bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThe 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.HighlightsPolysomes control the biophysical properties of cytoplasm.mRNP and GEM mobility is enhanced upon translation inhibition that leads to polysome disassemblyPerturbation 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

SummaryDespite 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

AbstractThe 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

AbstractRNA 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.
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

AbstractAs 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

1AbstractThe 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

ABSTRACTWe 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

AbstractThe 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

Abstractα-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

AbstractThe 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

AbstractRectification, 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 significanceIn 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

AbstractThe 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

AbstractDNA 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.