bluuebunny/crossref_metadata_2025 huggingface dataset:
Unravelling the universal spatial properties of coral reefs
Authors: Giménez-Romero Àlex , Matías Manuel A. , Duarte Carlos M.
Published: November 2024

Coral reefs are under rapid decline due to human pressures such as climate change. Achieving the Kunming-Montreal Global Biodiversity Framework goals, which include restoring 30% of degraded habitats like coral reefs by 2030, requires a comprehensive understanding of their extent and structure, which has been hitherto lacking. We address this limitation based on the unprecedented canonical inventory of coral reefs extracted from the Allen Coral Atlas of shallow-water tropical reefs. We identified a total of 1,579,772 individual reefs globally, extending over a total of 52,423km2of ocean area with mean and median sizes of 3.32 ha and 0.3 ha, respectively. We unravelled three universal laws that are common to all coral reef provinces: the size-frequency distribution, the inter-reef distance distribution and the area-perimeter relation, which follow power laws with an exponent of 1.8, 2.33 and 1.26, respectively. We demonstrate that coral reefs develop universal fractal patterns characterised by a perimeter fractal dimension ofDP= 1.3 and a surface fractal dimension ofDA= 1.6. Our analysis shows that coral reefs display intricate fractal-like geometries and exhibit universal macroecological patterns, largely independent of their geographical location. The universality of the observed patterns suggests that these features possibly stem from the highly conserved interactions of biological, physical, and chemical processes. Over geological scales, these processes lead to reef landscape patterns common among all provinces, providing new information relevant to reef growth modelling.
CGGBP1 from higher amniotes restricts cytosine methylation and drives a GC-bias in transcription factor binding sites at repressed promoters
Authors: Kumar Praveen , Morbia Ishani , Satish Aditi Lakshmi , Datta Subhamoy , Singh Umashankar
Published: November 2024

CGGBP1, a 20 kDa protein, has several functions associated with its DNA-binding through a C2H2 zinc finger. A range of studies have shown that GC richness, inter-strand G/C-skew and low cytosine methylation are associated with CGGBP1 occupancy. The non-preference of any sequence motif as CGGBP1 binding site suggests widespread association of CGGBP1 with DNA including at potent transcription factor binding sites (TFBSs) in promoter regions. The evolutionary advantage of such a design remains unclear. The regulatory interference by human CGGBP1 at TFBSs is supported by purifying selection in the DNA-binding domain of CGGBP1 and its requirement for gene repression as well as restriction of cytosine methylation at GC-rich TFBSs. Here we describe an evolutionary trajectory of this property of CGGBP1 by combining global gene expression and cytosine methylation analyses on human cells expressing CGGBP1 from four different vertebrates (representatives of coelacanth, reptiles, aves and mammals). We discover a potent cytosine methylation restriction by human CGGBP1 at some GC-rich TFBSs in repressed promoters. Further, we combine a high-throughput analysis of GC compositional bias of these CGGBP1-regulated TFBSs from available orthologous sequences from a pool of over 100 species. We show that cytosine methylation restriction by CGGBP1 is tightly linked to GC retention in a set of TFBSs. Orthology analyses demonstrate that this property of CGGBP1 has evolved in higher amniotes (aves and mammals) with lineage-specific heterogeneities in lower amniotes (reptiles). CGGBP1 ChIP-seq data suggest that occupancy of CGGBP1 at these target TFBSs plays a crucial role in their low methylation, GC-biased evolution and associated functions in gene repression.
Pangenome References Improve Biomarker Estimation from Tumor Sequencing Data
Authors: Arslan Elif , Turgut Deniz , Kalay Özem , Demirkaya-Budak Sinem , Budak Gungor , Jain Amit
Published: November 2024

It has recently been shown that patients from non-European ancestries are at a higher risk of inappropriate clinical intervention because of inaccurate biomarker estimation, arising from the reference bias inherent in standard methods for determining the tumor genome from sequencing data. Here we demonstrate that these inaccuracies can be reduced by using a pangenome reference appropriate for the patient’s population.

We constructed a novel secondary analysis workflow where the pangenome reference serves as a scaffold for mapping the sequencing reads, and is also included in the relevant ‘panel of normals’ needed to discriminate between germline and somatic mutations in tumor-only sequencing. This approach detects known somatic mutations in tumor-only sequencing more accurately than the standard GATK somatic calling workflow, prevalent in diagnostic settings for analysis of sequencing data from tumor-only assays, on a standard benchmark tumor sample, HCC1395 (33% relative increase in F1 score).

We also assessed the expected clinical impact of our approach by comparing the Tumor Mutational Burden (TMB) calculated from missense somatic mutations called in tumor/normal samples from 6 patients self-reported as belonging to African, 1 to Asian and 3 to European populations respectively. We find that the TMB values calculated from the tumor-only sequencing data analyzed by our workflow more closely approximate the TMB values calculated from the tumor-normal analysis of the same sample, being 35% higher on average, whereas GATK tumor-only analysis generates TMB values 56% higher on average than the tumor-normal analysis of the same sample. Tumor-normal TMB values calculated by the two methods do not vary as drastically, GATK generated values being 13% higher on average, indicating that GATK tumor-only analysis leads to significant overestimation of TMB values, which can be largely corrected by using our workflow when tumor-normal sequencing is not available.

These results indicate that pangenome based analysis has the potential to become the new standard for unbiased processing of somatic sequencing samples, following on from its increased adoption for germline sequencing analysis.
Jagged1 is a Notch-independent mechanotransducer in endothelial cells
Authors: Rodriguez Freddy Suarez , Virtanen Noora , Kiviluoto Elmeri , Driessen Rob C. H. , Zhao Feihu , Bouten Carlijn V. C. , Stassen Oscar M. J. A. , Sahlgren Cecilia M.
Published: November 2024

Fluid shear stress (FSS) from the blood flow is a crucial regulator of vascular physiology and is associated with major cardiovascular pathologies. Endothelial cells are the primary mechanotransducers of FSS. Here, we show that Jagged1, a canonical ligand of the Notch pathway, modulates biomechanical signaling in endothelial cells in response to FSS. We found that changes in FSS magnitude alter the expression and localization of Jagged1 independently of its effect on Notch expression or activation. Deletion of Jagged1 decreases FSS-induced VEGFR2 and ERK activity in vitro and causes attenuated kinase activity and cardiac defects in zebrafish embryos without significant changes in canonical Notch activity. We show that direct physical stimulation of Jagged1 induces mechanosignaling through the VEGFR2 pathway, independently of Notch signaling but mediated by Jagged1-induced Src activation. Our findings suggest a novel non-canonical role for Jagged1 as a mechanotransducer in endothelial cells with implications for cardiovascular morphogenesis and disease.

One Sentence Summary

Jag1 activates endothelial mechanosignaling through Src.
autoFISH - a modular toolbox for sequential smFISH experiments
Authors: Weber Christian , Defard Thomas , Lelek Mickael , Laporte Hugo , Mallick Ayan , Londoño-Vallejo José-Arturo , Walter Thomas , Fouillade Charles , Gariboldi Maria Isabella , Mueller Florian
Published: November 2024

Fluorescence in situ hybridization (FISH) allows for spatial and quantitative profiling of gene expression by visualizing individual RNA molecules. Here, we introduce automated FISH (autoFISH), a comprehensive toolbox to conduct automated single molecule FISH (smFISH) experiments that is both cost-effective and versatile. This includes detailed plans for constructing the necessary equipment, open-source software for control, reliable experimental protocols, and analysis workflows based on our FISH-quant analysis package. Validation experiments with both cell lines and tissue samples confirmed the system’s robustness. We demonstrate standard and amplified smFISH, along with a modified protocol for tissue clearing that enhances nuclear retention while preserving background reduction efficiency.
Quantifying key parameters of environmental transmission and age-specific susceptibility forMycobacterium aviumsubspeciesparatuberculosis (MAP)
Authors: Gao Yuqi , Bijma Piter , de Jong Mart C.M.
Published: November 2024

Paratuberculosis is a chronic disease in ruminants, caused byMycobacterium avium subspecies paratuberculosis(MAP). This research aims to improve the understanding of transmission dynamics on both exposure and susceptibility— factors influenced by the shedders and the recipients, respectively. We present an age-specific dose-response model, where the decrease in recipient’s susceptibility with age is quantified by a specific rate, and an environmental transmission model, where exposure from shedders is quantified by transmission rate parameters and theMAPdecay rate in the environment. Parameters of both models were estimated based on published experiments. The age-specific susceptibility decrease rate was calculated to be 0.0629 wk− 1. In the transmission model, two sub-models apply different standardization schemes for transiently infectious (Itr), low shedding (Il), high shedding (Ih): Model A standardized shedding rate at 2.29 wk− 1and varied transmission rates across states (and). Model B varied shedding rates across infectious states (and) while keeping the transmission rate constant at 0.0469 wk− 1. In both models, theMAPdecay rate was estimated at 0.424 wk− 1. Then, a scenario study was done, focusing on understanding: changes in environmental contamination levels over time, the timing of exposure, the duration of exposure, and the recipient’s age at exposure. Our findings enhance understanding ofMAPtransmission dynamics and support the development of future models that incorporate real-world complexities and interventions. The 95% confidence intervals for all estimates can be found in the main text.

Author Summary

Mycobacterium aviumsubspeciesparatuberculosis(MAP) causes paratuberculosis (Johne’s disease), a global concern in dairy farming that results in reduced milk production, health issues in cattle, and potential risk for food safety. In this study, we aimed to improve our understanding of MAP’s environmental transmission dynamics, including its build-up, decay, and transmission (via environmental exposure). We explored how the timing, duration of exposure, and recipient age affect infection probabilities. Our analysis of previous experimental data revealed that susceptibility to infection decreases at a specific rate as animals age. We also assess how the decay of MAP and shedding from three types of infectious animals contributes to contamination. Our findings provide new insights into the transmission dynamics of MAP and offer refined estimates of age-specific susceptibility decrease rate, three MAP shedding rates, three transmission rates and MAP natural decay rate. We hope this research can inform more effective control strategies, particularly those aimed at protecting younger animals and reducing environmental contamination.
Predicting semantic segmentation quality in laryngeal endoscopy images
Authors: Kist Andreas M. , Razi Sina , Groh René , Gritsch Florian , Schützenberger Anne
Published: November 2024

Endoscopy is a major tool for assessing the physiology of inner organs. Contemporary artificial intelligence methods are used to fully automatically label medical important classes on a pixel-by-pixel level. This so-called semantic segmentation is for example used to detect cancer tissue or to assess laryngeal physiology. However, due to the diversity of patients presenting, it is necessary to judge the segmentation quality. In this study, we present a fully automatic system to evaluate the segmentation performance in laryngeal endoscopy images. We showcase on glottal area segmentation that the predicted segmentation quality represented by the intersection over union metric is on par with human raters. Using a traffic light system, we are able to identify problematic segmentation frames to allow human-in-the-loop improvements, important for the clinical adaptation of automatic analysis procedures.
Leveraging chromatin packing domains to target chemoevasionin vivo
Authors: Frederick Jane , Virk Ranya K. A. , Ye I Chae , Almassalha Luay M. , Wodarcyk Greta M. , VanDerway David , Carrillo Gonzalez Paola , Nap Rikkert J. , Agrawal Vasundhara , Anthony Nicholas M. , Carinato John , Li Wing Shun , Dunton Cody L. , Medina Karla I. , Kakkaramadam Rivaan , Jain Surbhi , Shahabi Shohreh , Ameer Guillermo , Szleifer Igal G. , Backman Vadim
Published: November 2024

Cancer cells exhibit a remarkable resilience to cytotoxic stress, often adapting through transcriptional changes linked to alterations in chromatin structure. In several types of cancer, these adaptations involve epigenetic modifications and restructuring of topologically associating domains (TADs). However, the underlying principles by which chromatin architecture facilitates such adaptability across different cancers remain poorly understood. To investigate the role of chromatin in this process, we developed a physics-based mechanistic model that connects chromatin organization to cell fate decisions, specifically survival following chemotherapy. Our model builds on the observation that chromatin forms packing domains, which influence transcriptional efficiency through macromolecular crowding. The model accurately predicts chemoevasionin vitro, suggesting that changes in packing domains affect the likelihood of survival. Consistent results across diverse cancer types indicate that the model captures fundamental principles of chromatin-mediated adaptation, independent of the specific cancer or chemotherapy mechanisms involved. Based on these insights, we hypothesized that compounds capable of modulating packing domains, termed Transcriptional Plasticity Regulators (TPRs), could prevent cellular adaptation to chemotherapy. Using live-cell chromatin imaging, we conducted a compound screen that identified several TPRs which synergistically enhanced chemotherapyinduced cell death. The most effective TPR significantly improved therapeutic outcomes in a patient-derived xenograft (PDX) model of ovarian cancer. These findings underscore the central role of chromatin in cellular adaptation to cytotoxic stress and present a novel framework for enhancing cancer therapies, with broad potential across multiple cancer types.
Ranking protein-peptide binding affinities with protein language models
Authors: Chalas Charles Charbel , Dunne Michael P.
Published: November 2024

In this study we explore the use of protein language models for ranking protein-peptide interaction strength, extending the concept of binary protein interaction classification. We introduce a method that measures and ranks protein binding affinities in an unsupervised manner, eliminating the need for extensive labeled data, structural information, or complex biochemical features. We demonstrate the utility of our approach across five distinct protein-peptide datasets by comparing predicted interaction strength rankings with experimentally derived inhibitory concentration (IC50) values. Furthermore, we discuss limitations encountered during our study and present preliminary findings on extending our approach to more general protein-protein interactions. Finally, we highlight the need for comprehensive datasets specifically designed for ranking protein-protein interactions.
A whole-animal phenotypic drug screen identifies suppressors of atherogenic lipoproteins
Authors: Kelpsch Daniel J. , Zhang Liyun , Thierer James H. , Koren Kobe , Kumar Urmi , Lin Yuki , Hensley Monica R. , Sohn Mira , Liu Jun O. , Lectka Thomas , Mumm Jeff S. , Farber Steven A.
Published: November 2024

Lipoproteins are essential for lipid transport in all bilaterians. A single Apolipoprotein B (ApoB) molecule is the inseparable structural scaffold of each ApoB-containing lipoprotein (B-lps), which are responsible for transporting lipids to peripheral tissues. The cellular mechanisms that regulate ApoB and B-lp production, secretion, transport, and degradation remain to be fully defined. In humans, elevated levels of vascular B-lps play a causative role in cardiovascular disease. Previously, we have detailed that human B-lp biology is remarkably conserved in the zebrafish using anin vivochemiluminescent reporter of ApoB (LipoGlo) that does not disrupt ApoB function. Thus, the LipoGlo model is an ideal system for identifying novel mechanisms of ApoB modulation and, due to the ability of zebrafish to generate many progeny, is particularly amenable to large-scale phenotypic drug screening. Here, we report a screen of roughly 3000 compounds that identified 49 unique ApoB-lowering hits. Nineteen hits passed orthogonal screening criteria. A licorice root component, enoxolone, significantly lowered B-lps only in animals that express a functional allele of the nuclear hormone receptor Hepatocyte Nuclear Factor 4⍺ (HNF4⍺). Consistent with this result, inhibitors of HNF4⍺ also reduce B-lp levels. These data demonstrate that mechanism(s) of action can be rapidly determined from a whole animal zebrafish phenotypic screen. Given the well documented role of HNF4⍺ in human B-lp biology, these data validate the LipoGlo screening platform for identifying small molecule modulators of B-lps that play a critical role in a leading cause of worldwide mortality.
Polysomes and mRNA control the biophysical properties of the eukaryotic cytoplasm
Authors: Gade Vamshidhar R. , Heinrich Stephanie , Paloni Matteo , Gómez-García Pablo A. , Dzanko Ajla , Oswald Alexandra , Marchand Désirée , Khawaja Sarah , Barducci Alessandro , Weis Karsten
Published: November 2024

The organization and biophysical properties of the cytoplasm influence all cellular reactions, including molecular interactions and the mobility of biomolecules. It has become clear that the cytoplasm does not behave like a simple fluid but instead is a densely crowded and highly organized environment. Yet, the detailed properties of the cytoplasm, the molecular mechanisms that control them and how they influence the biochemistry of cells remain poorly understood. Here, we investigate the diffusive properties of the cytoplasmin silicoandin vivo,employing mRNPs (messengerribonucleoprotein) and GEM (geneticallyencodedmultimeric) particles as rheological probes in proliferating cells. We demonstrate that cytoplasmic diffusivity increases upon polysome disassembly due to translation inhibition or upon a reduction in mRNA levels. Reducing ribosome concentration by up to 20-25% without a change in polysome levels has no effectin vivo. In addition, we show that upon polysome disassembly, mRNA condensation into P-bodies does not affect cytosolic diffusion in budding yeast. Altogether, our results show that mRNAs and their organization into polysomes control the biophysical properties of the eukaryotic cytoplasm.

Highlights

Polysomes control the biophysical properties of cytoplasm.

mRNP and GEM mobility is enhanced upon translation inhibition that leads to polysome disassembly

Perturbation of mRNA levels leads to an increase in cytosolic diffusion.
Volumetric imaging and computation to explore contractile function in zebrafish hearts
Authors: Saberigarakani Alireza , Patel Riya P. , Almasian Milad , Zhang Xinyuan , Brewer Jonathan , Hassan Sohail S. , Chai Jichen , Lee Juhyun , Fei Baowei , Yuan Jie , Carroll Kelli , Ding Yichen
Published: November 2024

Despite advancements in cardiovascular engineering, heart diseases remain a leading cause of mortality. The limited understanding of the underlying mechanisms of cardiac dysfunction at the cellular level restricts the development of effective screening and therapeutic methods. To address this, we have developed a framework that incorporates light field detection and individual cell tracking to capture real-time volumetric data in zebrafish hearts, which share structural and electrical similarities with the human heart and generate 120 to 180 beats per minute. Our results indicate that the in-house system achieves an acquisition speed of 200 volumes per second, with resolutions of up to 5.02 ± 0.54 µm laterally and 9.02 ± 1.11 µm axially across the entire depth, using the estimated-maximized-smoothed deconvolution method. The subsequent deep learning-based cell trackers enable further investigation of contractile dynamics, including cellular displacement and velocity, followed by volumetric tracking of specific cells of interest from end-systole to end-diastole in an interactive environment. Collectively, our strategy facilitates real-time volumetric imaging and assessment of contractile dynamics across the entire ventricle at the cellular resolution over multiple cycles, providing significant potential for exploring intercellular interactions in both health and disease.
Common AAV gene therapy vectors show indiscriminate transduction of living human brain cell types
Authors: McGinnis JP , Ortiz-Guzman Joshua , Guevara Maria Camila , Mallannagari Sai , Belfort Benjamin D. W. , Bao Suyang , Srivastava Snigdha , Morkas Maria , Ji Emily , Addison Angela , Tantry Evelyne K. , Chen Sarah , Wang Ying , Chen Zihong , Katlowitz Kalman A. , Lange Jeffrey J. , Blessing Melissa M. , Mohila Carrie A. , Ljungberg M. Cecilia , Aldave Guillermo , Jalali Ali , Patel Akash , Sheth Sameer A. , Weiner Howard L. , Gopinath Shankar , Rao Ganesh , Harmanci Akdes Serin , Curry Daniel , Arenkiel Benjamin R.
Published: November 2024

The development of cell-type-specific gene therapy vectors for treating neurological diseases holds great promise, but has relied on animal models with limited translational utility. We have adapted anex vivoorganotypic model to evaluate adeno-associated virus (AAV) transduction properties in living slices of human brain tissue. Using fluorescent reporter expression and single-nucleus RNA sequencing, we found that common AAV vectors show broad transduction of normal cell types, with protein expression most apparent in astrocytes; this work introduces a pipeline for identifying and optimizing AAV gene therapy vectors in human brain samples.
Assessing the conservation and targets of putative sRNAs inStreptococcus pneumoniae
Authors: Eichelman Matthew C. , Meyer Michelle M.
Published: November 2024

RNA regulators are often found in complex regulatory networks and may mediate metabolism and virulence in bacteria. Small RNAs (sRNA’s), a class of non-coding RNAs that interact with an mRNA transcript via base pairing, modulate translation initiation and mRNA degradation. To better understand the role of sRNAs in pathogenicity several studies identified sRNAs inStreptococcus pneumoniae, however little functional characterization has followed. The goal of this study is threefold: 1) take an inventory of putative sRNAs inS. pneumoniae; 2) assess the conservation of these sRNAs; and 3) examine their predicted targets. Three previous studies inS. pneumoniaeidentified 287 putative sRNAs by high-throughput sequencing using a variety of distinct inclusion criteria. This study narrows the candidates to a list of 59 putative sRNAs. BLAST analysis shows that each of the 59 sequences are highly conserved across theS. pneumoniaepangenome while only 5 sRNAs have corresponding sequences with substantial similarity in other members of the Streptococcus genus. We used four RNA-RNA interaction prediction programs (IntaRNA, CopraRNA, sRNARFTarget, and TargetRNA3) to predict targets for each of the 59 putative sRNAs. Across all probable predictions, only seven sRNAs have overlap in the targets predicted by multiple programs, four of which target numerous transposases. Moreover, sRNAs targeting transposases do so with nearly identical and perfect base pairing. One sRNA, named M63 (Spd_sr37), has several probable targets in the CcpA regulon, a network responsible for global catabolite repression, suggesting a possible biological function in control of carbon metabolism. Further, each M63-target interaction exhibits unique base pairing increasing confidence in the biological relevance of the result. This study produces a curated list of S.pneumoniaeputative sRNAs whose predicted targets suggest functional significance in transposon and carbon metabolism regulation.
Transcriptional repression of SOX2 by p53 in cancer cells regulates cell identity and migration
Authors: Lado-Fernandez Patricia , Vilas Jessica Maria , Fernandes Tania , Carneiro Carmen , Da Silva-Alvarez Sabela , Estevez-Souto Valentin , Pedrosa Pablo , Gonzalez-Barcia Miguel , Abatti Luis E , Mitchell Jennifer A , Rivas Carmen , Moreno-Bueno Gema , Vidal Anxo , Collado Manuel
Published: November 2024

During cancer development and progression, many genetic alterations lead to the acquisition of novel features that confer selective advantage to cancer cells and that resemble developmental programs. SOX2 is one of the key pluripotency transcription factors, expressed during embryonic development and active in adult stem cells. In cancer, SOX2 is frequently dysregulated and associated with tumor stemness and poor patient survival. SOX2 expression is suppressed in differentiated cells by tumor suppressor proteins that form a transcriptional repressive complex. We previously identified some of these proteins and found that their absence combined with deficiency in Trp53, leads to maximal dysregulated expression of Sox2. Using cancer cell lines of different origin and with different p53 status, we show here that manipulating TP53 to restore or decrease its activity results in repression or induction of SOX2, respectively. Mechanistically, we observed that the regulation of SOX2 expression by TP53 is transcriptional and identified Trp53 bound to the promoter region and the SRR2 enhancer of Sox2. Forcing high levels of SOX2 in cancer cells leads to morphological changes that molecularly correspond to the acquisition of a more mesenchymal phenotype correlating with an increased migratory capacity. Finally, the analysis of human breast cancer samples shows that this correlation between TP53 status, levels of expression of SOX2 and a more metastatic phenotype is also observed in cancer patients. Our results support the notion that lack of TP53 in tumor cells results in deregulated expression of developmental gene SOX2 with phenotypic consequences related with increased malignization.
Species biology and demographic history determines species vulnerability to climate change in tropical island endemic birds
Authors: Karjee Ratnesh , Iyer Vikram , Chatterjee Durbadal , Ray Rajasri , Garg Kritika M. , Chattopadhyay Balaji
Published: November 2024

Climate change and associated habitat fluctuations can expedite the diversification of insular lineages, or lead to isolation and extinction. Tropical island birds are a model system to assess responses to climate change owing to their insular nature and ability to diversify rapidly. While there is some understanding of the diversification of tropical island avian clades, we are yet to understand the vulnerability of these species to climate change. Long-term species genetic diversity and demography are critical predictors of this. Therefore, we investigated the sensitivity of tropical island endemic birds to climate change and analysed how species traits determine these responses by comparing species traits with demographic histories and paleohabitat fluctuations during the Last Glacial Period (LGP). From publicly available whole genome and paleoclimatic datasets, we reconstructed tropical island endemics' past demographic histories (effective population size (Ne)) using Pairwise Sequential Markovian Coalescent (PSMC) (n = 22) and suitable habitat (n = 28) during the LGP and the Holocene. We observed that most species experienced an increase in suitable habitat from the Last Interglacial and Last Glacial Maxima. However, a concomitant increase Ne was only observed in the hyper-diverse passerine clade, attesting to their ability to rapidly diversify. Overall, diet specialists and large-bodied species showed a decrease in Ne during the LGP. Our results indicate that species traits dictate tropical island endemics' demographic responses to climate, and plastic response to habitat availability could be a consequence of clades' abilities to rapidly occupy new niches and diversify. Further, our analyses revealed that most species entered the Holocene with low genetic diversity. Given that tropical island endemics have small geographic ranges and are groups vulnerable to climate change, special efforts are necessary to conserve them. We recommend that conservation management policies add components like historical demography and species traits while assessing extinction threats for island populations.
Generating Biomedical Knowledge Graphs from Knowledge Bases, Registries, and Multiomic Data
Authors: Qin Guangrong , Narsinh Kamileh , Wei Qi , Roach Jared C. , Joshi Arpita , Goetz Skye L. , Moxon Sierra T. , Brush Matthew H. , Xu Colleen , Yao Yao , Glen Amy K. , Morris Evan D. , Ralevski Alexandra , Roper Ryan , Belhu Basazin , Zhang Yue , Shmulevich Ilya , Hadlock Jennifer , Glusman Gwênlyn
Published: November 2024

As large clinical and multiomics datasets and knowledge resources accumulate, they need to be transformed into computable and actionable information to support automated reasoning. These datasets range from laboratory experiment results to electronic health records (EHRs). Barriers to accessibility and sharing of such datasets include diversity of content, size and privacy. Effective transformation of data into information requires harmonization of stakeholder goals, implementation, enforcement of standards regarding quality and completeness, and availability of resources for maintenance and updates. Systems such as the Biomedical Data Translator leverage knowledge graphs (KGs), structured and machine learning readable knowledge representation, to encode knowledge extracted through inference. We focus here on the transformation of data from multiomics datasets and EHRs into compact knowledge, represented in a KG data structure. We demonstrate this data transformation in the context of the Translator ecosystem, including clinical trials, drug approvals, cancer, wellness, and EHR data. These transformations preserve individual privacy. We provide access to the five resulting KGs through the Translator framework. We show examples of biomedical research questions supported by our KGs, and discuss issues arising from extracting biomedical knowledge from multiomics data.
Selection, Evolution and Persistence of Paleoecological Systems
Authors: Roopnarine Peter D.
Published: November 2024

1

The Phanerozoic fossil record can be organized as a nested set of persistent paleoecological units, ranging from paleocommunities to the Evolutionary Faunas. This paper argues that the basis for ecological persistence on geological timescales is rooted in the robustness of ecological communities, that is, the resistance and resilience of communities when perturbed by the environment. Here I present the Ecological Functional Networks Hypothesis (EFNH) that proposes that networks of species functions, or Ecological Functional Networks (EFNs), underlie ecological stasis and persistence, and that EFNs are both subject to selection and evolve. An EFN varies if the species composition and hence functional structures of its constituent communities vary, and EFNs may differ from each other based on the robustness of those constituent communities, numerical representation, and biogeographic distribution. That variation is subject to selection acting on EFN community composition, and determines both the persistence of an EFN and the differential persistence among multiple EFNs. Selection pressures on EFNs in turn exert top-down influence on species evolution and extinction. Evidence is presented to both establish the reality of EFNs in the fossil record, for example community structures that persist even as species composition changes, and the selection of EFNs, which is apparent during and after episodes of severe biotic turnover such as mass extinctions. Finally, tests are suggested that make the EFNH falsifiable, including testing the correlation between EFNs or EFN emergent traits and geological persistence, and using models of paleocommunity dynamics to examine the relationship between community or EFN robustness and geological persistence. The tests should be applied broadly throughout the Phanerozoic and diverse environments. The EFNH is part of a growing body of hypotheses that address multilevel selection and evolution of non-reproducing systems, including ecosystems and entire biospheres, and addresses those concepts on geological timescales.
Characteristic of KPC-14, a KPC Variant Conferring Resistance to Ceftazidime-Avibactam in the Extensively Drug-resistant ST463Pseudomonas aeruginosaClinical Isolate
Authors: Xiao Yanyan , Wang Le , Jia Huiqiong , Jiang Yan , Li Yue , Han Jiamin , Li Shengchao , Gu Yaxi , Yang Qing
Published: November 2024

We studied two KPC-14 variants from clinicalPseudomonas aeruginosaisolates, C137 and C159, to better understand genomic diversity, mechanisms, and genes that confer antibiotic resistance and pathogenicity. C137 and C159, a sequence type 463 ExoU-positive multidrug-resistant strain, were concurrently resistant to carbapenems and ceftazidime-avibactam (CZA). Both strains possessed five intrinsic antimicrobial resistance genes (fosA, catB7, crpP, blaPAO, and ablaOXA-486variant), as well as theblaKPC-14gene in the chromosome. In strain C137,blaKPC-14gene was situated on the plasmid pC137. KPC-14-harbouring transformants of pC137 exhibited resistance to CZA and restored sensitivity to carbapenems, signifying a “see-saw” effect. Both strains demonstrated the expression of theblaKPC-14gene, concurrent inactivation of the outer membrane protein OprD, overexpression of the efflux pump MexX, and a pronounced capacity for biofilm formation. The genomic environment of KPC-14 consisted of IS26/IS26/TnpR_Tn3/ISKpn27/ISKpn6/IS26, which was classified as pseudo-compound transposons (PCTs). Plasmid pC137 closely resembled the previously described plasmid p94, which possesses the same genomic architecture, implying that IS26-mediated PCTs may store a variety of resistance genes, includingblaKPC-2and KPC variants, and were currently disseminating in the region. The KPC-14 variant presents significant challenges for clinical treatment. TheblaKPC-14gene, carried by the PCTs, was integrated into the chromosome, exhibiting stability throughout bacterial inheritance. Our research highlights the necessity for improved clinical surveillance ofKlebsiella pneumoniaecarbapenemase-producingP. aeruginosa.
A reconstruction of the mammalian secretory pathway identifies mechanisms regulating antibody production
Authors: Masson Helen , Tat Jasmine , Di Giusto Pablo , Antonakoudis Athanasios , Shamie Isaac , Baghdassarian Hratch , Samoudi Mojtaba , Robinson Caressa M. , Kuo Chih-Chung , Koga Natalia , Singh Sonia , Gezalyan Angel , Li Zerong , Movsessian Alexia , Richelle Anne , Lewis Nathan E.
Published: November 2024

The secretory pathway processes >30% of mammalian proteins, orchestrating their synthesis, modification, trafficking, and quality control. However, its complexity— spanning multiple organelles and dependent on coordinated protein interactions—limits our ability to decipher how protein secretion is controlled in biomedical and biotechnological applications. To advance such research, we present secRecon—a comprehensive reconstruction of the mammalian secretory pathway, comprising 1,127 manually curated genes organized within an ontology of 77 secretory process terms, annotated with functional roles, subcellular localization, protein interactions, and complex composition. Using secRecon to integrate multi-omics data, we identified distinct secretory topologies in antibody-producing plasma cells compared to CHO cells. Genes within proteostasis, translocation, and N-glycosylation are deficient in CHO cells, highlighting them as potential engineering targets to boost secretion capacity. Applying secRecon to single-cell transcriptomics and SEC-seq data, we uncovered secretory pathway signatures underlying secretion diversity among IgG-secreting plasma cells. Different transcriptomic clusters had unique secretory phenotypes characterized by variations in the unfolded protein response (UPR), endoplasmic reticulum-associated degradation (ERAD), and vesicle trafficking pathways. Additionally, we discovered specific secretory machinery genes as new markers for plasma cell differentiation. These findings demonstrate secRecon can identify mechanisms regulating protein secretion and guide diverse studies in biomedical research and biotechnology.

Graphical Abstract
Lipid Packing Defects are Necessary and Sufficient for Membrane Binding of α-Synuclein
Authors: Johnson David H. , Kou Orianna H. , White John M. , Ramirez Stephanie Y. , Margaritakis Antonis , Chung Peter J. , Jaeger Vance W. , Zeno Wade F.
Published: November 2024

α-Synuclein (αSyn), an intrinsically disordered protein implicated in Parkinson’s disease, is potentially thought to initiate aggregation through binding to cellular membranes. Previous studies have suggested that anionic membrane charge is necessary for this binding. However, these studies largely focus on unmodified αSyn, while nearly all αSyn in the body is N-terminally acetylated (NTA). NTA dramatically shifts the narrative by diminishing αSyn’s reliance on anionic charge for membrane binding. Instead, we demonstrate that membrane packing defects are the dominant forces driving NTA-αSyn interactions, challenging the long-standing paradigm that anionic membranes are essential for αSyn binding. Using fluorescence microscopy and circular dichroism spectroscopy, we monitored the binding of NTA-αSyn to reconstituted membrane surfaces with different lipid compositions. Phosphatidylcholine and phosphatidylserine concentrations were varied to control surface charge, while phospholipid tail unsaturation and methylation were varied to control lipid packing. All-atom molecular dynamics simulations of lipid bilayers supported the observation that membrane packing defects are necessary for NTA-αSyn binding and that defect-rich membranes are sufficient for NTA-αSyn binding regardless of membrane charge. We further demonstrated that this affinity for membrane defects persisted in reconstituted, cholesterol-containing membranes that mimicked the physiological lipid composition of synaptic vesicles. Increasing phospholipid unsaturation in these mimics led to more membrane packing defects and a corresponding increase in NTA-αSyn binding. Altogether, our results point to a mechanism for the regulation of NTA-αSyn binding in biological membranes that extends beyond phospholipid charge to the structural properties of the lipids themselves.
Identifying the Copper Coordination Environment Between Interacting Neurodegenerative Proteins: A New Approach Using Pulsed EPR with14N/15N Isotopic Labelling
Authors: Smart Amanda , Singewald Kevin , Hasanbasri Zikri , Britt R. David , Millhauser Glenn L.
Published: November 2024

The trafficking and aggregation of neurodegenerative proteins often involves the interaction between intrinsically disordered domains, stabilized by the inclusion of physiologic metal ions such as copper or zinc. Characterizing the metal ion coordination environment is critical for assessing the stability and organization of these relevant protein-protein interactions but is challenging given the lack of regular molecular order or global structure. The cellular prion protein (PrPC) binds both monomers and aggregates of the Alzheimer’s amyloid-beta peptide (Aβ), promoting interactions of relevance to Aβ internalization across the cellular plasma membrane and aberrant signaling in neurodegenerative disease, respectively. Both proteins bind Cu2+with high affinity, suggesting the existence of a ternary complex with copper bridging between the two proteins through His coordination. In this work, we describe a novel approach utilizing multiple EPR experiments to characterize the simultaneous Cu2+coordination of PrPCand Aβ. Uniformly15N-labeled PrPCis used in conjunction with natural abundance14N Aβ, the combination of which leads to distinct energy manifolds for paramagnetic Cu2+and resolved by the pulsed EPR experiments ESEEM and HYSCORE. We develop acquisition parameters to simultaneously optimize14N (I = 1) and15N (I = ½) pulsed EPR signals and we also advance the theory of ESEEM and HYSCORE to quantitatively describe multiple15N imidazole coordination. Together, these findings provide a detailed view of how Cu2+bridges between the two proteins in this complex, along with a global strategy for assessing the copper environment with other interacting neurodegenerative proteins.
Dissecting current rectification through asymmetric nanopores
Authors: Lin Yichun , Lacroix Jerome J. , Sterling James D. , Luo Yun Lyna
Published: November 2024

Rectification, the tendency of bidirectional ionic conductors to favor ion flow in a specific direction, is an intrinsic property of many ion channels and synthetic nanopores. Despite its frequent occurrence in ion channels and its phenomenological explanation using Eyring’s rate theory, a quantitative relationship between the rectified current and the underlying ion-specific and voltage-dependent free energy profile has been lacking. In this study, we designed nanopores in which potassium and chloride current rectification can be manipulated by altering the electrostatic pore polarity. Using molecular dynamics-based free energy simulations, we quantified voltage-dependent changes of free energy barriers in six ion-nanopore systems. Our results illustrate how the energy barriers for inward and outward fluxes become unequal in the presence of an electromotive driving force, leading to varying degrees of rectification for cation and anion currents. This work establishes a direct link between equilibrium potential of mean force and current rectification rate and demonstrates that rectification caused by energy barrier asymmetry depends on the nature of the permeating ion, can be tuned by pore polarity, does not require ion binding sites, conformational flexibility, or specific pore geometry, and, as such, may be widespread among ion channels.

Statement of significance

In many ion channels, ions flow faster in one direction than the other, even under equal magnitude of driving forces. This phenomenon, known as rectification, often arises as an intrinsic biophysical property of the channel pore and has significant physiological implications. Our molecular dynamics simulations provide a unified framework to dissect the free energy profiles that underpin current rectification. This approach has broad applications in the field of ion channel biology and material design.
Optimized recess design in artificial structures dramatically enhances coral settlement and survival
Authors: Reichert Jessica , Jorissen Hendrikje , Drury Crawford , Hancock Joshua , Haynes Corryn , Nims Allison , Rova Lomani H. , Schiettekatte Nina M. D. , Madin Joshua S.
Published: November 2024

The rapid decline of coral reefs prompts the need for new, scalable restoration approaches. Focusing on coral larvae has a great potential for scalability, as a single coral colony can release many thousands of offspring of which the vast majority do not find suitable habitat and die. Here, we designed a range of adaptable modules with distinct geometric features hypothesized to enhance coral settlement and survival. In tank and field experiments, we explored the properties and dimensions of the most successful modules and structural features, and examined the influence of hydrodynamics. Modules with spiral recesses outperformed others, increasing settlement by about 80-fold and post-settlement survival over a year by 20−50-fold compared to controls. Settlement was greatest on cryptic edges with 17 mm deep and 15 mm wide recesses with ∼56 µmol m-2s-1photosynthetic active radiation (i.e., ∼28% of the incoming light). Settlement was more pronounced under high-flow conditions, suggesting a crucial role of micro-scale hydrodynamics in entraining settling coral larvae. Integrating spiral recesses of informed dimensions into restoration modules or engineering structures can provide a novel, scalable, cheap, and self-sustaining approach to reef restoration.
Reduction of DNA Topoisomerase Top2 reprograms the epigenetic landscape and extends health and life span across species
Authors: Zhu Man , Ma Meng , Luo Lunan , Li Feiyang , Zhang Jiashun , Pan Yan , Yang Lu , Xiao Ying , Wang Ziyan , Xian Bo , Zheng Yi , Li Hao , Yang Jing
Published: November 2024

DNA topoisomerases are essential molecular machines that manage DNA topology in the cell and play important roles in DNA replication and transcription. We find that knocking down the enzyme Topoisomerase Top2 or its mammalian homolog Top2b increases the life span ofS. cerevisiae,C. elegans, and mice. Top2b reduction also extends the health span of mice and alleviates the pathologies of aging in multiple tissues. At the cellular/molecular level, Top2b reduction attenuates the major hallmarks of aging, such as cellular senescence, de-regulated nutrient sensing, epigenetic alteration, and lysosomal biogenesis. We observed that Top2b reduction significantly changes the epigenetic landscape in various mouse tissues toward those of the young animals, and differentially down-regulates genes with active promoter and high expression. Our observations suggest that Top2 reduction confers longevity effect across species via a conserved mechanism, and may be used as a novel therapeutic strategy for countering aging.
Self-restrained sex chromosome drive through sequential asymmetric meiosis
Authors: Meng Xuefeng , Yamashita Yukiko M.
Published: November 2024

Meiotic drivers are selfish genetic elements that bias their own transmission, violating Mendel’s Law of Equal Segregation. It has long been recognized that sex chromosome-linked drivers present a paradox: their success in transmission can severely distort populations’ sex ratio and lead to extinction. How sex chromosome drivers may resolve this paradox remains unknown. Here, we show thatD. melanogaster’sStellate (Ste)is an X chromosome-linked driver with a self-restraining mechanism that weakens its drive and prevents extinction. Ste protein asymmetrically segregates into Y-bearing cells during meiosis I, subsequently causing their death. Surprisingly, Ste segregates asymmetrically again during meiosis II, sparing half of the Y-bearing spermatids from Ste-induced defects. Our findings reveal a novel class of sex chromosome drivers that resolve the paradox of suicidal success.