bluuebunny/crossref_metadata_2025_split huggingface dataset:
RoAM: computational reconstruction of ancient methylomes and identification of differentially methylated regions
Authors: Mathov Yoav , Rosen Naomi , Leibson Chen , Meshorer Eran , Yakir Benjamin , Carmel Liran 
Published: August 2024

AbstractIdentifying evolutionary changes in DNA methylation bears a huge potential for unraveling adaptations that have occurred in modern humans. Over the past decade, computational methods to reconstruct DNA methylation patterns from ancient DNA sequences have been developed, allowing for the exploration of DNA methylation changes during the past hundreds of thousands of years of human evolution. Here, we introduce a new version of RoAM (Reconstruction of Ancient Methylation), a flexible tool that allows for the reconstruction of ancient methylomes, as well as the identification of differentially methylated regions between ancient populations. RoAM incorporates a series of filtering and quality control steps, resulting in highly reliable DNA methylation maps that exhibit similar characteristics to modern maps. To showcase RoAM’s capabilities, we used it to compare ancient methylation patterns between pre- and post-Neolithic revolution samples from the Balkans. Differentially methylated regions separating these populations are shown to be associated with genes related to regulation of sugar metabolism. Notably, we provide evidence for overexpression of the gene PTPRN2 in post-Neolithic revolution samples. PTPRN2 is a key regulator of insulin secretion, and our finding is compatible with hypoinsulinism in pre-Neolithic revolution hunter-gatherers. Additionally, we observe methylation changes in the genes EIF2AK4 and SLC2A5, which provide further evidence to metabolic adaptations to a changing diet during the Neolithic transition. RoAM offers powerful algorithms that position it as a key asset for researchers seeking to identify evolutionary regulatory changes through the lens of paleoepigenetics.
StrainR2 accurately deconvolutes strain-level abundances in synthetic microbial communities
Authors: Heber Kerim , Tian Shuchang , Betancurt-Anzola Daniela , Koo Heejung , Bisanz Jordan E. 
Published: August 2024

ABSTRACTBackgroundSynthetic microbial communities offer an opportunity to conduct reductionist research in tractable model systems. However, deriving abundances of highly related strains within these communities is currently unreliable. 16S rRNA gene sequencing does not resolve abundance at the strain level, standard methods for analysis of shotgun metagenomic sequencing do not account for ambiguous mapping between closely related strains, and other methods such as quantitative PCR (qPCR) scale poorly and are resource prohibitive for complex communities. We present StrainR2, which utilizes shotgun metagenomic sequencing paired with a k-mer-based normalization strategy to provide high accuracy strain-level abundances for all members of a synthetic community, provided their genomes.ResultsBothin silico,and using sequencing data derived from gnotobiotic mice colonized with a synthetic fecal microbiota, StrainR2 resolves strain abundances with greater accuracy than other tools utilizing shotgun metagenomic sequencing reads and can resolve complex mixtures of highly related strains. Through experimental validation and benchmarking, we demonstrate that StrainR2’s accuracy is comparable to that of qPCR on a subset of strains resolved using absolute quantification. Further, it is capable of scaling to communities of hundreds of strains and efficiently utilizes memory being capable of running both on personal computers and high-performance computing nodes.ConclusionsUsing shotgun metagenomic sequencing reads is a viable method for determining accurate strain-level abundances in synthetic communities using StrainR2.
FACT-(H3-H4) complex stimulates Pol α activity to coordinate DNA synthesis with nucleosome assembly
Authors: Zhang Wenshuo , Xu Jiawei , Yang Jiayi , Shi Guojun , Wu Jiale , Gao Ning , Feng Jianxun , Li Qing 
Published: August 2024

AbstractDeficiencies in replication-coupled (RC) nucleosome assembly often lead to reduced DNA replication rate, but the precise mechanism underlying this process remains unsolved. Here, we discovered that H3-H4, but not H2A-H2B, mediates the interaction between FACT and the primase-polymerase complex DNA Pol α. This interaction stimulates the DNA polymerase activity of Pol α, and is indispensable for Okazaki fragment synthesis and replication fork progression. Moreover, the Pol1-N domain of Pol α provides a specific binding site for FACT and H3-H4. Furthermore, CAF-1 and Rtt106-mediated replication-coupled nucleosome assembly pathways regulate this interaction. Together, we propose that the FACT-(H3-H4)-Pol α interaction acts as a “Pre-Warning System” that regulates DNA replication, ensuring proper coordination between DNA synthesis and nucleosome assembly.
Mitochondrial Ca2+controls pancreatic cancer growth and metastasis by regulating epithelial cell plasticity
Authors: Weissenrieder Jillian S. , Peura Jessica , Paudel Usha , Bhalerao Nikita , Weinmann Natalie , Johnson Calvin , Wengyn Maximilian , Drager Rebecca , Furth Emma Elizabeth , Simin Karl , Ruscetti Marcus , Stanger Ben Z. , Rustgi Anil K. , Pitarresi Jason R. , Foskett J. Kevin 
Published: August 2024

AbstractEndoplasmic reticulum to mitochondria Ca2+transfer is important for cancer cell survival, but the role of mitochondrial Ca2+uptake through the mitochondrial Ca2+uniporter (MCU) in pancreatic adenocarcinoma (PDAC) is poorly understood. Here, we show that increased MCU expression is associated with malignancy and poorer outcomes in PDAC patients. In isogenic murine PDAC models,Mcudeletion (McuKO) ablated mitochondrial Ca2+uptake, which reduced proliferation and inhibited self-renewal. Orthotopic implantation of MCU-null tumor cells reduced primary tumor growth and metastasis.Mcudeletion reduced the cellular plasticity of tumor cells by inhibiting epithelial-to-mesenchymal transition (EMT), which contributes to metastatic competency in PDAC. Mechanistically, the loss of mitochondrial Ca2+uptake reduced expression of the key EMT transcription factor Snail and secretion of the EMT-inducing ligand TGFβ. Snail re-expression and TGFβ treatment rescued deficits inMcuKOcells and restored their metastatic ability. Thus, MCU may present a therapeutic target in PDAC to limit cancer-cell-induced EMT and metastasis.
A synthetic cell-free pathway for biocatalytic upgrading of one-carbon substrates
Authors: Landwehr Grant M. , Vogeli Bastian , Tian Cong , Singal Bharti , Gupta Anika , Lion Rebeca , Sargent Edward H. , Karim Ashty S. , Jewett Michael C. 
Published: August 2024

AbstractBiotechnological processes hold tremendous potential for the efficient and sustainable conversion of one-carbon (C1) substrates into complex multi-carbon products. However, the development of robust and versatile biocatalytic systems for this purpose remains a significant challenge. In this study, we report a hybrid electrochemical-biochemical cell-free system for the conversion of C1 substrates into the universal biological building block acetyl-CoA. The synthetic reductive formate pathway (ReForm) consists of five core enzymes catalyzing non-natural reactions that were established through a cell-free enzyme engineering platform. We demonstrate that ReForm works in a plug-and-play manner to accept diverse C1 substrates including CO2equivalents. We anticipate that ReForm will facilitate efforts to build and improve synthetic C1 utilization pathways for a formate-based bioeconomy.
Ion channels that mediate calcium-dependent control of spike patterns are spatially organized across the soma in relation to a cytoskeletal assembly
Authors: Sahu Giriraj , Greening Dylan , Nicola Wilten , Turner Ray W. 
Published: August 2024

AbstractSodium and potassium channels that regulate axonal spike propagation are highly organized at nodes of Ranvier by a spectrin-actin membrane periodic skeleton. STORM-TIRF microscopy was used to define the spatial organization over the soma of a complex of Cav1.3 calcium, RyR2, and IK potassium channels (CaRyK complex) that generate a slow AHP in hippocampal neurons. Nearest neighbor distance and non-negative matrix factorization analyses identified two spatial patterns as linear rows of 3-8 immuno-labeled clusters with 155 nm periodicity that extended to branchpoints, or as isolated clusters with 600-800 nm separation. The rows and isolated clusters for each of the CaRyK complex proteins closely overlapped with the patterns for spectrin βII and the actin linking proteins actinin I and II. Together the data reveal a close correspondence between the placement of CaRyK complex proteins and that of a net-like organization of spectrin βII across the soma. The regularity in the pattern of expression of these proteins at ER-PM junctions suggest their role as functional nodes of calcium- and calcium-gated potassium channels to control the pattern of spike output at the soma.
Structural basis of human 20S proteasome biogenesis
Authors: Zhang Hanxiao , Zhou Chenyu , Mohammad Zarith , Zhao Jianhua 
Published: August 2024

ABSTRACTNew proteasomes are produced to accommodate increases in cellular catabolic demand and prevent the accumulation of cytotoxic proteins. Formation of the proteasomal 20S core complex relies on the function of the five chaperones PAC1-4 and POMP. To understand how these chaperones facilitate proteasome assembly, we tagged the endogenous chaperones using CRISPR/Cas gene editing and examined the chaperone-bound complexes by cryo-EM. We observed an early α-ring intermediate subcomplex that is stabilized by PAC1-4, which transitions to β-ring assembly upon dissociation of PAC3/PAC4 and rearrangement of the PAC1 N-terminal tail. Completion of the β-ring and dimerization of half-proteasomes repositions critical lysine K33 to trigger cleavage of the β pro-peptides, leading to the concerted dissociation of POMP and PAC1/PAC2 to yield mature 20S proteasomes. This study reveals structural insights into critical points along the assembly pathway of the human proteasome and provides a molecular blueprint for 20S biogenesis.
Top-down Proteomics for the Characterization and Quantification of Calreticulin Arginylation
Authors: Searfoss Richard M. , Liu Xingyu , Garcia Benjamin A. , Lin Zongtao 
Published: August 2024

AbstractArginylation installed by arginyltransferase 1 (ATE1) features an addition of arginine (Arg) to the reactive amino acids (e.g., Glu and Asp) at the proteinN-terminus or side chain. Systemic removal of arginylation after ATE1 knockout (KO) in mouse models resulted in heart defects leading to embryonic lethality. The biological importance of arginylation has motivated the discovery of arginylation sites on proteins using bottom-up approaches. While bottom-up proteomics is powerful in localizing peptide arginylation, it lacks the ability to quantify proteoforms at the protein level. Here we developed a top-down proteomics workflow for characterizing and quantifying calreticulin (CALR) arginylation. To generate fully arginylated CALR (R-CALR), we have inserted an R residue after the signaling peptide (AA1-17). Upon overexpression in ATE1 KO cells, CALR and R-CALR were purified by affinity purification and analyzed by LCMS in positive mode. Both proteoforms showed charge states ranging from 27-68 with charge 58 as the most intense charge state. Their MS2 spectra from electron-activated dissociation (EAD) showed preferential fragmentation at the proteinN-terminals which yielded sufficientcions facilitating precise localization of the arginylation sites. The calcium-binding domain (CBD) gave minimum characteristic ions possibly due to the abundant presence of >100 D and E residues. Ultraviolet photodissociation (UVPD) compared with EAD and ETD significantly improved the sequence coverage of CBD. This method can identify and quantify CALR arginylation at absence, endogenous (low), and high levels. To our knowledge, our work is the first application of top-down proteomics in characterizing post-translational arginylationin vitroandin vivo.
Dissecting the metabolic costs of up- and down-hill walking
Authors: Jessup Luke N. , Kelly Luke A. , Cresswell Andrew G. , Lichtwark Glen A. 
Published: August 2024

AbstractWork- and collision-based models of locomotion are often used to describe the relationship between the body’s mechanical work requirements and metabolic energy expenditure. While work- and collision-based models do a reasonable job of relating mechanical work to metabolic cost at a system level, these models may not map to the underlying force and work demands of muscle, which directly affects energy expenditure. We collected motion capture, force, electromyography and ultrasound data from the main power producing muscles during uphill and downhill walking between +/− 15% grade. These data were used to evaluate a musculoskeletal modelling approach to simulate muscle force- and work-related costs that could be compared to metabolic power that we measured using indirect calorimetry. Muscle force-related costs (activation heat rate + maintenance heat rate) increased at steeper up- and down-hill grades and were moderately correlated with mean joint moments. Muscle work-related costs (mechanical work rate + shortening / lengthening heat rate) increased as grade became more positive and were strongly correlated with net joint work. Compared to traditional models, the inclusion of a term to account for muscle force-related costs should lead to a more explanatory cost model that maps directly to the mechanical demands of muscle.
Biomolecular condensates bridge experiment and theory of mass-conserving reaction-diffusion systems in phase separation
Authors: Li Cheng , Guo Man-Ting , He Xiaoqing , Liu Quan-Xing , Qi Zhi 
Published: August 2024

AbstractPhase separation is crucial in biological processes and ecological resilience, yet experimental evidence supporting validity of mass-conserving reaction-diffusion (MCRD) models in describing phase separation remains rare. Here, we identified one type of biomolecular condensates – double-stranded DNA (dsDNA) and the human transcription factor p53 as forming dsDNA-protein interactive co-condensates (DPICs) as an experimental model, where dynamic DPICs evolve into droplet-like patterns through reversible autocatalytic biochemical reactions. Thus, we can use the MCRD model to describe this experimental system. The pattern formation depends on concentration of protein and dsDNA and their local nonlinear interactions, which were experimentally tested at meso-scale and integrated into an MCRD model. Our results provide direct evidence that the experimental data-driven MCRD models can reproduce the observed phase diagram and scaling-invariance coarsening patterns, thus, providing a compelling mechanism for phase-separation pattern in other systems.
The ameliorative effect ofC-Kitposhepatic endothelial Mertk deficiency on nonalcoholic steatohepatitis
Authors: Fu Seng-Wang , Gao Yu-Xuan , Li Hui-Yi , Ren Yi-Fan , Wu Jun-Cheng , Li Zheng-Hong , Xu Ming-Yi 
Published: August 2024

AbstractRecently, Mer tyrosine kinase (Mertk) and KIT proto-oncogene (C-Kit) were reported play a role in liver sinusoidal endothelial cells (LSECs) in patients with nonalcoholic steatohepatitis (NASH). In this study, lower levels of C-Kit and higher levels of Mertk/p-Mertk were confirmed in steatotic LSECs and in the livers of patients and mice with NASH. C-Kit was suggested to negatively regulate Mertk signaling in steatotic LSECs. The steatotic LSECs in which Mertk was knocked down displayed high fenestration and reduced expression of procapillarized CD31/VN; showed antiangiogenic features and decreased expression of proangiogenic VEGF/ERK1/2; and exhibited intact mitophagy and upregulation of the Pink1/Parkin pathway. Bone marrow transplantation (BMT) ofC-Kitpos-BMCssh-Mertkto MCD mice could equivalently protect endothelial functions. Steatotic hepatocytes (HCs) or hepatic stellate cells (HSCs) cocultured with LSECssh-Mertkexhibited diminished lipid deposition; decreased expression of prolipogenic LXR/SREBP-1c, proinflammatory TNF-α/IL-6 and profibrotic α-SMA/ColI; and increased expression of prolipolytic FXR/ADPN. Similarly, the BMT ofC-Kitpos-BMCssh-Mertkto MCD mice ameliorated NASH.C-Kitpos-LSECs that underwent Mertk cleavage were found to limit NASH progression. Therefore, Mertk deficiency should be a novel therapeutic agent for restoring LSECs in patients with NASH.
Unraveling the Role of Viral Interference in Disrupting Biennial RSV Epidemics in Northern Stockholm
Authors: Li Ke , Hamrin Johan , Weinberger Daniel M. , Pitzer Virginia E. 
Published: August 2024

AbstractRespiratory syncytial virus (RSV) primarily impacts infants and older adults, with seasonal winter outbreaks in temperate countries. Biennial cycles of RSV activity have also been identified in Northern Europe and some states in the United States. Delayed RSV activity was reported worldwide during the 2009 influenza pandemic, and a disrupted biennial pattern of RSV activity was observed in northern Stockholm following the pandemic. Biennial patterns shifted to early/large outbreaks in even-numbered years and late/small outbreaks in odd-numbered years. However, the mechanisms underpinning this change in pattern remain unknown. In this work, we constructed an age-stratified mechanistic model to explicitly test three factors that could lead to the change in RSV transmission dynamics: 1) birth rates, 2) temperatures, and 3) viral interference. By fitting the model to weekly RSV admission data over a 20-year period and comparing different models, we found that viral interference from influenza was the only mechanism that explained the shifted biennial pattern. Our work demonstrates the complex interplay between different respiratory viruses, providing evidence that supports the presence of interactions between the H1N1 pandemic influenza virus and RSV at the population level, with implications for future public health interventions.
Standardized clinical data capture to describe cerebral palsy
Authors: Kim Susie , Steffen Kelsey , Gottschalk-Henneberry Lauren , Miros Jennifer , Leger Katie , Robichaux-Viehoever Amy , Taca Karen , Aravamuthan Bhooma 
Published: August 2024

AbstractObjectiveTo describe a standardized methodology for capturing clinically valuable information on young people with cerebral palsy (CP) from caregivers and clinicians during routine clinical care.MethodsWe developed a caregiver-facing intake form and clinician-facing standardized note template and integrated both into routine clinical care at a tertiary care CP center (https://bit.ly/CP-Intake-Methodology). We extracted this caregiver and clinician-entered data on people with an ICD10 diagnosis of CP seen between 3/22/23 and 12/28/23. We used this data to describe how CP manifests in this group and which medical features affected the odds of walking, oral feeding, and speech by age 5.ResultsOf 686 visits, 663 (97%) had caregiver- and clinician-entered data and 633 had a clinician-confirmed CP diagnosis (mean age 9.1, 53.4% Male, 78.5% White). It was common to have quadriplegia (288/613, 47.0%), both spasticity and dystonia (257/632, 40.7%), walk independently (368/633, 58.1%), eat all food and drink safely by mouth (288/578, 55.9%), and produce understandable speech (249/584, 42.6%). Cortical grey matter injury and duration of initial critical care unit stay affected the odds of walking, oral feeding, and speech (binary logistic regression, p<0.001).ConclusionsWe comprehensively captured caregiver and clinician-entered data on 97% of people seen in a tertiary care CP Center and used this data to determine medical features affecting the odds of three functional outcomes. By sharing our methodology, we aim to facilitate replication of this dataset at other sites and grow our understanding of how CP manifests in the US.Article summaryUsing caregiver and clinician-entered data on people seen in a tertiary-care CP center, we determined medical features affecting the odds of three functional outcomes.What’s known on this subjectDetailed CP characterization can be limited if using population-based registries and retrospective chart review alone, including limited data on recently validated functional classification systems for CP.What this study addsWe comprehensively captured caregiver and clinician-entered data on 97% of people seen in our CP Center to describe how CP manifests and show that cortical injury and initial ICU stay duration affect the odds of walking, oral feeding, and speech.Contributors StatementSusie Kim helped design the study, aggregated data, carried out data analyses, and critically reviewed and revised the manuscript.Kelsey Steffen helped conceptualize and design the study and critically reviewed and revised the manuscript.Lauren Gottschalk, Jennifer Miros, Katie Leger, Amy Viehoever, and Karen Taca helped design the study and critically reviewed and revised the manuscript.Bhooma Aravamuthan conceptualized and designed the study, supervised data collection and analysis, drafted the initial manuscript, and critically reviewed and revised the manuscript.
Molecular Feature-Based Classification of Retroperitoneal Liposarcoma: A Prospective Cohort Study
Authors: Xiao Mengmeng , Li Xiangji , Bu Fanqin , Ma Shixiang , Yang Xiaohan , Chen Jun , Zhao Yu , Cananzi Ferdinando , Luo Chenghua , Min Li 
Published: August 2024

ABSTRACTBackgroundRetroperitoneal liposarcoma (RPLS) is a critical malignant disease with various clinical outcomes. However, the molecular heterogeneity of RPLS was poorly elucidated, and few biomarkers were proposed to monitor its progression.MethodsRNA sequencing was performed on a training cohort of 88 RPLS patients to identify dysregulated genes and pathways using clusterprofiler. The GSVA algorithm was utilized to assess signaling pathways levels in each sample, and unsupervised clustering was employed to distinguish RPLS subtypes. Differentially expressed genes (DEGs) between RPLS subtypes were identified to construct a simplified dichotomous clustering via nonnegative matrix factorization. The feasibility of this classification was validated in a separate validation cohort (n=241) using immunohistochemistry (IHC) from the Retroperitoneal SArcoma Registry (RESAR). The study is registered withClinicalTrials.govunder numberNCT03838718.ResultsCell cycle, DNA damage & repair, and Metabolism were identified as the most aberrant biological processes in RPLS, enabling the division of RPLS patients into two distinct subtypes with unique molecular signatures, tumor microenvironment, clinical features and outcomes (overall survival, OS and disease-free survival, DFS). A simplified RPLS classification based on representative biomarkers (LEP and PTTG1) demonstrated high accuracy (AUC>0.99), with patients classified as LEP+ and PTTG1-showing lower aggressive pathological composition ratio and fewer surgery times, along with better OS (HR=0.41,P<0.001) and DFS (HR=0.60,P=0.005).ConclusionsOur study provided an ever-largest gene expression landscape of RPLS and established an IHC-based molecular classification that was clinically relevant and cost-effective for guiding treatment decisions.