bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimation of the Achilles tendon twist in vivo by individual triceps surae muscle stimulation
Authors: Laura Lecompte , Marion Crouzier , Stéphane Baudry , Benedicte Vanwanseele 
Published: March 2024

AbstractThe Achilles tendon (AT) is comprised of three distinct subtendons, each arising from the one of the three heads of the triceps surae muscles: gastrocnemius medialis (GM), gastrocnemius lateralis (GL) and soleus (SOL). These subtendons exhibit a twisted structure, classified as low (Type I), medium (Type II), and high (Type III) twist, based on cadaveric studies. Nevertheless, the in-vivo investigation of AT twist is notably scarce, resulting in a limited understanding of its functional significance. The aim of this study was to give insights into the complex 3D AT structure in vivo. 30 healthy participants underwent individual stimulation of each of the triceps surae muscles at rest with the foot attached to the pedal of an isokinetic dynamometer. Ultrasound images were captured to concomitantly examine the displacement of the superficial, middle and deep AT layers. SOL stimulation resulted in the highest AT displacement followed by GM and GL stimulation. Independent of the muscle stimulated, non-uniformity within the AT was observed with the deep layer exhibiting more displacement compared to the middle and superficial layers, hence important inter-individual differences in AT displacement were noticeable. By leveraging these individual displacement patterns during targeted stimulations in conjunction with cadaveric twist classifications providing insights into the area of each specific subtendon, our classification identified 19 subjects with a ’low’ and 11 subjects with a ’high’ AT twist. More research is needed to understand the complexity of the AT twisted structure in vivo to further understand its effect on AT properties and behaviour.
Transfer learning of multicellular organization via single-cell and spatial transcriptomics
Authors: Tan Yecheng , Wang Ai , Wang Zezhou , Lin Wei , Yan Yan , Nie Qing , Shi Jifan 
Published: March 2024

ABSTRACTSpatial tissues exhibit complex gene expression and multicellular patterns that are difficult to dissect. Single-cell RNA sequencing (scRNA-seq) provides full coverages of genes, but lacking spatial information, whereas spatial transcriptomics (ST) measures spatial locations of individual or group of cells, with more restrictions on gene information. To integrate scRNA-seq and ST data, we introduce a transfer learning method to decipher spatial organization of cells named iSORT. iSORT trains a neural network that maps gene expressions to spatial locations using scRNA-seq data along with ST slices as references. iSORT can find spatial patterns at single-cell scale, identify key genes that drive the patterning, and infer pseudo-growth trajectories using a concept of SpaRNA velocity. Benchmarking on simulation data and comparing with multiple existing tools show iSORT’s robustness and accuracy in reconstructing spatial organization. Using our own new human artery datasets, iSORT shows its capability of dissecting atherosclerosis. Applications to a range of biological systems, such as mouse embryo, mouse brain,Drosophilaembryo, and human developmental heart, demonstrate that iSORT can utilize both scRNA-seq and ST datasets to uncover multilayer spatial information of single cells.
Expansion microscopy for super-resolution imaging of collagen-abundant tissues
Authors: Chuang Ya-Han , Wu Yueh-Feng , Lin Ya-Hui , Zhou Yu-Xian , Hsu Shao-Chun , Lin Sung-Jan , Chu Li-An 
Published: March 2024

AbstractExpansion microscopy (ExM) is popular for three-dimensional ultrastructural imaging of cultured cells and tissue slices at nanoscale resolution with conventional microscopes via physical expansion of biological tissues. However, the application of this technology to collagen-abundant thick tissues is challenging. We demonstrate a new method, collagen expansion microscopy (ColExM), optimized for expanding tissues containing more than 70% collagen. ColExM succeeded in 4.5-fold linear expansion with minimal structural distortion of corneal and skin tissues. It was also compatible with immunostaining, allowing super-resolution visualization of three-dimensional neural structures innervating hair follicles and corneas. With ColExM, we succeeded in identifying individual mitochondria and previously unrecognized dendritic spine-like structures of corneal nerves. ColExM also enabled fine mapping of structural rearrangement of tight junctions and actin cytoskeletons. Therefore, this method can facilitate the exploration of three-dimensional nanoscale structures in collagen-rich tissues.
Breaking the Burst: Unveiling Mechanisms Behind Fragmented Network Bursts in Patient-derived Neurons
Authors: Doorn Nina , Voogd Eva J.H.F. , Levers Marloes R. , van Putten Michel J.A.M. , Frega Monica 
Published: March 2024

AbstractFragmented network bursts (NBs) are observed as a phenotypic driver in many patient-derived neuronal networks on multi-electrode arrays (MEAs), but the pathophysiological mechanisms underlying this phenomenon are unknown. Here, we used our previously developed biophysically detailedin silicomodel to investigate these mechanisms. Fragmentation of NBs in our model simulations occurred only when the level of short-term synaptic depression (STD) was enhanced, suggesting that STD is a key player. Experimental validation with Dynasore, an STD enhancer, induced fragmented NBs in healthy neuronal networksin vitro. Additionally, we showed that strong asynchronous neurotransmitter release, NMDA currents, or short-term facilitation (STF) can support the emergence of multiple fragments in NBs by producing excitation that persists after high-frequency firing stops. Our results provide important insights into disease mechanisms and potential pharmaceutical targets for neurological disorders modeled using hiPSC-derived neurons.
Exploring the potential ofCeltis aetnensis compoundsthrough Molecular Docking for Hepatocellular carcinoma
Authors: Kavitha K.N. , Revathi K. , Tamiraikani Tamilamban 
Published: March 2024

AbstractHepatocellular carcinoma (HCC) accounts for 1% of the liver malignances; HCC progresses in hepatocytes primarily as a result of inflammation, oxidative stress, and primary liver disease. Thanks to the in-silico methods that help in the identification of the targets and the drugs/potential drugs that can inhibit these proteins that cater to the growth of the cancer cells. Plant actives have been long considered as potential sources of anticancer drugs. In this regard, we studied the actives fromCeltis tournefortii Lam (Celtis aetnensis) usingGCMS analysis. The protein structures of three receptors—NF-B P50 homodimer, FGF receptor 4, and vascular endothelial growth factor receptor 2 (VEGFR2)—were then subjected to docking studies using phytocompounds fromCeltis aetnensis. Three receptor proteins were used in the docking analysis against 7 ligands. In this study, the PDB was used to obtain the structures of 3 cancer-related receptor proteins. The proteins were produced by eliminating water molecules, ligands using PyMol, and were then exposed to docking experiments. Docking studies revealed that the compounds with a binding energy ranging from -1.83 kcal/mol to -6.12 kcal/mol. The docking results revealed that eicosatetraenoic acid has a binding energy of-6.12 kcal/mol against the FGFR4 receptor. Sulfadoxine’s binding energy to the VEGFR2 receptor protein was-4.9 kcal/mol. Promethazine sulfoxide docks with an energy of -5.36 kcal/mol against NFKB P50. By attaching to the protein, these substances demonstrated good inhibitory activity. The results are supportive that these compounds may be used to treat HCC.
Light-directed evolution of dynamic, multi-state, and computational protein functionalities
Authors: Gligorovski Vojislav , Labagnara Marco , Rahi Sahand Jamal 
Published: March 2024

AbstractDirected evolution is a powerful method in biological engineering. Current approaches draw on time-invariant selection mechanisms, ideal for evolving steady-state properties such as enzymatic activity or fluorescence intensity. A fundamental problem remains how to continuously evolve dynamic, multi-state, or computational functionalities, e.g., on-off kinetics, state-specific activity, stimulus-responsiveness, or switching and logic capabilities. These require selection pressure on all of the states of a protein of interest (POI) and the transitions between them. We realized that optogenetics and cell cycle oscillations could be leveraged for a novel directed evolution paradigm (‘optovolution’) that is germane for this need: We designed a signaling cascade in budding yeast where optogenetic input switches the POI between off (0) and on (1) states. In turn, the POI controls a Cdk1 cyclin, which in the re-engineered cell cycle system is essential for one cell cycle stage but poisonous for another. Thus, the cyclin must oscillate (1-0-1-0…) for cell proliferation. In this system, evolution can act efficiently on the dynamics, transient states, and input-output relations of the POI in every cell cycle. Further, controlling the pacemaker, light, directs and tunes selection pressures. Optovolution is in vivo, continuous, self-selecting, and efficient. We first evolved two optogenetic systems, which relay 0/1 input to 0/1 output: We obtained 25 new variants of the widely used LOV transcription factor El222 that were stronger, less leaky, or green-and red-responsive. The latter was conjectured to be impossible for LOV domains but is needed for multiplexing and lowering phototoxicity. Evolving the PhyB-Pif3 optogenetic system, we discovered that loss of YOR1 makes supplementing the expensive and unstable chromophore phycocyanobilin (PCB) unnecessary. Finally, we demonstrate the generality of the method by evolving a destabilized rtTA transcription factor, which performs an AND operation between transcriptional and doxycycline input. Optovolution makes coveted, difficult-to-change protein functionalities continuously evolvable.
Next Generation Neuropeptide Y Receptor Small Molecule Agonists Inhibit Mosquito Biting Behavior
Authors: Zeledon Emely V. , Baxt Leigh A. , Khan Tanweer A. , Michino Mayako , Miller Michael , Huggins David J. , Jiang Caroline S. , Vosshall Leslie B. , Duvall Laura B. 
Published: March 2024

AbstractFemaleAedes aegyptimosquitoes can spread disease-causing pathogens when they bite humans to obtain blood nutrients required for egg production. Following a complete blood meal, host-seeking is suppressed until eggs are laid. Neuropeptide Y-like Receptor 7 (NPYLR7) plays a role in endogenous host-seeking suppression and previous work identified small molecule NPYLR7 agonists that suppress host-seeking and blood feeding when fed to mosquitoes at high micromolar doses. Using structure activity relationship analysis and structure-guided design we synthesized 128 compounds with similarity to known NPYLR7 agonists. Althoughin vitropotency (EC50) was not strictly predictive ofin vivoeffect, we identified 3 compounds that suppressed blood feeding from a live host when fed to mosquitoes at a 1 μM dose, a 100-fold improvement over the original reference compound. Exogenous activation of NPYLR7 represents an innovative vector control strategy to block mosquito biting behavior and prevent mosquito/human host interactions that lead to pathogen transmission.
Quantitative profiling of human translation initiation reveals regulatory elements that potently affect endogenous and therapeutically modified mRNAs
Authors: Lewis Cole J.T. , Xie Li , Bhandarkar Shivani , Jin Danni , Abdallah Kyrillos S. , Draycott Austin S. , Chen Yixuan , Thoreen Carson C. , Gilbert Wendy V. 
Published: March 2024

AbstractmRNA therapeutics offer a potentially universal strategy for the efficient development and delivery of therapeutic proteins. Current mRNA vaccines include chemically modified nucleotides to reduce cellular immunogenicity. Here, we develop an efficient, high-throughput method to measure human translation initiation on therapeutically modified as well as endogenous RNAs. Using systems-level biochemistry, we quantify ribosome recruitment to tens of thousands of human 5′ untranslated regions and identify sequences that mediate 250-fold effects. We observe widespread effects of coding sequences on translation initiation and identify small regulatory elements of 3-6 nucleotides that are sufficient to potently affect translational output. Incorporation of N1-methylpseudouridine (m1Ψ) selectively enhances translation by specific 5′ UTRs that we demonstrate surpass those of current mRNA vaccines. Our approach is broadly applicable to dissect mechanisms of human translation initiation and engineer more potent therapeutic mRNAs.HighlightsMeasurement of >30,000 human 5′ UTRs reveals a 250-fold range of translation outputSystematic mutagenesis demonstrates the causality of short (3-6nt) regulatory elementsN1-methylpseudouridine alters translation initiation in a sequence-specific mannerOptimal modified 5′ UTRs outperform those in the current class of mRNA vaccines
Voluntary co-contraction of ankle muscles alters motor unit discharge characteristics and reduces estimates of persistent inward currents
Authors: Gomes Matheus M. , Jenz Sophia T. , Beauchamp James A. , Negro Francesco , Heckman C.J. , Pearcey Gregory E.P. 
Published: March 2024

ABSTRACTMotoneuronal persistent inward currents (PICs) are both facilitated by neuromodulatory inputs and highly sensitive to local inhibitory circuits (e.g., Ia reciprocal inhibition). Methods aimed to increase group Ia reciprocal inhibition from the antagonistic muscle have been successful in decreasing PICs, and the diffuse actions of neuromodulators released during activation of remote muscles have increased PICs. However, it remains unknown how motoneurons function in the presence of simultaneous excitatory and inhibitory commands. To probe this topic, we investigated motor unit (MU) discharge patterns and estimated PICs during voluntary co-contraction of ankle muscles, which simultaneously demands the contraction of agonist-antagonist pairs. Twenty young adults randomly performed triangular ramps (10s up and down) of both co-contraction (simultaneous dorsiflexion and plantarflexion) and isometric dorsiflexion to a peak of 30% of their maximum muscle activity from a maximal voluntary contraction. Motor unit spike trains were decomposed from high-density surface electromyography recorded over the tibialis anterior (TA) using blind source separation algorithms. Voluntary co-contraction altered motor unit discharge rate characteristics, decreasing estimates of PICs by 20% (4.47 pulses per second (pps) vs 5.57 pps during isometric dorsiflexion). These findings suggest that, during voluntary co-contraction, the inhibitory input from the antagonist muscle overcomes the additional excitatory and neuromodulatory drive that may occur due to the co-contraction of the antagonist muscle, which constrains PIC behavior.KEY POINTSVoluntary co-contraction is a unique motor behavior that concurrently provides increases in excitatory and inhibitory inputs to motoneurons.During co-contraction of agonist-antagonist pairs, agonist motor unit discharge characteristics are altered, consistent with reductions in persistent inward current magnitude.Reciprocal inhibition from the antagonist likely becomes proportional to the increase in neural drive to the agonist, dampening the magnitude of persistent inward currents.
“Identification of microRNAs regulated by E2F transcription factors in human pluripotent stem cells”
Authors: Rodríguez-Varela María Soledad , Vautier Mercedes Florencia , Mucci Sofía , Isaja Luciana , Fernández Elmer , Sevlever Gustavo Emilio , Scassa María Elida , Romorini Leonardo 
Published: March 2024

ABSTRACTHuman pluripotent stem cells (hPSCs), which include embryonic and induced pluripotent stem cells (hESCs and hiPSCs, respectively), have an unusual cell cycle structure which consists of a short G1 phase and the absence of the G1/S checkpoint regulation. E2F transcription factors (E2Fs) play an important role in the G1/S transition. G1 duration contributes to hPSC fate determination, and microRNAs (miRNAs) play critical roles in this commitment. As little is known about the interplay between E2Fs and miRNAs in hPSCs, we aimed to identify miRNAs that are regulated by E2Fs in these cells. We first found that mRNA expression levels of canonical E2F repressors were more expressed than most E2F activators in G1-arrested hPSCs. Moreover, we observed higher mRNA and protein expression levels of canonicalE2F2,E2F3A,andE2F5in G1 synchronized hPSCs compared to human fibroblasts (HF). However,E2F1andE2F4protein expression levels were higher in HF. We next found that E2F inhibition with HLM006474 induced an increase in the G1 cell population without affecting hPSC viability, concomitantly with a decrease inOCT-4mRNA levels and the percentage of OCT-4+hPSCs. Next, by RNA-seq analysis we found 52 differentially expressed (DEGs) miRNAs in HLM006474-treated hESCs. RT-qPCR validation of some of the DEGs let us conclude that miR-19a-3p, miR-19b-3p, miR-4454, miR-1260a, miR-1260b, miR-454-3p and miR-301a-3p are regulated by E2Fs in hPSCs. Interestingly, gene target and ontology analysis of these miRNAs revealed a possible implication in proliferation and cell cycle regulation, development, and neural differentiation.
Latest RNA and DNA nanopore sequencing allows for rapid avian influenza profiling
Authors: Perlas Albert , Reska Tim , Croville Guillaume , Tarrés-Freixas Ferran , Guérin Jean-Luc , Majó Natàlia , Urban Lara 
Published: March 2024

AbstractAvian influenza virus (AIV) currently causes a panzootic with extensive mortality in wild birds, poultry, and wild mammals, thus posing a major threat to global health and underscoring the need for efficient monitoring of its distribution and evolution. Here, we utilized a well-defined AIV strain to systematically investigate AIV characterization through rapid, portable nanopore sequencing by (i) benchmarking the performance of fully portable RNA extraction and viral detection; (ii) comparing the latest DNA and RNA nanopore sequencing approaches for in-depth AIV profiling; and (iii) evaluating the performance of various computational pipelines for viral consensus sequence creation and phylogenetic analysis. Our results show that the latest RNA-specific nanopores can accurately genomically profile AIV from native RNA while additionally detecting RNA epigenetic modifications. We further identified an optimal laboratory and bioinformatic pipeline for reconstructing viral consensus genomes from nanopore sequencing data at various rarefaction thresholds, which we validated by application to real-world environmental samples for AIV monitoring in livestock.Author SummaryWe tested portable, rapid, and easy-to-use technology to obtain more information about the potentially zoonotic RNA virus avian influenza virus, or AIV. AIV has spread globally via the migratory paths of wild birds, and endangers domestic birds, mammals, and human populations given past evidence of infections of different animal species. We here used novel genomic technology that is based on nanopores to explore the genomes of the virus; we established optimized ways of creating the viral genome by comparing different laboratory and computational approaches and the performance of nanopores that either sequence the viral RNA directly or the converted DNA. We then applied the optimized protocol to dust samples which were collected from a duck farm in France during an AIV outbreak. We showed that we were able to use the resulting data to reconstruct the relationship between the virus responsible for the outbreak and previously detected AIV. Altogether, we showed how novel easy-to-use genomic technology can support the surveillance of potentially zoonotic pathogens by accurately recreating the viral genomes to better understand evolution and transmission of these pathogens.
On the Evolution of Chromosomal Regions with High Gene Strand Bias in Bacteria
Authors: Tomasch Jürgen , Kopejtka Karel , Shivaramu Sahana , Mujakic Izabela , Koblížek Michal 
Published: March 2024

AbstractOn circular bacterial chromosomes, the majority of genes are coded on the leading strand. This gene strand bias (GSB) ranges from up to 85% in some Bacillota to little more than 50% in other phyla. The factors defining the extent of the GSB remain to be found. Here, we report that species in the phylum Gemmatimonadota share a unique chromosome architecture, distinct from neighboring phyla: In a conserved 600 kb region around the terminus of replication, almost all genes were located on the leading strands while on the remaining part of the chromosome the strand preference was more balanced. The high strand bias (HSB) region harbors the rRNA clusters, core, and highly expressed genes. Selective pressure for reduction of collisions with DNA replication to minimize detrimental mutations can explain the conservation of essential genes in this region. Repetitive and mobile elements are underrepresented, suggesting reduced recombination frequency by structural isolation from other parts of the chromosome. We propose that the HSB region forms a distinct chromosomal domain. Gemmatimonadota chromosomes evolved mainly by expansion through horizontal gene transfer and duplications outside of the ancient HSB region. In support of our hypothesis, we could further identify two Spiroplasma strains on a similar evolutionary path.ImportanceOn bacterial chromosomes, a preferred location of genes on the leading strand has evolved to reduce conflicts between replication and transcription. Despite a vast body of research, the question why bacteria show large differences in their GSB is still not solved. The discovery of ‘hybrid’ chromosomes in different phyla, including Gemmatimonadota, in which a conserved high GSB is found exclusively in a region atter, points towards a role of nucleoid structure, additional to replication, in the evolution of strand preferences. A fine-grained structural analysis of the ever-increasing number of available bacterial genomes could help to better understand the forces that shape the sequential and spatial organization of the cell’s information content.