bluuebunny/crossref_metadata_2025 huggingface dataset:
The human genetic variant rs6190 unveils Foxc1 and Arid5a as novel pro-metabolic targets of the glucocorticoid receptor in muscle
Authors: Prabakaran Ashok Daniel , Chung Hyun-Jy , McFarland Kevin , Govindarajan Thirupugal , Soussi Fadoua El Abdellaoui , Durumutla Hima Bindu , Villa Chiara , Piczer Kevin , Latimer Hannah , Werbrich Cole , Akinborewa Olukunle , Horning Robert , Quattrocelli Mattia
Published: March 2024

The genetic determinants of the glucocorticoid receptor (GR) metabolic action remain largely unelucidated. This is a compelling gap in knowledge for the GR single nucleotide polymorphism (SNP) rs6190 (p.R23K), which has been associated in humans with enhanced metabolic health but whose mechanism of action remains completely unknown. We generated transgenic knock-in mice genocopying this polymorphism to elucidate how the mutant GR impacts metabolism. Compared to non-mutant littermates, mutant mice showed increased insulin sensitivity on regular chow and high-fat diet, blunting the diet-induced adverse effects on adiposity and exercise intolerance. Overlay of RNA-seq and ChIP-seq profiling in skeletal muscle revealed increased transactivation ofFoxc1andArid5Agenes by the mutant GR. Using myotropic adeno-associated viruses for in vivo overexpression or knockdown in muscle, we found thatFoxc1was required and sufficient for normal expression levels of insulin response pathway genesInsrandIrs1, promoting muscle insulin sensitivity. In parallel,Arid5awas required and sufficient to transcriptionally repress the lipid uptake genesC 36andFabp4, reducing muscle triacylglycerol accumulation. Moreover, the Foxc1 and Arid5a programs in muscle were divergently changed by glucocorticoid regimens with opposite metabolic outcomes in muscle. Finally, we found a direct human relevance for our mechanism of SNP action in the UK Biobank and All of Us datasets, where the rs6190 SNP correlated with pro-metabolic changes in BMI, lean mass, strength and glucose control according to zygosity. Collectively, our study leveraged a human nuclear receptor coding variant to unveil novel epigenetic regulators of muscle metabolism.

Graphical abstract
Current forest carbon offset buffer pools do not adequately insure against disturbance-driven carbon losses
Authors: Anderegg William R. L. , Trugman Anna T. , Vargas German , Wu Chao , Yang Linqing
Published: March 2024

Nature-based climate solutions in Earth’s forests could strengthen the land carbon sink and contribute to climate mitigation, but must adequately account for climate risks to the durability of carbon storage. Forest carbon offset protocols use a ‘buffer pool’ to insure against disturbance risks that may compromise durability. However, current buffer pool tools and allocations are not based on existing scientific data or models. Here, we use a tropical forest stand biomass model and an extensive set of long-term tropical forest plots to test whether current buffer pools are adequate to insure against observed disturbance regimes. We find that forest age and disturbance regime both influence necessary buffer pool sizes. In the vast majority of disturbance scenarios, current buffer pools are substantially smaller than required by carbon cycle science. Buffer pool estimates urgently need to be updated based on rigorous, open scientific datasets for nature-based climate solutions to succeed.

Plain Language Summary

Forests could contribute to climate mitigation through conservation and restoration activities. Carbon offsets are a widespread pathway to fund these nature-based climate solutions in forests, but must account for the risks to durability that forests face in a changing climate. Current carbon offset protocols have a buffer pool to insure against risk in different disturbance regimes, but the buffer pool contributions have not been tested with observed disturbance regimes and rigorous models. We tested these contributions using widespread tropical forest plot data and a carbon cycle model and find that the current buffer pool contributions are generally not adequate for most disturbance regimes. Our results highlight that better datasets, models, and tools are urgently needed in forest carbon offset protocols.

Key points

Nature-based climate solutions in forests face substantial and rising climate risks to durability

Carbon offsets use a buffer pool to insure against disturbance, which is not currently based on rigorous evidence

Our results reveal current carbon offset protocols do not have an adequate buffer pool for most tropical forest disturbance regimes
Metabolic modeling reveals the aging-associated decline of host-microbiome metabolic interactions in mice
Authors: Best Lena , Dost Thomas , Esser Daniela , Flor Stefano , Haase Madlen , Kadibalban A. Samer , Marinos Georgios , Walker Alesia , Zimmermann Johannes , Simon Rowena , Schmidt Silvio , Taubenheim Jan , Kunzel Sven , Hasler Robert , Groth Marco , Waschina Silvio , Witte Otto W. , Schmitt-Kopplin Phillipe , Baines John F. , Frahm Christiane , Kaleta Christoph
Published: March 2024

Aging is the predominant cause of morbidity and mortality in industrialized countries. The specific molecular mechanisms that drive aging are poorly understood, especially the contribution of the microbiota in these processes. Here, we combined multi-omics with metabolic modeling in mice to comprehensively characterize host-microbiome interactions and how they are affected by aging. Our findings reveal a complex dependency of host metabolism on microbial functions, including previously known as well as novel interactions. We observed a pronounced reduction in metabolic activity within the aging microbiome, which we attribute to reduced beneficial interactions in the microbial community and a reduction in its metabolic output. These microbial changes coincided with a corresponding downregulation of key host pathways predicted by our model to be dependent on the microbiome that are crucial for maintaining intestinal barrier function, cellular replication, and homeostasis. Our results elucidate microbiome-host interactions that potentially influence host aging processes, focusing on microbial nucleotide metabolism as a pivotal factor in aging dynamics. These pathways could serve as future targets for the development of microbiome-based therapies against aging.
Timing of standard chow exposure determines the variability of mouse phenotypic outcomes and gut microbiota profile
Authors: Knuth Megan M. , Campos Carolina Vieira , Smith Kirsten , Hutchins Elizabeth K. , Lewis Shantae , York Mary , Coghill Lyndon M. , Franklin Craig , MacFarlane Amanda , Ericsson Aaron C. , Magnuson Terry , Ideraabdullah Folami
Published: March 2024

Standard chow diet contributes to reproducibility in animal model experiments since chows differ in nutrient composition, which can independently influence phenotypes. However, there is little evidence of the role of timing in the extent of variability caused by chow exposure. Here, we measured the impact of diet (5V5M, 5V0G, 2920X, and 5058) and timing of exposure (adult exposure (AE), lifetime exposure (LE), and developmental exposure (DE)) on growth & development, metabolic health indicators, and gut bacterial microbiota profiles across genetically identical C57BL6/J mice. Diet drove differences in macro-and micronutrient intake for all exposure models. AE had no effect on measured outcomes. However, LE mice exhibited significant sex-dependent diet effects on growth, body weight, and body composition. LE effects were mostly absent in the DE model, where mice were exposed to chow differences from conception to weaning. Both AE and LE models exhibited similar diet-driven beta diversity profiles for the gut bacterial microbiota, with 5058 diet driving the most distinct profile. Diet-induced beta diversity profiles were sex-dependent for LE mice. Compared to AE, LE drove 9X more diet-driven differentially abundant genera, majority of which were the result of inverse effects of 2920X and 5058. Our findings demonstrate that lifetime exposure to different chow diets has the greatest impact on reproducibility of experimental measures that are common components of preclinical mouse model studies. Importantly, weaning DE mice onto a uniform diet is likely an effective way to reduce unwanted phenotypic variability among experimental models.
Symmetry in levels of axon-axon homophilic adhesion establishes topography in the corpus callosum and development of connectivity between brain hemispheres
Authors: Poulopoulos Alexandros , Davis Patrick , Brandenburg Cheryl , Itoh Yasuhiro , Galazo Maria J , Greig Luciano C. , Romanowski Andrea J. , Budnik Bogdan , Macklis Jeffrey D
Published: March 2024

Specific and highly diverse connectivity between functionally specialized regions of the nervous system is controlled at multiple scales, from anatomically organized connectivity following macroscopic axon tracts to individual axon target-finding and synapse formation. Identifying mechanisms that enable entire subpopulations of related neurons to project their axons with regional specificity within stereotyped tracts to form appropriate long-range connectivity is key to understanding brain development, organization, and function. Here, we investigate how axons of the cerebral cortex form precise connections between the two cortical hemispheres via the corpus callosum. We identify topographic principles of the developing trans-hemispheric callosal tract that emerge through intrinsic guidance executed by growing axons in the corpus callosum within the first postnatal week in mice. Using micro-transplantation of regionally distinct neurons, subtype- specific growth cone purification, subcellular proteomics, and in utero gene manipulation, we investigate guidance mechanisms of transhemispheric axons. We find that adhesion molecule levels instruct tract topography and target field guidance. We propose a model in which transcallosal axons in the developing brain perform a "handshake" that is guided through co- fasciculation with symmetric contralateral axons, resulting in the stereotyped homotopic connectivity between the brain's hemispheres.
Type I interferon drives a cellular state inert to TCR-stimulation and could impede effective T-cell differentiation in cancer
Authors: Corvino Dillon , Batstone Martin , Hughes Brett G.M , Kempchen Tim , Ng Susanna S , Salim Nazhifah , Schneppenheim Franziska , Rommel Denise , Kumar Ananthi , Pearson Sally , Madore Jason , Koufariotis Lambross T. , Steinheuer Lisa Maria , Pathirana Dilan , Thurley Kevin , Hölzel Michael , Borcherding Nicholas , Braun Matthias , Bald Tobias
Published: March 2024

Head and neck squamous cell carcinoma (HNSCC) arises from the mucosal epithelium of the oral cavity, pharynx, or larynx and is linked to exposure to classical carcinogens and human papillomavirus (HPV) infection. Due to molecular, immunological, and clinical disparities between HPV+ and HPV-HNSCC, they are recognized as distinct cancer types. While immune checkpoint inhibition (ICI) has demonstrated efficacy in recurrent/metastatic HNSCC, response variability persists irrespective of HPV status. To gain insights into the CD8+ T-cell landscape of HPV-HNSCC, we performed multimodal sequencing (RNA and TCR) of CD8+ tumor-infiltrating lymphocytes (TILs) from treatment-naïve HPV-HNSCC patients. Additionally, we subjected cells toex vivoTCR-stimulation, facilitating the tracing of clonal transcriptomic responses. Our analysis revealed a subset of CD8+ TILs highly enriched for interferon-stimulated genes (ISG), which were found to be clonally related to a subset of granzyme K (GZMK)-expressing cells. Trajectory inference suggests ISG transition via GZMK cells towards terminal effector states. However, unlike GZMK cells, which rapidly an effector-like phenotype in response to TCR stimulation, ISG cells remain transcriptionally inert. Consequently, ISG cells may impede effective T-cell differentiation within the TME. Although, the functional consequences of ISG cells are poorly understood, we revealed that they possess receptors and ligands enabling cell-cell communication networks with key TME immunomodulators such as dendritic cells. Additionally, ISG cells were found to be a core feature across various tumor entities and were specifically enriched within tumor tissue. Thus, our findings illuminate the complexity of T-cell heterogeneity in HPV-HNSCC and reveal an overlooked population of IFN-stimulated CD8+ TILs. Further exploration of their functional significance may offer insights into therapeutic strategies for HPV-HNSCC and other cancer types.
Development of a Two-Leaf Photosynthetic Model Sensitive to Chlorophyll and Its Coupling with a Wheat Growth Model
Authors: Tang Yining , Wang Jiacheng , Hong Yifan , Guo Caili , Zheng Hengbiao , Yao Xia , Cheng Tao , Zhu Yan , Cao Weixing , Tian Yongchao
Published: March 2024

Crop growth models (CGMs) commonly simulates the response of photosynthetic rate to nitrogen (N) dynamic by calculating critical N concentration. However, critical N concentration makes it hard to describe the physiological effect of N dynamic on photosynthesis. Meanwhile, the effect of diffuse light on photosynthesis was limited in previous studies. In this study, we introduced a Two-leaf Photosynthetic Model Sensitive to Chlorophyll Content (TPMSCC) and coupled it with the crop growth model (WheatGrow) to enhance our understanding of how N dynamic and diffuse light affects photosynthesis. By coupling the Farquhar-von Caemmerer-Berry (FvCB) C3photosynthesis model with a canopy radiative transfer model (PROSAIL), TPMSCC simulated the light interception of direct and diffuse light, and employed leaf chlorophyll content (LCC) to simulate the light absorption and electron transfer rate of leaves. Result showed that TPMSCC well simulated the light absorption of the wheat canopy and found the canopy photosynthetic rate benefited from the increase of diffuse radiation fraction (DRF) except for when the condition of a dense canopy at a high solar zenith angle was present. Research found the logarithmic and linear relationships of LCC to the initial light use efficiency (ɑ) and the maximum photosynthetic rate (Amax), respectively, which followed the field measurements. Additionally, the optimized WheatGrow model outperforms its predecessor in describing the response of N application rate on photosynthesis.
Establishing the foundations for a data-centric AI approach for virtual drug screening through a systematic assessment of the properties of chemical data
Authors: Chong Allen , Phua Ser-Xian , Xiao Yunzhi , Ng Woon Yee , Li Hoi Yeung , Goh Wilson Wen Bin
Published: March 2024

Researchers have adopted model-centric artificial intelligence (AI) approaches in cheminformatics by using newer, more sophisticated AI methods to take advantage of growing chemical libraries. It has been shown that complex deep learning methods outperform conventional machine learning (ML) methods in QSAR and ligand-based virtual screening1–3but such approaches generally lack explanability. Hence, instead of developing more sophisticated AI methods (i.e., pursuing a model-centric approach), we wanted to explore the potential of a data-centric AI paradigm for virtual screening. A data-centric AI is an intelligent system that would automatically identify the right type of data to collect, clean and curate for later use by a predictive AI and this is required given the large volumes of chemical data that exist in chemical databases – PubChem alone has over 100 million unique compounds. However, a systematic assessment of the attributes and properties of suitable data is needed. We show here that it is not the result of deficiencies in current AI algorithms but rather, poor understanding and erroneous use of chemical data that ultimately leads to poor predictive performance. Using a new benchmark dataset of BRAF ligands that we developed, we show that our best performing predictive model can achieve an unprecedented accuracy of 99% with a conventional ML algorithm (SVM) using a merged molecular representation (Extended + ECFP6 fingerprints), far surpassing past performances of virtual screening platforms using sophisticated deep learning methods. Thus, we demonstrate that it is not necessary to resort to the use of sophisticated deep learning algorithms for virtual screening because conventional ML can perform exceptionally well if given the right data and representation. We also show that the common use of decoys for training leads to high false positive rates and its use for testing will result in an over-optimistic estimation of a model’s predictive performance. Another common practice in virtual screening is defining compounds that are above a certain pharmacological threshold as inactives. Here, we show that the use of these so-called inactive compounds lowers a model’s sensitivity/recall. Considering that some target proteins have a limited number of known ligands, we wanted to also observe how the size and composition of the training data impact predictive performance. We found that an imbalance training dataset where inactives outnumber actives led to a decrease in recall but an increase in precision, regardless of the model or molecular representation used; and overall, we observed a decrease in the model’s accuracy. We highlight in this study some of the considerations that one needs to take into account in future development of data-centric AI for CADD.
Communication of perceptual predictions from the hippocampus to the deep layers of the parahippocampal cortex
Authors: Warrington Oliver , Graedel Nadine N. , Callaghan Martina F. , Kok Peter
Published: March 2024

Current evidence points to the hippocampus as an essential region coordinating learning and exploiting predictive relationships in the service of perception. However, it remains unclear whether the hippocampus drives the communication of predictions to the sensory cortex or acts as a recipient of predictions from else-where. Here, we collected sub-millimetre 7T fMRI data to investigate neural signals in the medial temporal lobe (MTL). We used layer-specific fMRI to infer the direction of communication between the hippocam-pus and cortex. Specifically, superficial layers of the MTL cortex project to the hippocampus, while deep MTL layers receive feedback projections. Participants performed a task in which auditory cues predicted abstract shapes. Crucially, we omitted the expected shape on 25% of trials, thus isolating the prediction signal from bottom-up input and allowing us to ask: In which direction are predictions communicated between the hippocampus and neocortex? Neural patterns in CA23, pre/parasubiculum and the parahippocampal cortex (PHC) reflected shape-specific predictions. Layer-specific informational connectivity analyses revealed that communication between CA23 and PHC was specific to the deep layers of PHC. These findings are in line with the hippocampus generating predictions through pattern completion in CA23 and feeding these pre-dictions back to the neocortex.
Preservation of an Aging-Associated Mitochondrial Signature in Advanced Human Neuronal Models
Authors: Varghese Nimmy , Szabo Leonora , Cader Zameel , Lejri Imane , Grimm Amandine , Eckert Anne
Published: March 2024

1.

This study investigated whether induced pluripotent stem cell-derived neurons (iPSCsNs) and directly converted neurons (iNs) generated from the same cells of origin (human fibroblasts) represent aging-related characteristics on mitochondrial levels. There is still uncertainty regarding the potential for rejuvenation or preservation of an aging-associated donor signature in aged iPSCsNs upon transition through pluripotent states, while direct conversion retains the aging-associated mitochondrial impairments. Surprisingly, both aged neuronal models exhibited age-associated donor phenotypes, including decreased ATP, mitochondrial membrane potential, mitochondrial respiration, NAD+/NADH ratio, and increased radical levels and mitochondrial mass. Besides, a fragmented mitochondrial network was observed in both aged neuronal models. However, unlike aged iNs, aged iPSCsNs did not show a metabolic shift towards anaerobic glycolysis to compensate for the energy deficit. Moreover, the mRNA expression profile significantly differed between aged iPSCsNs and aged iNs. Our study indicates that aged iPSCsNs may experience rejuvenation in certain parameters, such as transcriptomics and the aging-associated glycolytic shift. Nevertheless, aged iPSCsNs can be a valuable tool for studying neuronal aging of mitochondrial parametersin vitroalongside aged iNs.
Exploring protein-mediated compaction of DNA by coarse-grained simulations and unsupervised learning
Authors: de Jager Marjolein , Kolbeck Pauline J. , Vanderlinden Willem , Lipfert Jan , Filion Laura
Published: March 2024

Protein-DNA interactions and protein-mediated DNA compaction play key roles in a range of biological processes. The length scales typically involved in DNA bending, bridging, looping, and compaction (≥1 kbp) are challenging to address experimentally or by all-atom molecular dynamics simulations, making coarse-grained simulations a natural approach. Here we present a simple and generic coarse-grained model for the DNA-protein and protein-protein interactions, and investigate the role of the latter in the protein-induced compaction of DNA. Our approach models the DNA as a discrete worm-like chain. The proteins are treated in the grand-canonical ensemble and the protein-DNA binding strength is taken from experimental measurements. Protein-DNA interactions are modeled as an isotropic binding potential with an imposed binding valency, without specific assumptions about the binding geometry. To systematically and quantitatively classify DNA-protein complexes, we present an unsupervised machine learning pipeline that receives a large set of structural order parameters as input, reduces the dimensionality via principal component analysis, and groups the results using a Gaussian mixture model. We apply our method to recent data on the compaction of viral genome-length DNA by HIV integrase and we find that protein-protein interactions are critical to the formation of looped intermediate structures seen experimentally. Our methodology is broadly applicable to DNA-binding proteins and to protein-induced DNA compaction and provides a systematic and quantitative approach for analyzing their mesoscale complexes.

SIGNIFICANCE

DNA is central to the storage and transmission of genetic information and is frequently compacted and condensed by interactions with proteins. Their size and dynamic nature make the resulting complexes difficult to probe experimentally and by all-atom simulations. We present a simple coarse-grained model to explore ∼kbp DNA interacting with proteins of defined valency and concentration. Our analysis uses unsupervised learning to define conformational states of the DNA-protein complexes and pathways between them. We apply our simulations and analysis to the compaction of viral genome-length DNA by HIV integrase. We find that protein-protein interactions are critical to account for the experimentally observed intermediates and our simulated complexes are in good agreement with experimental observations.
Expanding the use of reindeer foetal bone measurements for zooarchaeological applications
Authors: Discamps Emmanuel , Soulier Marie-Cécile
Published: March 2024

When foetal bones are preserved in archaeological sites, they are often used to identify the seasonality of prey acquisition by past human populations and, subsequently, to discuss their lifestyle, their management of food resources, nomadic cycles, etc. To do so, zooarchaeologists use charts to estimate foetal age based on the growth of their bones. For reindeer (Rangifer tarandus), a species that was widely exploited since the Palaeolithic throughout Eurasia, existing reference data are limited and require the measurement of complete bones, a procedure that is rarely applicable to archaeological contexts in which bones are often fragmented. In this study we present a wide range of measurements (9-10 measurements per bone) taken on the humerus, radius, metacarpal, femur, tibia and metatarsal of 31 individuals housed at the Zoological Museum of the University of Oulu (Finland). With this large data set, a more accurate estimation of the time of death of reindeer foetus can be achieved using skeletal measurements, even in the case of fragmented bones. To facilitate the use of this referential, an open-access web interface (foetusmeteR) was designed in RShiny. This interface allows for the direct estimation of foetal age and season of death by entering a single skeletal measurement, as well as the possibility of estimating if two bones might correspond to the same individual using two different measurements. This new tool should help to discuss in more detail the condition of reindeer herds hunted in the past, the hunting techniques and strategies that may have been used by human groups, and allow for a more detailed reconstruction of the seasonal nomadic cycle of past societies that focused their subsistence onRangiferpopulations.
A pangenomic perspective of the Lake Malawi cichlid radiation reveals extensive structural variation driven by transposable elements
Authors: Quah Fu Xiang , Almeida Miguel Vasconcelos , Blumer Moritz , Yuan Chengwei Ulrika , Fischer Bettina , See Kirsten , Jackson Ben , Zatha Richard , Rusuwa Bosco , Turner George F. , Santos M. Emília , Svardal Hannes , Hemberg Martin , Durbin Richard , Miska Eric
Published: March 2024

The East African Rift Lakes, namely Lake Malawi, Victoria, and Tanganyika, host a remarkable diversity of cichlid fishes, representing one of nature’s most striking vertebrate radiations. Despite rich phenotypic diversity, single nucleotide polymorphism (SNP)-based sequencing studies have revealed little sequence divergence between cichlids, with 0.1 to 0.25% pairwise divergence within Lake Malawi. These studies were based on aligning short reads to a single linear reference genome, which ignores the contribution of larger scale structural variants (SVs). To complement existing SNP-based studies, we adopted a pangenomic approach by constructing a multiassembly graph of haplochromine cichlids in Lake Malawi. We produced six new long read genome assemblies, alongside two publicly available ones, to span most of the major eco-morphological clades in the lake. This approach not only identifies longer SVs, but also visually represents complex and nested variation. Strikingly, the SV landscape is dominated by large insertions, many exclusive to individual assemblies. From a pangenomic perspective, we observed an exceptional amount of extra sequence, totaling up to 33.1% additional bases with respect to a single cichlid genome. Approximately 4.73 to 9.86% of the cichlid assemblies were estimated to be interspecies structural variation, suggesting substantial genomic diversity underappreciated in previous SNP-based studies. While coding regions remain highly conserved, our analysis uncovers a significant contribution of SVs from transposable element (TE) insertions, especially DNA, LINE, and LTR transposons. These findings underscore the intricate interplay of evolutionary forces shaping cichlid genome diversity, including both small nucleotide mutations and large TE-derived sequence alterations.
CRISPR/Cas9 gene editing inDrosophilavia visual selection in a summer classroom
Authors: Kockel Lutz , Zhang Valentina , Wang Jenna , Gulick Clara , Laws Madeleine E. , Rajan Arjun , Lantz Nicole , Asgarova Ayla , Dai Lillian , Garcia Kristian , Kim Charlene , Li Michelle , Ordonez-Acosta Patricio , Peng Dongshen , Shull Henry , Tse Lauren , Wang Yixang , Yu Wenxin , Zhou Zee , Rankin Anne , Park Sangbin , Kim Seung K.
Published: March 2024

CRISPR/Cas9 methods are a powerfulin vivoapproach to edit the genome ofDrosophila melanogaster. To convert existingDrosophila GAL4lines toLexAdriver lines in a secondary school classroom setting, we applied the CRISPR-based genetic approach to a collection ofGal4‘driver’ lines. The integration of theyellow+coat color marker into homology-assisted CRISPR knock-in (HACK) enabled visual selection ofGal4-to-LexAconversions using brightfield stereo-microscopy available in a broader set of standard classrooms. Here, we report the successful conversion of elevenGal4lines with expression in neuropeptide-expressing cells into corresponding, novelLexAdrivers. The conversion was confirmed byLexA-andGal4-specific GFP reporter gene expression. This curriculum was successfully implemented in a summer course running 16 hours/week for seven weeks. The modularity, flexibility, and compactness of this course should enable development of similar classes in secondary schools and undergraduate curricula, to provide opportunities for experience-based science instruction, and university-secondary school collaborations that simultaneously fulfill research needs in the community of science.
Diel Partitioning in Microbial Phosphorus Acquisition in the Sargasso Sea
Authors: Muratore Daniel , Gilbert Naomi E. , LeCleir Gary R. , Wilhelm Steven W. , Weitz Joshua S.
Published: March 2024

The daily cycle of photosynthetic primary production at the base of marine food webs is often limited by the availability of scarce nutrients. According to temporal niche partitioning theory, competition for scarce resources can be alleviated insofar as the intensity of nutrient uptake and assimilation activities are distributed heterogeneously across organisms over periodic input cycles. Recent analysis of community transcriptional dynamics in the nitrogen-limited subtropical North Pacific gyre revealed evidence of temporal partitioning of nitrogen uptake and assimilation between eukaryotic phytoplankton, cyanobacteria, and heterotrophic bacteria over day-night cycles. Here, we present results from a Lagrangian metatranscriptomic time series survey in the Sargasso Sea and demonstrate temporally partitioned phosphorus uptake in this phosphorus-limited environment. In the Sargasso, heterotrophic bacteria, eukaryotic phytoplankton, and cyanobacteria express genes for phosphorus assimilation during the morning, day, and dusk, respectively. These results support the generality of temporal niche partitioning as an emergent mechanism structuring uptake of limiting nutrients and facilitating coexistence of diverse microbes in open ocean ecosystems.
Mesenchymal Stromal Cell Senescence Induced byDnmt3a-Mutant Hematopoietic Cells is a Targetable Mechanism Driving Clonal Hematopoiesis and Initiation of Hematologic Malignancy
Authors: Mistry Jayna J. , Young Kira A. , Colom Díaz Patricia A. , Maestre Inés Fernández , Levine Ross L. , Trowbridge Jennifer J.
Published: March 2024

Clonal hematopoiesis (CH) can predispose to blood cancers due to enhanced fitness of mutant hematopoietic stem and progenitor cells (HSPCs), but the mechanisms driving this progression are not understood. We hypothesized that malignant progression is related to microenvironment-remodelling properties of CH-mutant HSPCs. Single-cell transcriptomic profiling of the bone marrow microenvironment inDnmt3aR878H/+mice revealed signatures of cellular senescence in mesenchymal stromal cells (MSCs).Dnmt3aR878H/+HSPCs caused MSCs to upregulate the senescence markers SA-β-gal, BCL-2, BCL-xL,Cdkn1a(p21) andCdkn2a(p16),ex vivoandin vivo. This effect was cell contact-independent and can be replicated by IL-6 or TNFα, which are produced byDnmt3aR878H/+HSPCs. Depletion of senescent MSCsin vivoreduced the fitness ofDnmt3aR878H/+hematopoietic cells and the progression of CH to myeloid neoplasms using a sequentially inducibleDnmt3a;Npm1-mutant model. Thus,Dnmt3a-mutant HSPCs reprogram their microenvironment via senescence induction, creating a self-reinforcing niche favoring fitness and malignant progression.

Statement of Significance

Mesenchymal stromal cell senescence induced byDnmt3a-mutant hematopoietic stem and progenitor cells drives clonal hematopoiesis and initiation of hematologic malignancy.
Tools forCre-mediated conditional deletion of floxed alleles from developing cerebellar Purkinje cells
Authors: Jahncke Jennifer N. , Wright Kevin M.
Published: March 2024

The Cre-lox system is an indispensable tool in neuroscience research for targeting gene deletions to specific cellular populations. Here we assess the utility of several transgenicCrelines, along with a viral approach, for targeting cerebellar Purkinje cells. Using a combination of a fluorescent reporter line (Ai14) to indicateCre-mediated recombination and a floxedDystroglycanline (Dag1flox) we show that reporter expression does not always align precisely with loss of protein. The commonly usedPcp2Creline exhibits a gradual mosaic pattern ofCrerecombination in Purkinje cells from P7-P14, while loss of Dag1 protein is not complete until P30.Ptf1aCredrives recombination in precursor cells that give rise to GABAergic neurons in the embryonic cerebellum, including Purkinje cells and molecular layer interneurons. However, due to its transient expression in precursors,Ptf1aCreresults in stochastic loss of Dag1 protein in these neurons.NestinCre, which is often described as a “pan-neuronal”Creline for the central nervous system, does not driveCre-mediated recombination in Purkinje cells. We identify aCalb1Creline that drives efficient and complete recombination in embryonic Purkinje cells, resulting in loss of Dag1 protein before the period of synaptogenesis.AAV8-mediated delivery ofCreat P0 results in gradual transduction of Purkinje cells during the second postnatal week, with loss of Dag1 protein not reaching appreciable levels until P35. These results characterize several tools for targeting conditional deletions in cerebellar Purkinje cells at different developmental stages and illustrate the importance of validating the loss of protein following recombination.

Significance Statement

The development ofCrelines for targeting gene deletions to defined cellular populations has led to important discoveries in neuroscience. As with any tool, there are inherent limitations that must be carefully considered. Here we describe severalCrelines available for targeting of cerebellar Purkinje cells at various developmental stages. We use the combination of aCre-dependent fluorescent reporter line and conditional deletion of the synaptic scaffolding molecule Dystroglycan as an example to highlight the potential disconnect between the presence of a fluorescent reporter and the loss of protein.
Overwintering performance of juvenile temperate estuarine fish
Authors: Bellotto Clara , Fowler Ashley M. , Booth David J.
Published: March 2024

Estuaries, rich in biodiversity and economically valuable species, are increasingly threatened by climate change-induced factors that challenge fish resilience and survival. This study compared the performance of estuarine fishes between water temperatures reflecting two scenarios: current Sydney winters (16°C) and future winters under climate change (20°C), and at two food levels, for three estuarine fish species (eastern fortescue,Centropogon australis, common silverbiddy,Gerres subfasciatus,and eastern striped trumpeter,Pelates sexlineatus) Overall, as expected from metabolic theory, fish performance was generally higher at higher temperatures, with growth rates higher at 20°C forG. subfasciatusandC. australis.Bite rates and aerobic scope were generally higher at the higher temperature for all species.G. subfasciatusandP. sexlineatusexhibited increased escape responses at 20°C, withP. sexlineatusalso showing greater boldness. Boldness was positively associated with bite rates inP. sexlineatus, potentially indicating foraging advantages under future warming for this species. The order of temperature treatment (20°C then 16°C, vs 16°C then 20°C) affected boldness forG. subfasciatusand growth rate, total length, bite rate and burst speed forP. sexlineatus.

Contrary to expectations, food had no effect on fish performance either directly or interacting with temperature, and all three species generally performed better at 20°C than 16°C, suggesting this study was conducted below the species’ thermal optima. Future climate change may therefore favour temperate estuarine fishes at winter temperatures, with potential benefits differing among these species.
Stacking haplotypes from the Vavilov wheat collection to accelerate breeding for multiple disease resistance
Authors: Tong Jingyang , Tarekegn Zerihun T. , Alahmad Samir , Hickey Lee T. , Periyannan Sambasivam K. , Dinglasan Eric , Hayes Ben J.
Published: March 2024

Wheat production is threatened by numerous fungal diseases, but the potential to breed for multiple disease resistance (MDR) mechanisms is yet to be explored. Here, significant global genetic correlations and underlying local genomic regions were identified in the Vavilov wheat diversity panel for six major fungal diseases, including biotrophic leaf rust (LR), yellow rust (YR), stem rust (SR), hemibiotrophic crown rot (CR), and necrotrophic tan spot (TS) and Septoria nodorum blotch (SNB). By adopting haplotype-based local genomic estimated breeding values, derived from an integrated set of 34,899 SNP and DArT markers, we established a novel haplotype catalogue for resistance to the six diseases in over 20 field experiments across Australia and Ethiopia. Haploblocks with high variances of haplotype effects in all environments were identified for three rusts and pleiotropic haploblocks were identified for at least two diseases, with four haploblocks affecting all six diseases. Through simulation we demonstrated that stacking optimal haplotypes for one disease could improve resistance substantially, but indirectly affected resistance for other five diseases, which varied depending on the genetic correlation with the non-target disease trait. On the other hand, our simulation results combining beneficial haplotypes for all diseases increased resistance to LR, YR, SR, CR, TS and SNB, by up to 48.1%, 35.2%, 29.1%, 12.8%, 18.8% and 32.8%, respectively. Overall, our results highlight the genetic potential to improve MDR in wheat. The haploblock-based catalogue with novel forms of resistance provides a useful resource to guide desirable haplotype stacking for breeding future wheat cultivars with MDR.
Acute promyelocytic leukemia with torque teno mini virus (TTMV)::RARAfusion: an approach to screening and diagnosis
Authors: Tsai Harrison K. , Sabbagh Mark F. , Montesion Meagan , Williams Erik A. , Arbini Arnaldo , Boué Daniel R. , Harris Emily M. , Wachter Franziska , Grimmett Leslie , Place Andrew E. , Lucas Fabienne , Nardi Valentina , Kim Annette S. , Brugnara Carlo , Degar Barbara , Pollard Jessica , Harris Marian H. , Bledsoe Jacob R.
Published: March 2024

Acute promyelocytic leukemia (APL) with variantRARAtranslocation is linked to over 15 partner genes. Recent publications encompassing six cases have expanded the spectrum ofRARApartners to torque teno mini virus (TTMV). This entity is likely under-recognized due to lack of clinician and pathologist familiarity, inability to detect the fusion using routine testing modalities, and informatic challenges in its recognition within next-generation sequencing (NGS) data. We describe a clinicopathologic approach and provide necessary tools to screen and diagnose APL with TTMV::RARAusing existing clinical DNA or RNA-based NGS assays, which led to identification of four cases, all without other known cytogenetic/molecular drivers. One was identified prospectively and three retrospectively, including two from custom automated screening of multiple data sets (50,257 cases of hematopoietic malignancy, including 4809 acute myeloid leukemia (AML)/myeloid sarcoma/APL cases). Two cases presented as myeloid sarcoma, including one with multiple relapses after AML-type chemotherapy and hematopoietic stem cell transplant (HSCT). Two cases presented as leukemia, had a poor response to induction chemotherapy, but achieved remission upon re-induction (including all-trans retinoic acid (ATRA) in one case) and subsequent HSCT. Neoplastic cells demonstrated features of APL including frequent azurophilic granules and dim/absent CD34 and HLA-DR expression.RARArearrangement was not detected by karyotype or FISH. Custom analysis of NGS fusion panel data identified TTMV::RARArearrangements, and in the prospectively identified case, facilitated monitoring in sequential bone marrow samples. APL with TTMV::RARAis a rare leukemia with a high rate of treatment failure in described cases. The diagnosis should be considered in leukemias with features of APL that lack detectableRARAfusions and other drivers, and may be confirmed by appropriate NGS tests with custom informatics. Incorporation of ATRA may have a role in treatment but requires accurate recognition of the fusion for appropriate classification as APL.
Reverse Mendelian randomization separates causes from early proteomic biomarkers of glioma
Authors: Andrews Lily J , Thornton Zak A , Zheng Jie , Robinson Jamie W , Hemani Gibran , Kurian Kathreena M
Published: March 2024

Background/Objectives

Glioma represents the largest entity of primary brain tumours in adults, with an overall survival of less than 20% over 5 years. Glioblastoma is the most frequent and aggressive glioma subtype. At present, there are few well-established pre-clinical predictors for glioma incidence. Due to the availability and size of prognostic studies in glioma, we utilised a Mendelian randomization framework to identify non-causal protein biomarkers which are associated with early-onset of glioma in the European population.

Methods

We generated polygenic risk scores (PRS) for glioma (n=12,496), glioblastoma (n=6,191), and non-glioblastoma (n=5,819) cases. We used reverse Mendelian randomization (MR) to examine the relationship between the genetic liability of glioma and 1,463 and 90 proteins were measured using an Olink panel (UKBB, n=35,571 and SCALLOP, n=21,758), additionally 4,907 and 2,994 aptamers were assayed using SOMAscan assays (deCODE n=35,559 and INTERVAL, n=3,301). We further performed a forward cis-MR and colocalization analysis leveraging the circulating protein markers in risk of glioma, glioblastoma and non-glioblastoma.

Results

Reverse MR identified 161 unique proteins associated with the PRS of glioma, 79 proteins associated with the PRS of glioblastoma, and 11 proteins associated with the PRS of non-glioblastoma. Enrichment analyses identified a proportion of plasma proteins to be associated with the PRS of glioma to be correlated with response to external stimulus. A group of plasma proteins linked to the PRS of glioma and glioblastoma were related to the immune system process. Forward MR of the putative relationships were found to have little or no evidence of association on the causal pathway. Candidate markers ETFA, RIR1 and BT3A1 are evidenced in glioma risk.

Conclusion

Our findings identify a high genetic liability to glioma is associated with the immune system processes. Non-causal plasma biomarkers identified through PRS associations could indicate novel non-causal biomarkers of early glioma development.
Regional Variation in the Interpretation of Contact Precautions for Multidrug-resistant Gram-negative bacteria: a cross-sectional survey
Authors: van Veen Anneloes , de Goeij Inge , Damen Marjolein , Huijskens Elisabeth G.W. , Paltansing Sunita , van Rijn Michiel , Bentvelsen Robbert G. , Veenemans Jacobien , van der Linden Michael , Vos Margreet C. , Severin Juliëtte A.
Published: March 2024

Background

Contact precautions (CP) are recommended when caring for patients with carbapenemase-producing Enterobacterales (CPE), carbapenemase-producingPseudomonas aeruginosa(CPPA), and extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E).

Aim

Our aim was to determine the interpretation of CP and associated infection prevention and control (IPC) measures in the non-ICU hospital setting for patients with CPE, CPPA or ESBL-E in 11 hospitals in the Southwest of the Netherlands.

Methods

A cross-sectional survey was developed to collect information on all implemented IPC measures, including use of personal protective equipment, IPC measures for visitors, cleaning and disinfection, precautions during outpatient care and follow-up strategies. All eleven hospitals were invited to participate between November 2020 and April 2021.

Findings

The survey was filled together with each hospital. All hospitals installed isolation precautions for patients with CPE and CPPA during inpatient care and day admissions, whereas ten hospitals (90.9%) applied isolation precautions for patients with ESBL-E. Gloves and gowns were always used during physical contact with the patient in isolation. Large variations were identified in IPC measures for visitors, cleaning and disinfection products used, and precautions during outpatient care. Four hospitals (36.4%) actively followed up on CPE or CPPA patients with the aim to declare them CPE- or CPPA-negative as timely as possible, and two hospitals (20.0%) actively followed up on ESBL-E patients.

Conclusion

CP are interpreted differently between hospitals, leading to regional differences in IPC measures applied in clinical settings. Harmonizing infection-control policies between the hospitals could facilitate patient transfers and benefit collective efforts of preventing transmission of MDR-GNB.
LOMIA-T: A Transformer-based LOngitudinal Medical Image Analysis framework for predicting treatment response of esophageal cancer
Authors: Sun Yuchen , Li Kunwei , Chen Duanduan , Hu Yi , Zhang Shuaitong
Published: March 2024

Deep learning models based on medical images have made significant strides in predicting treatment outcomes. However, previous methods have primarily concentrated on single time-point images, neglecting the temporal dynamics and changes inherent in longitudinal medical images. Thus, we propose a Transformer-based longitudinal image analysis framework (LOMIA-T) to contrast and fuse latent representations from pre- and post-treatment medical images for predicting treatment response. Specifically, we first design a treatment response- based contrastive loss to enhance latent representation by discerning evolutionary processes across various disease stages. Then, we integrate latent representations from pre- and post-treatment CT images using a cross-attention mechanism. Considering the redundancy in the dual-branch output features induced by the cross-attention mechanism, we propose a clinically interpretable feature fusion strategy to predict treatment response. Experimentally, the proposed framework outperforms several state-of-the-art longitudinal image analysis methods on an in-house Esophageal Squamous Cell Carcinoma (ESCC) dataset, encompassing 170 pre- and post-treatment contrast-enhanced CT image pairs from ESCC patients underwent neoadjuvant chemoradiotherapy. Ablation experiments validate the efficacy of the proposed treatment response-based contrastive loss and feature fusion strategy. The codes will be made available athttps://github.com/syc19074115/LOMIA-T.