the timing of cortical maturation, yet regulators of human developmental chronology are not well understood. Given evidence from animal models that thalamic axons modulate windows of cortical plasticity7–12, here we evaluate the overarching hypothesis that structural connections between the thalamus and cortex help to coordinate cortical maturational heterochronicity during youth. We first introduce, cortically annotate, and anatomically validate a new atlas of human thalamocortical connections using diffusion tractography. By applying this atlas to three independent youth datasets (ages 8-23 years; totalN= 2,676), we reproducibly demonstrate that thalamocortical connections develop along a maturational gradient that aligns with the cortex’s sensorimotor-association axis. Associative cortical regions with thalamic connections that take longest to mature exhibit protracted expression of neurochemical, structural, and functional markers indicative of higher circuit plasticity as well as heightened environmental sensitivity. This work highlights a central role for the thalamus in the orchestration of hierarchically organized and environmentally sensitive windows of cortical developmental malleability.
Electrophysiology and Morphology of Human Cortical Supragranular Pyramidal Cells in a Wide Age Range
Authors: Barzó Pál , Szöts Ildikó , Tóth Martin , Csajbók Éva Adrienn , Molnár Gábor , Tamás Gábor 
Published: June 2024

AbstractThe basic excitatory neurons of the cerebral cortex, the pyramidal cells, are the most important signal integrators for the local circuit. They have quite characteristic morphological and electrophysiological properties that are known to be largely constant with age in the young and adult cortex. However, the brain undergoes several dynamic changes throughout life, such as in the phases of early development and cognitive decline in the aging brain. We set out to search for intrinsic cellular changes in supragranular pyramidal cells across a broad age range: from birth to 85 years of age and we found differences in several biophysical properties between defined age groups. During the first year of life, subthreshold and suprathreshold electrophysiological properties changed in a way that shows that pyramidal cells become less excitable with maturation, but also become temporarily more precise. According to our findings, the morphological features of the three-dimensional reconstructions from different life stages showed consistent morphological properties and systematic dendritic spine analysis of an infantile and an old pyramidal cell showed clear significant differences in the distribution of spine shapes. Overall, the changes that occur during development and aging may have lasting effects on the properties of pyramidal cells in the cerebral cortex. Understanding these changes is important to unravel the complex mechanisms underlying brain development, cognition and age-related neurodegenerative diseases.
A neural alternative splicing program controls cellular function and growth in Pancreatic Neuroendocrine tumours
Authors: Potiri M. , Moschou C. , Erpapazoglou Z , Rouni G. , Kotsoni A. , Andreadou M. , Dragolia M. , Ntafis V. , Schrader J. , Juan-Mateu J. , Kostourou V. , Dedos S.G. , Rogalska M.E. , Kafasla P. 
Published: June 2024

AbstractPancreatic neuroendocrine tumours (PanNETs) are a rare heterogeneous group of neoplasms that arise from pancreatic islet cells. The hormone secreting function of pancreatic neuroendocrine cells is altered in PanNETs, rendering these tumours functional or non— functional (secreting excessive or lower levels of hormones, respectively). Genome wide approaches have revealed the genomic landscape of PanNETs but have not shed light on this problematic hormone secretion. In the present work, we show that alternative splicing (AS) deregulation is responsible for changes in the secretory ability of PanNET cells. We reveal a group of alternative microexons that are regulated by the RNA binding protein SRRM3 and are preferentially included in mRNAs in PanNET cells, where SRRM3 is also upregulated. These microexons are part of a larger neural program regulated by SRRM3. We show that their inclusion gives rise to protein isoforms that change stimulus-induced secretory vesicles and their trafficking in PanNET cells. Moreover, the increased inclusion of these microexons results in an enhanced neuronal component in PanNET tumours. Using knock-down and splicing switching oligonucleotides in cellular and animal PanNET models, we show that decrease of the SRRM3 levels or even of the inclusion levels of the three most deregulated microexons can significantly alter the PanNET cell characteristics. Collectively, our study links secretory impairment and nerve dependency to alternative splicing deregulation in PanNETs, providing promising therapeutic targets for PanNET treatment.
Centrosomes act as organizing centers to promote Polo kinase-mediated adaptation to persistent DNA damage
Authors: Langlois-Lemay Laurence , D’Amours Damien 
Published: June 2024

AbstractThe ability of cells to overcome cell cycle arrest and adapt to the presence of unrepairable DNA damage is under the control of polo-like kinases (PLKs) in eukaryotes. How DNA damage checkpoints are silenced or bypassed during the adaptation response is unknown, but the process requires enrichment of the Cdc5 PLK to microtubule organizing centers (MTOCs), such as the yeast centrosomes or spindle pole bodies (SPBs). Here we found that SPBs play an active role as supramolecular organizing centers that coordinate Cdc5 recruitment and signaling to downstream effectors during the adaptation response to DNA damage. We show that SPB components Nud1, Spc110, and Spc72 are key effectors of Cdc5 recruitment to SPB in the presence of sustained DNA damage. Following recruitment, Cdc5 transduces a phospho-signal to key structural subunits of the SPB, including Cnm67 and Mps3. We demonstrate these phosphorylation events are required to bypass cell cycle checkpoint arrest and enable effective adaptation to DNA damage. This response is specific because it cannot be recapitulated by a generic inactivation of MTOC activity. Collectively, our results indicate that centrosomes can act as supramolecular platforms to coordinate dynamic recruitment and substrate selection of PLKs during the DNA damage response.