bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new mRNA structure prediction based approach to identifying improved signal peptides for bone morphogenetic protein 2
Authors: Wilkinson Piers , Jackson Brian , Fermor Hazel , Davies Robert 
Published: January 2024

AbstractBackgroundSignal peptide (SP) engineering has proven able to improve production of many proteins yet is a laborious process that still relies on trial and error. mRNA structure around the translational start site is important in translation initiation and has rarely been considered in this context, with recent improvements inin silicomRNA structure potentially rendering it a useful predictive tool for SP selection. Here we attempt to create a method to systematically screen candidate signal peptide sequencesin silicobased on both their nucleotide and amino acid sequences. Several recently released computational tools were used to predict signal peptide activity (SignalP), localization target (DeepLoc) and predicted mRNA structure (MXFold2). The method was tested with Bone Morphogenetic Protein 2 (BMP2), an osteogenic growth factor used clinically for bone regeneration. It was hoped more effective BMP2 SPs could improve BMP2-based gene therapies and reduce the cost of recombinant BMP2 production.ResultsAmino acid sequence analysis indicated 2,611 SPs from the TGF-β superfamily were predicted to function when attached to BMP2. mRNA structure prediction indicated structures at the translational start site were likely highly variable. The five sequences with the most accessible translational start sites, a codon optimized BMP2 SP variant and the well-established hIL2 SP sequence were taken forward toin vitrotesting. The top five candidates showed non-significant improvements in BMP2 secretion in HEK293T cells. All showed reductions in secretion versus the native sequence in C2C12 cells, with several showing large and significant decreases. None of the tested sequences were able to increase alkaline phosphatase activity above background in C2C12s. The codon optimized control sequence and hIL2 SP showed reasonable activity in HEK293T but very poor activity in C2C12.ConclusionsThese results support the use of peptide sequence basedin silicotools for basic predictions around signal peptide activity in a synthetic biology context. However, mRNA structure prediction requires improvement before it can produce reliable predictions for this application. The poor activity of the codon optimized BMP2 SP variant in C2C12 emphasizes the importance of codon choice, mRNA structure, and cellular context for SP activity.
Functional benefit of CRISPR/Cas9-induced allele deletion forRYR1dominant mutation
Authors: Beaufils Mathilde , Melka Margaux , Brocard Julie , Benoit Clement , Debbah Nagi , Mamchaoui Kamel , Romero Norma B. , Dalmas-Laurent Anne Frédérique , Quijano-Roy Susana , Fauré Julien , Rendu John , Marty Isabelle 
Published: January 2024

AbstractMore than 700 pathogenic or probably pathogenic variations have been identified in theRYR1gene causing various myopathies collectively known as “RYR1-related myopathies”. Currently, there is no treatment for these myopathies, and gene therapy stands out as one of the most promising approaches. In the context of a dominant form of Central Core Disease due to aRYR1mutation, we aimed at showing the functional benefit of inactivating specifically the mutatedRYR1allele by guiding CRISPR/Cas9 cleavages onto frequent single nucleotide polymorphisms (SNPs) segregating on the same chromosome. Whole-genome sequencing was used to pinpoint SNPs localized on the mutantRYR1allele and identified specific CRISPR/Cas9 guide-RNAs. Lentiviruses encoding these guide-RNAs and theSpCas9nuclease were used to transduce immortalized patient muscle cells, inducing the specific deletion of the mutantRYR1allele. The efficiency of the deletion was assessed at both DNA and RNA levels and at the functional level after monitoring calcium release induced by the stimulation of the RyR1-channel. This study providesin-celluloproof of concept regarding the benefits of mutantRYR1allele deletion, in the case of a dominantRYR1mutation, from both a molecular and functional perspective.Graphical abstracteTOC synopsisMutations in theRYR1gene, encoding a calcium channel required for muscle contraction, cause severe myopathies. In this study, Marty and colleagues demonstrate the functional benefit of suppression of a mutantRYR1allele using CRISPR/Cas9, in the case of a dominant mutation, leaving the wild type allele alone.
CHMP4B contributes to maintaining the follicular cells integrity in the panoistic ovary of the cockroachBlattella germanica
Authors: Farrus N. , Maestro J.L. , Piulachs M.D. 
Published: January 2024

AbstractThe Endosomal Sorting Complex Required for Transport (ESCRT) is a highly conserved cellular machinery essential for many cellular functions, including transmembrane protein sorting, endosomal trafficking and membrane scission. CHMP4B is a key component of ESCRT-III subcomplex and has been thoroughly studied in the meroistic ovaries ofDrosophila melanogastershowing its relevance in maintaining this reproductive organ during the life of the fly. However, the role of the CHMP4B in the most basal panoistic ovaries remains elusive. Using RNAi, we examined the function of CHMP4B in the ovary ofBlattella germanicain two different physiological stages: in last instar nymphs, with proliferative follicular cells, and in vitellogenic adults when follicular cells enter in polyploidy and endoreplication.InChmp4b-depleted specimens, the expression of actin in the basal pole of the follicular cells increased, leading to an excess of actin bundles that surrounded the basal ovarian follicle and modifying their shape. Depletion ofChmp4balso caused a loss of planar polarity in the follicular epithelium due to the actin increase in cell membranes, resulting in different cell morphologies and sizes, as well as an absence of patency. In these cells, the nuclei appeared unusually elongated, suggesting an incomplete karyokinesis.These results proved CHMP4B essential in preserving the proper expression of cytoskeleton proteins vital for basal ovarian follicle growth and maturation, and for yolk proteins incorporation. Moreover, the correct distribution of actin fibers in the basal ovarian follicle emerged as a critical factor for the successful completion of ovulation and oviposition. The overall of the results, obtained in two different proliferative stages, suggest that the function of CHMP4B inB. germanicafollicular epithelium is independent of the proliferative stage of the tissue.
Grasp context-dependent uncertainty alters the relative contribution of anticipatory and feedback-based mechanisms in object manipulation
Authors: Dutta Swarnab , SKM Varadhan 
Published: January 2024

AbstractPredictive control within dexterous object manipulation while allowing for the choice of contact points has been shown to employ a predominantly feedback-based force modulation. Anticipation is thought to be facilitated through the internal representation of the object dynamics being integrated and updated on a trial-to-trial basis with the feedback of contact locations on the object. This is as opposed to the classically studied memory representation-based fingertip force control for grasping with pre-selected contact locations. We designed a study to examine this grasp context-dependent asymmetry in sensorimotor integration by introducing binary uncertainty about the grasp type before movement initiation within the framework of motor planning. An inverted T-shaped instrumented object was presented to 24 participants as the manipulandum, and they were asked to reach, grasp, and lift it while minimising the roll. We dissociated the planning and the execution phases by pseudo-randomly manipulating the availability of visual contact cues on the object after movement onset. Our results suggest that uncertainty about the grasp type during movement preparation anterogradely modulated the differential weighting of feedback and feedforward mechanisms in anticipatory coordination.
Elucidating the effect of cations onKlebsiella pneumoniaebiofilm and related genes
Authors: Murugavel Aravind , Gunasekaran Srinithi , Ramakrishnan Jayapradha 
Published: January 2024

AbstractK. pneumoniaeis a non-motile, encapsulated bacterium from the Enterobacteriaceae family. The illnesses related to this opportunistic pathogen are pneumonia, Urinary Tract Infection (UTI), pyogenic liver abscess, endophthalmitis, and meningitis. Among them, UTI is predominant due to its biofilm formation leading to the mortality of 150 million people worldwide. The function of monovalent and divalent ions onKlebsiellabiofilm, aside from physiochemical variables, remains unclear. Hence the present study was performed to analyze the role of K+, Ca2+, Na+, Mg2+, NH+4in biofilm formation and its influence on biofilm-related genes. Among the tested cations, K+and Ca2+yielded strong biofilm in clinical and environment isolates in pH between 6.5 to 9.5. Increasing Ca2+ions concertation reduced theKlebsiellabiofilm. When compared to the hypercalciuria condition (Ca2+level > 5 mM), 2.5 mM resulted in high biofilm mass. Cations concurrently enhanced the size of the capsule and cell density ofKlebsiellabut were not correlated with biofilm mass. Expression of the LPS gene (WbaG) either in planktonic or biofilm stage promoted biofilm formation in the presence of K+, Ca2+and Na+. Whereas, expression of fimbriae genes (FimHandmrkD) was co- regulation, and capsule genes (RmpAandWcab) were absent. Stating, the primary component needed for theKlebsiellabiofilm is not the capsule or fimbriae, rather LPS. Resulting as a potent target in the treatment ofKlebsiellabiofilm in UTI. To the best of our knowledge, this is the first kind of study on the effect of cation ions on biofilm and planktonic cells ofKlebsiellaspp. and demonstrating the role of LPS biosynthesis gene (WbaG) in biofilm development.
High-speed two-photon microscopy with adaptive line-excitation
Authors: Li Yunyang , Guo Shu , Mattison Ben , Yang Weijian 
Published: January 2024

AbstractWe present a two-photon fluorescence microscope designed for high-speed imaging of neural activity in cellular resolution. Our microscope uses a new adaptive sampling scheme with line illumination. Instead of building images pixel by pixel via scanning a diffraction-limited spot across the sample, our scheme only illuminates the regions of interest (i.e., neuronal cell bodies), and samples a large area of them in a single measurement. Such a scheme significantly increases the imaging speed and reduces the overall laser power on the brain tissue. Using this approach, we performed high-speed imaging of the neural activity of mouse cortexin vivo. Our method provides a new sampling strategy in laser-scanning two-photon microscopy, and will be powerful for high-throughput imaging of neural activity.
A small molecule VHL molecular glue degrader for cysteine dioxygenase 1
Authors: Tutter Antonin , Buckley Dennis , Golosov Andrei A. , Ma Xiaolei , Shu Wei , McKay Daniel J. J. , Darsigny Veronique , Dovala Dustin , Beckwith Rohan , Solomon Jonathan , Rao Pasupuleti , Xu Lei , Fazal Aleem , Lingel Andreas , Wartchow Charles , Cobb Jennifer S. , Hachey Amanda , Tullai Jennifer , Michaud Gregory A. 
Published: January 2024

AbstractThe Von Hippel-Lindau Tumor Suppressor gene product (pVHL) is an E3 ligase substrate receptor that binds proline-hydroxylated HIF1-α, leading to its ubiquitin-dependent degradation. By using protein arrays, we identified a small molecule that binds the HIF1-α binding pocket on pVHL and functions as a molecular glue degrader of the neosubstrate cysteine dioxygenase (CDO1) by recruiting it into the VHL-cullin-ring E3 ligase complex and leading to its selective degradation. The CDO1 binding region involved in VHL recruitment was characterized through a combination of mutagenesis and protein-protein docking coupled with molecular dynamics-based solvation analysis. The X-ray structure of the ternary complexes of VHL, CDO1, and degrader molecules confirms the binding region prediction and provides atomic insights into key molecular glue interactions.
Regional specialization manifests in the reliability of neural population codes
Authors: Guidera Jennifer A. , Gramling Daniel P. , Comrie Alison E. , Joshi Abhilasha , Denovellis Eric L. , Lee Kyu Hyun , Zhou Jenny , Thompson Paige , Hernandez Jose , Yorita Allison , Haque Razi , Kirst Christoph , Frank Loren M. 
Published: January 2024

SUMMARYThe brain has the remarkable ability to learn and guide the performance of complex tasks. Decades of lesion studies suggest that different brain regions perform specialized functions in support of complex behaviors1–3. Yet recent large-scale studies of neural activity reveal similar patterns of activity and encoding distributed widely throughout the brain4–6. How these distributed patterns of activity and encoding are compatible with regional specialization of brain function remains unclear. Two frontal brain regions, the dorsal medial prefrontal cortex (dmPFC) and orbitofrontal cortex (OFC), are a paradigm of this conundrum. In the setting complex behaviors, the dmPFC is necessary for choosing optimal actions2,7,8, whereas the OFC is necessary for waiting for3,9and learning from2,7,9–12the outcomes of those actions. Yet both dmPFC and OFC encode both choice- and outcome-related quantities13–20. Here we show that while ensembles of neurons in the dmPFC and OFC of rats encode similar elements of a cognitive task with similar patterns of activity, the two regions differ in when that coding is consistent across trials (“reliable”). In line with the known critical functions of each region, dmPFC activity is more reliable when animals are making choices and less reliable preceding outcomes, whereas OFC activity shows the opposite pattern. Our findings identify the dynamic reliability of neural population codes as a mechanism whereby different brain regions may support distinct cognitive functions despite exhibiting similar patterns of activity and encoding similar quantities.
Stepwise recruitment of Hsc70 by DNAJB1 produces ordered arrays primed for bursts of amyloid fibre disassembly
Authors: Monistrol Jim , Beton Joseph G , Johnston Erin C , Saibil Helen R 
Published: January 2024

AbstractTo understand the action of co-chaperones of the J-domain protein family in the assembly of disaggregation-active Hsc70 complexes on the surface of amyloid fibres, we used cryo-EM and tomography to compare the assemblies with wild-type co-chaperones or an activity deficient mutant. We show that human DNAJB1 binds uniformly and densely along α-synuclein amyloid fibres in an asymmetric orientation, with one subunit of the DNAJB1 dimer lying along the fibre surface and the other subunit further away. It acts in a 2-step recruitment of Hsc70 to the fibres, first releasing DNAJB1 auto-inhibition and then activating the Hsc70 ATPase by the J domain, with ATPase recycling stimulated by the nucleotide exchange factor Apg2. When the auto-inhibition is removed by mutating the H5 inhibitory binding site on DNAJB1 (Δ1H5 DNAJB1 mutant), Hsc70 is recruited to the fibres at a normal level, but the resulting complex is inactive in disaggregation. Cryo tomography of the wild-type DNAJB1:Hsc70:Apg2:αSyn fibre complex shows dense arrays of the chaperones extending out from the fibre surface along spiral tracks, with the Hsc70 density on the outer surface of the DNAJB1 layer. The Δ1H5 DNAJB1:Hsc70:Apg2:αSyn fibre complex results in equally dense but less organised binding all over the fibre surface and lacks the ordered clusters. On the basis of these findings, we propose that 2-step activation of DNAJB1 regulates Hsc70 access to the fibre substrate. Since the DNAJB1 dimers are bound every 40 Å, the J domain released by Hsc70 binding to one dimer could activate the ATPase of an Hsc70 bound to the adjacent dimer. This could trigger a cascade of recruitment and activation in a localised, dense cloud of Hsc70 molecules to give coordinated, sequential binding and disaggregation from an exposed fibre end, as observed by cryo-EM and earlier fluorescence and AFM studies.
Excessive F-Actin and Microtubule Formation Mediates Primary Cilia Shortening and Loss in Response to Increased Extracellular Osmotic Pressure
Authors: Otani Hiroshi , Nakazato Ryota , Ijaz Faryal , Koike Kanae , Ikegami Koji 
Published: January 2024

ABSTRACTThe primary cilium is a small organelle protruding from the cell surface and is recognized as an antenna for signals from the extracellular milieu. Maintenance of primary cilia structure is crucial for proper behaviors of cells, tissues, and organs. While a dozen of studies have reported that several genetic factors impair the structure of primary cilia, evidence for environmental stimuli affecting primary cilia structures is limited. Here, we investigated an extracellular stress that affected primary cilia morphology and its underlying mechanisms. Hyperosmotic shock with increased extracellular sodium chloride concentration induced shortenings and disassembly of primary cilia in murine intramedullary collecting ducts cells. The shortening of primary cilia caused by hyperosmotic shock followed a loss of axonemal microtubules and delocalization of pericentriolar materials (PCMs). The primary cilia shortening/disassembly and PCMs delocalization were reversible. In parallel with these hyperosmotic shock-induced changes of primary cilia and PCMs, excessive microtubule and F-actin formation occurred in the cytoplasm. A microtubule-disrupting agent, Nocodazole, prevented the hyperosmotic shock-induced primary cilia disassembly partially, while preventing the delocalization of PCMs almost 100%. An actin polymerization inhibitor, Latrunculin A, also prevented partially the hyperosmotic shock-induced primary cilia shortening and disassembly, while preventing the delocalization of PCMs almost 100%. Taken together, we demonstrate that hyperosmotic shock induces reversible morphological changes in primary cilia and PCMs in a manner dependent on excessive formation of microtubule and F-actin.
Human stem cell model of neural crest cell differentiation reveals a requirement of SF3B4 in survival, maintenance, and differentiation
Authors: Griffin Casey , Saint-Jeannet Jean-Pierre 
Published: January 2024

AbstractIn vitromodeling is a powerful approach to investigate the pathomechanisms driving human congenital conditions. Here we use human embryonic stem cells (hESCs) to model Nager and Rodriguez syndromes, two craniofacial conditions characterized by hypoplastic neural crest-derived craniofacial bones, caused by pathogenic variants of SF3B4, a core component of the spliceosome. We observed that siRNA-mediated knockdown ofSF3B4interferes with the production of hESC-derived neural crest cells, as seen by a marked reduction in neural crest gene expression. This phenotype is associated with an increase in neural crest cell apoptosis and premature neuronal differentiation. Altogether these results point at a role of SF3B4 in neural crest cell survival, maintenance, and differentiation. We propose that the dysregulation of these processes may contribute to Nager/Rodriguez syndrome associated craniofacial defects.
The Temporal Dynamics of Aperiodic Neural Activity Track Changes in Sleep Architecture
Authors: Ameen Mohamed S , Jacobs Joshua , Schabus Manuel , Hoedlmoser Kerstin , Donoghue Thomas 
Published: January 2024

AbstractThe aperiodic (1/f-like) component of electrophysiological data - whereby power systematically decreases with increasing frequency, as quantified by the aperiodic exponent - has been shown to differentiate sleep stages. Earlier work, however, has typically focused on measuring the aperiodic exponent across a narrow frequency range. In this work, we sought to further investigate aperiodic activity during sleep by extending these analyses across broader frequency ranges and considering alternate model definitions. This included measuring ‘knees’ in the aperiodic component, which reflect bends in the power spectrum, indicating a change in the exponent. We also sought to evaluate the temporal dynamics of aperiodic activity during sleep. To do so, we analyzed data from two sources: intracranial EEG (iEEG) from 106 epilepsy patients and high-density EEG from 17 healthy individuals, and measured aperiodic activity, explicitly comparing different frequency ranges and model forms. In doing so, we find that fitting broadband aperiodic models and incorporating a ‘knee’ feature effectively captures sleep-stage-dependent differences in aperiodic activity as well as temporal dynamics that relate to sleep stage transitions and responses to external stimuli. In particular, the knee parameter shows stage-specific variation, suggesting an interpretation of varying timescales across sleep stages. These results demonstrate that examining broader frequency ranges with the more complex aperiodic models reveals novel insights and interpretations for understanding aperiodic neural activity during sleep.
Exploring the Categorical Nature of Colour Perception: Insights from Artificial Networks
Authors: Akbarinia Arash 
Published: January 2024

AbstractThis study delves into the categorical aspects of colour perception, employing the odd-one-out paradigm on artificial neural networks. We reveal a significant alignment between human data and unimodal vision networks (e.g., ImageNet object recognition). Vision-language models (e.g., CLIP text-image matching) account for the remaining unexplained data even in non-linguistic experiments. These results suggest that categorical colour perception is a language-independent representation, albeit partly shaped by linguistic colour terms during its development. Exploring the ubiquity of colour categories in Taskonomy unimodal vision networks highlights the task-dependent nature of colour categories, predominantly in semantic and 3D tasks, with a notable absence in low-level tasks. To explain this difference, we analysed kernels’ responses before the winnertaking-all, observing that networks with mismatching colour categories align in continuous representations. Our findings quantify the dual influence of visual signals and linguistic factors in categorical colour perception, thereby formalising a harmonious reconciliation of the universal and relative debates.