bluuebunny/crossref_metadata_2025_split huggingface dataset:
Benchmarking Bayesian colocalization methods in validating Mendelian randomization-based target discoveries from circulating proteins for cardiometabolic diseases
Authors: Zhang Wenmin , Yoshiji Satoshi , Sladek Robert , Dupuis Josée , Lu Tianyuan 
Published: October 2024

AbstractBackgroundMendelian randomization (MR) is an important tool for identifying potential biomarkers and drug targets. Colocalization analysis is crucial for validating MR findings and guarding against potential confounding due to linkage disequilibrium. We aim to systematically benchmark the performance of four Bayesian colocalization methods in validating MR-based target discoveries from circulating proteins for cardiometabolic diseases.ResultsWe conducted MR analyses to assess the associations between circulating levels of 1,535 proteins and five cardiometabolic traits, followed by colocalization analyses using coloc, coloc+SuSiE, PWCoCo and SharePro. All methods demonstrated well-controlled false discoveries in the colocalization analysis of 611 pairs of circulating proteins and cardiometabolic traits with a nominal p-value > 0.9 in MR. SharePro demonstrated the highest frequency in supporting 160 (79.6%) of the 201 Bonferroni-significant protein-trait associations identified by MR, compared to coloc (supporting 40.3% of these associations), coloc+SuSiE (46.8%), and PWCoCo (45.8%), and was robust to varying prior colocalization probabilities. Moreover, protein-trait associations identified by MR and supported by SharePro were more likely to agree with significant gene-level associations based on rare variants detected in exome-wide association studies and implicate known drug targets for cardiometabolic diseases. Eight protein-trait associations were exclusively supported by SharePro and did not demonstrate a high risk of horizontal pleiotropy, suggesting potential cardiometabolic biomarkers or drug targets, such as HSF1 and HAVCR2.ConclusionsSharePro most often supports high-confidence associations identified through MR for cardiometabolic diseases. Combining multiple lines of evidence using different methods may substantially increase the yield of biomarker and drug target discovery programs.
DDX41 dissolves G-quadruplexes to maintain erythroid genome integrity and prevent cGAS-mediated cell death
Authors: Bi Honghao , Ren Kehan , Wang Pan , Li Ermin , Han Xu , Wang Wen , Yang Jing , Aydemir Inci , Tao Kara , Godley Lucy , Liu Yan , Shukla Vipul , Bartom Elizabeth T. , Tang Yuefeng , Blanc Lionel , Sukhanova Madina , Ji Peng 
Published: October 2024

AbstractDeleterious germlineDDX41variants constitute the most common inherited predisposition disorder linked to myeloid neoplasms (MNs). The role of DDX41 in hematopoiesis and how its germline and somatic mutations contribute to MNs remain unclear. Here we show that DDX41 is essential for erythropoiesis but dispensable for the development of other hematopoietic lineages. Using stage-specific Cre models for erythropoiesis, we reveal that Ddx41 knockout in early erythropoiesis is embryonically lethal, while knockout in late-stage terminal erythropoiesis allows mice to survive with normal blood counts. DDX41 deficiency induces a significant upregulation of G-quadruplexes (G4), noncanonical DNA structures that tend to accumulate in the early stages of erythroid precursors. We show that DDX41 co-localizes with G4 on the erythroid genome. DDX41 directly binds to and dissolves G4, which is significantly compromised in MN-associatedDDX41mutants. Accumulation of G4 by DDX41 deficiency induces erythroid genome instability, defects in ribosomal biogenesis, and upregulation of p53. However, p53 deficiency does not rescue the embryonic death of Ddx41 hematopoietic-specific knockout mice. In parallel, genome instability also activates the cGas-Sting pathway, which is detrimental to survival since cGas-deficient and hematopoietic-specific Ddx41 knockout mice are viable without detectable hematologic phenotypes, although these mice continue to show erythroid ribosomal defects and upregulation of p53. These findings are further supported by data from aDDX41mutated MN patient and human iPSC-derived bone marrow organoids. Our study establishes DDX41 as a G4 dissolver, essential for erythroid genome stability and suppressing the cGAS-STING pathway.
Bringing Attomolar Detection to the Point-of-Care with Nanopatterned DNA Origami Nanoantennas
Authors: Yaadav Renukka , Trofymchuk Kateryna , Dass Mihir , Behrendt Vivien , Hauer Benedikt , Schütz Jan , Close Cindy , Scheckenbach Michael , Ferrari Giovanni , Maeurer Leoni , Sebina Sophia , Glembockyte Viktorija , Liedl Tim , Tinnefeld Philip 
Published: October 2024

AbstractCreating increasingly sensitive and cost-effective nucleic acid detection methods is critical for enhancing point-of-care (POC) applications. This involves capturing all desired biomarkers in a sample with high specificity and transducing the capture events to a detector. However, the signal from biomarkers present at extremely low amounts often falls below the detection limit of typical fluorescence-based methods, making molecular amplification a necessary step. Here, we present a nucleic acid detection assay of a 151-nucleotide sequence specific to antibiotics-resistantKlebsiella pneumoniae, based on single-molecule fluorescence detection of non-amplified DNA down to the attomolar level, using Trident NanoAntennas with Cleared HOtSpots (NACHOS). Our NACHOS-diagnostics assay leverages a compact microscope with a large field-of-view and cost-efficient components, including microfluidic flow to enhance capturing efficiency. Fluorescence enhancement is provided by DNA origami NanoAntennas, arranged in a dense array using a combination of nanosphere lithography and site-specific DNA origami placement. Our method can detect 200 ± 50 out of 600 molecules in a 100 µL sample volume within an hour. This represents typical number of pathogens in clinical samples commonly detected by Polymerase Chain Reaction but without the need for molecular amplification. We achieve similar sensitivity in untreated human blood plasma, enhancing the practical applicability of the system. Our platform can be adapted to detect shorter nucleic acid fragments that are not compatible with traditional amplification-based technologies. This broadens its potential for diverse diagnostic and healthcare applications, providing a robust and scalable solution for sensitive nucleic acid detection in various clinical settings.
An iPSC model of fragile X syndrome reflects clinical phenotypes and reveals m6A- mediated epi-transcriptomic dysregulation underlying synaptic dysfunction
Authors: Lu Lu , Sarkar Avijite Kumer , Dao Lan , Liu Yanchen , Ma Chunlong , Thwin Phyo Han , Chang Xuyao , Yoshida George , Li Annie , Wang Cenjing , Westerkamp Crace , Schmitt Lauren , Chelsey Maag , Stephanie Monzon , Zhao Yu , Liu Yaping , Wang Xiong , Zhu Ling-Qiang , Liu Dan , Tchieu Jason , Miyakoshi Makoto , Zhu Haining , Gross Christina , Pedapati Ernest , Salomonis Nathan , Erickson Craig , Guo Ziyuan 
Published: October 2024

AbstractFragile X syndrome (FXS), the leading genetic cause of intellectual disability, arises fromFMR1gene silencing and loss of the FMRP protein. N6-methyladenosine (m6A) is a prevalent mRNA modification essential for post-transcriptional regulation. FMRP is known to bind to and regulate the stability of m6A-containing transcripts. However, how loss of FMRP impacts on transcriptome-wide m6A modifications in FXS patients remains unknown. To answer this question, we generated cortical neurons differentiated from induced pluripotent stem cells (iPSC) derived from healthy subjects and FXS patients. In electrophysiology recordings, we validated that synaptic and neuronal network defects in iPSC-derived FXS neurons corresponded to the clinical EEG data of the patients from which the corresponding iPSC line was derived. In analysis of transcriptome-wide methylation, we show that FMRP deficiency led to increased translation of m6A writers, resulting in hypermethylation that primarily affecting synapse-associated transcripts and increased mRNA decay. Conversely, in the presence of an m6A writer inhibitor, synaptic defects in FXS neurons were rescued. Taken together, our findings uncover that an FMRP-dependent epi-transcriptomic mechanism contributes to FXS pathogenesis by disrupting m6A modifications in FXS, suggesting a promising avenue for m6A- targeted therapies.
Endurance exercise with reduced muscle glycogen content influences substrate utilization and attenuates acute mTORC1- and autophagic signaling in human type I and type II muscle fibers
Authors: Horwath O , Cornet L , Strömlind H , Moberg M , Edman S , Söderlund K , Checa A , Ruas J L , Blomstrand E 
Published: October 2024

AbstractBackgroundExercising with low muscle glycogen content can improve training adaptation, but the mechanisms underlying the muscular adaptation are still largely unknown. In this study, we measured substrate utilization and cell signaling in different muscle fiber types during exercise and investigated a possible link between these variables.MethodsFive subjects performed a single leg cycling exercise in the evening (day 1) with the purpose of reducing glycogen stores. The following morning (day 2), they performed two-legged cycling at ∼70% of VO2peak for 1h. Muscle biopsies were taken from both legs pre- and post-exercise for enzymatic analyses of glycogen, metabolite concentrations using LC-MS/MS-based quantification, and protein signaling using Western blot in pools of type I or type II fibers.ResultsGlycogen content was 60-65% lower for both fiber types (P<0.01) in the leg that exercised on day 1 (low leg) compared to the other leg with normal level of glycogen (normal leg) before the cycling exercise on day 2. Glycogen utilization during exercise was significantly less in both fiber types in the low compared to the normal leg (P<0.05). In the low leg, there was a 14- and 6-fold increase in long-chain fatty acids conjugated to carnitine in type I and type II fibers, respectively, post-exercise. This increase was 3-4 times larger than in the normal leg (P<0.05). Post-exercise, mTORSer2448phosphorylation was increased in both fiber types in the normal leg (P<0.05) but remained unchanged in both fiber types in the low leg together with an increase in eEF2Thr56phosphorylation in type I fibers (P<0.01). Exercise induced a reduction in the autophagy marker LC3B-II in both fiber types and legs, but the post-exercise level was higher in both fiber types in the low leg (P<0.05). Accordingly, the LC3B-II/I ratio decreased only in the normal leg (75% for type I and 87% for type II, P<0.01).ConclusionsStarting an endurance exercise session with low glycogen availability leads to profound changes in substrate utilization in both type I and type II fibers. This may reduce the mTORC1 signaling response, primarily in type I muscle fibers, and attenuate the normally observed reduction in autophagy.
Simulating 3D refractive index distributions of suspended cells
Authors: Borrelli Francesca , Pirone Daniele , Miccio Lisa , Memmolo Pasquale , Ferraro Pietro , Bianco Vittorio 
Published: October 2024

AbstractThe introduction of holo-tomographic flow cytometry has unlocked the possibility of imaging the 3D refractive index (RI) distribution of suspended cells while they flow and rotate in microfluidic streams. Similarly, approaches that optically trap and rotate the samples can image them in suspension conditions. Great effort has been spent in developing robust algorithms for the tomogram estimation, as well as denoising and 3D segmentation algorithms. However, the lack of a ground-truth dataset for suspended cells significantly hinders the development of image processing pipelines, limiting the advancement of the associated technology field. Here we propose a novel method for simulating 3D refractive index tomograms of suspended cells. We start with prior knowledge of the statistics of the 3D RI distribution and morphometry of various cell sub-compartments gathered from holo-tomographic flow cytometry experiments and combined with literature data to create realistic 3D distributions. Next, we introduce a simple method to obtain a simulation of the tomogram obtainable from each cell, which approximates the effects of the limited numerical aperture of the system, the speckle noise and the inversion algorithm itself. As a benchmark for the simulator, we created a shared dataset of RI tomograms with various levels of complexity, simulating yeast eukaryotic cells at different budding stages with various phenotypes of cytoplasmic vacuoles, and the presence of cytoplasmic vacuoles and lipid droplets in monocyte cells. We believe that this shared dataset and the simulation method will contribute to the development of a wide plethora of tomogram estimation and processing algorithms.
Representations of stimulus meaning in the hippocampus
Authors: Biane Jeremy S. , Ladow Max A. , Fan Austin , Choi Hye Sun , Zhou Lexi Zichen , Hassan Shazreh , Apodaca-Montano Daniel L. , Kwon Andrew O. , Bratsch-Prince Joshua X. , Kheirbek Mazen A. 
Published: October 2024

SUMMARYThe ability to discriminate and categorize the meaning of environmental stimuli and respond accordingly is essential for survival. The ventral hippocampus (vHPC) controls emotional and motivated behaviors in response to environmental cues and is hypothesized to do so in part by deciphering the positive or negative quality of these cues. Yet, what features of the environment are represented in the activity patterns of vCA1 neurons, and whether the positive or negative meaning of a stimulus is present at this stage, remains unclear. Here, using 2-photon calcium imaging across six different experimental paradigms, we consistently found that vCA1 ensembles encode the identity, sensory features, and intensity of learned and innately salient stimuli, but not their overall valence. These results offer a reappraisal of vCA1 function, wherein information corresponding to individual stimulus features and their behavioral saliency predominates, while valence-related information is attached elsewhere.
Genetic removal of Nlrp3 protects against sporadic and R345W Efemp1-induced basal laminar deposit formation
Authors: Ortega Antonio J. , Daniel Steffi , Renwick Marian , Kambhampati Pravallika , Thompson Krista N. , Collier Gracen E. , Baker Emily L. , Zaki Hasan , Hulleman John D. 
Published: October 2024

ABSTRACTChronic, unresolved inflammation has long been speculated to serve as an initiating and propagating factor in numerous neurodegenerative diseases, including a leading cause of irreversible blindness in the elderly, age-related macular degeneration (AMD). Intracellular multiprotein complexes called inflammasomes in combination with activated caspases facilitate production of pro-inflammatory cytokines such as interleukin 1 beta. Specifically, the nucleotide-binding oligomerization (NOD)-like receptor protein 3 (NLRP3) has received heightened attention due to the wide range of stimuli to which it can respond and its potential involvement in AMD. In this study, we directly tested the role of Nlrp3 and its downstream effector, caspase 1 (Casp1) in mediating early AMD-like pathology (i.e., basal laminar deposits [BLamDs]) in wild-type (WT) mice and the Malattia Leventinese/Doyne honeycomb retinal dystrophy (ML/DHRD) mouse model (p.R345W mutation in Efemp1). Compared to aged-matched controls, R345W+/+knockin mice demonstrated increased Muller cell gliosis, subretinal Iba-1+microglial cells, higher Nlrp3 immunoreactivity in the retina, as well as significant transcriptional upregulation of complement component 3, Nlrp3, pro-Il1b, pro-caspase-1, and tissue inhibitor of matrix metalloproteinase 3 in the retinal pigmented epithelium (RPE)/choroid. These findings were accompanied by an age-related increase in BLamD formation in the R345W+/+mice. Genetic elimination of either Nlrp3 or Casp1 significantly reduced both the size and coverage of BLamDs in the R345W+/+background, highlighting an important and underappreciated pathway that could affect ML/DHRD onset and progression. Moreover, Nlrp3 knockout reduced spontaneous, idiopathic BLamDs in WT mice, suggesting translatability of our findings not only to rare inherited retinal dystrophies, but also potentially to AMD itself.
Metabolic modeling of microbial communities in the chicken ceca reveals a landscape of competition and co-operation
Authors: Utkina Irina , Fan Yi , Willing Benjamin P. , Parkinson John 
Published: October 2024

ABSTRACTWith their ability to degrade dietary fibers to liberate otherwise unavailable substrates, members of the Bacteroidales exert a substantial influence on the microbiome of the lower intestine. Currently our knowledge of how this influence translates to the metabolic interactions that support community structure is limited. Here we applied constraints-based modeling to chicken cecal communities to investigate metabolic interactions in the presence and absence ofBacteroides. From metagenomic datasets previously generated from 33 chicken ceca, we constructed 237 metagenome-assembled genomes. Metabolic modeling of communities built from these genomes generated profiles of short chain fatty acids largely consistent with experimental assays and confirmed the role ofB. fragilisas a metabolic hub, central to the production of metabolites consumed by other taxa. In its absence, communities undergo significant functional reconfiguration, with metabolic roles typically fulfilled byB. fragilisassumed by multiple taxa. BeyondB. fragilis, we foundEscherichia coliandLactobacillus crispatusalso mediate influential metabolic roles that vary in the presence or absence ofB. fragilis. Compensatory adaptations adopted by the microbiome in the absence ofB. fragilisresulted in metabolic profiles previously associated with inflammatory bowel disease in humans, including energy deficiency, increased lactate production and altered amino acid metabolism. This work demonstrates the potential of chicken cecal microbiomes to investigate the complex metabolic interactions and key contributions that drive community dynamics.
Further characterization and engineering of a 11-amino acid motif for enhancing recombinant protein expression
Authors: Bi Jiawu , Tiong Elaine , Zhou Weibiao , Wong Fong Tian 
Published: October 2024

AbstractBackgroundRecombinant protein production inEscherichia coli(E. coli) is a widely used system in both academic and industrial research owing to its low cost and wide availability of genetic tools. Despite its advantages, this system still struggles with soluble expression of recombinant proteins. To address this, various solubility-enhancing and yield-improving methods such as the addition of fusion tags have been developed. However, traditional tags such as small ubiquitin-related modifier (SUMO) and Glutathione S-transferase (GST) can interfere with protein folding or require removal post-translation, which adds complexity and cost to production. To circumvent these issues, smaller solubility tags (<10 kDa) are preferred. This study specifically focuses on an 11-amino acid solubility-enhancing tag (NT11) derived from the N-terminal domain of a duplicated carbonic anhydrase fromDunaliellaspecies.ResultsA comprehensive analysis was performed to improve the characteristics of the 11-amino acid tag. By investigating the alanine-scan library of NT11, we increased its activity and identified key residues for further development. Screening with the alanine mutant library consistently led to at least a two-fold improvement in protein yield for three different proteins. We also discovered that the NT11 tag is not limited to the N-terminal position and can function at either the N- or C-terminal of the protein, providing flexibility in designing protein expression constructs. With these new insights, we have successfully doubled the recombinant protein yields of valuable growth factors, such as fibroblast growth factor 2 (FGF2) and an originally low-yielding human epidermal growth factor (hEGF), inE. coli.ConclusionThe further characterisation and development of the NT11 tag have provided valuable insights into the optimization process for such small tags and expanded our understanding of its potential applications. The ability of NT11 tag to be positioned at different locations within the protein construct without compromising its effectiveness to enhance recombinant protein yields, makes it a valuable tool across a diverse range of proteins. Collectively, these findings have the potential to simplify and enhance the efficiency of recombinant protein production.
Functional characterization of luciferase in a brittle star indicates parallel evolution influenced by genomic availability of haloalkane dehalogenase
Authors: Lau Emily S , Majerova Marika , Hensley Nicholai M , Mukherjee Arnab , Vasina Michal , Pluskal Daniel , Damborsky Jiri , Prokop Zbynek , Delroisse Jérôme , Bayaert Wendy-Shirley , Parey Elise , Oliveri Paola , Marletaz Ferdinand , Marek Martin , Oakley Todd H 
Published: October 2024

AbstractDetermining why convergent traits use distinct versus shared genetic components is crucial for understanding how evolutionary processes generate and sustain biodiversity. However, the factors dictating the genetic underpinnings of convergent traits remain incompletely understood. Here, we use heterologous protein expression, biochemical assays, and phylogenetic analyses to confirm the origin of a luciferase gene from haloalkane dehalogenases in the brittle starAmphiura filiformis. Through database searches and gene tree analyses, we also show a complex pattern of presence and absence of haloalkane dehalogenases across organismal genomes. These results first confirm parallel evolution across a vast phylogenetic distance, because octocorals likeRenillaalso use luciferase derived from haloalkane dehalogenases. This parallel evolution is surprising, even though previously hypothesized, because many organisms that also use coelenterazine as the bioluminescence substrate evolved completely distinct luciferases. The inability to detect haloalkane dehalogenases in the genomes of several bioluminescent groups suggests that the distribution of this gene family influences its recruitment as a luciferase. Together, our findings highlight how biochemical function and genomic availability help determine whether distinct or shared genetic components are used during the convergent evolution of traits like bioluminescence.