bluuebunny/crossref_metadata_2025 huggingface dataset:
Time, Space and Single-Cell Resolved Molecular Trajectory of Cell Populations and the Laterality of the Body Plan at Gastrulation
Authors: Wang Ran , Yang Xianfa , Chen Jiehui , Zhang Lin , Griffiths Jonathan A. , Cui Guizhong , Chen Yingying , Qian Yun , Peng Guangdun , Li Jinsong , Wang Liantang , Marioni John C. , Tam Patrick P.L. , Jing Naihe
Published: April 2023

Understanding of the molecular drivers of lineage diversification and tissue patterning during primary germ layer development requires in-depth knowledge of the dynamic molecular trajectories of cell lineages across a series of developmental stages of gastrulation1–7. Through computational modeling, we constructed at single-cell resolution a spatio-temporal compendium of the molecular trajectories of germ-layer derivatives in gastrula-stage mouse embryos. This molecular atlas infers the developmental trajectories of single-cell populations and the molecular network activity underpinning the specification and differentiation of the germ-layer lineages. Analysis of the heterogeneity of cellular composition of cell populations at defined positions in the epiblast revealed progressive diversification of cell types, mirroring the process of lineage allocation during gastrulation. A novel observation is the difference in the contribution of cells on contralateral sides of the epiblast to mesoderm derivatives of the early organogenesis embryo, and the enhanced BMP signaling activity in right-side mesoderm of E7.5 embryo. Perturbation of BMP signaling activity at late gastrulation led to randomization of left-right (L-R) molecular asymmetry in the lateral mesoderm of early-somite-stage embryo. Our findings indicate the asymmetric BMP activity during gastrulation may be critical for the symmetry breaking process associated with specification of L-R body asymmetry ahead of the acquisition of functionality of the L-R organizer.
Electrophysiological correlates of attention in the locus coeruleus - anterior cingulate cortex circuit during the rodent continuous performance test
Authors: Hallock Henry L. , Adiraju Suhaas , Miranda-Barrientos Jorge , McInerney Jessica M. , Oh Seyun , DeBrosse Adrienne C. , Li Ye , Carr Gregory V. , Martinowich Keri
Published: April 2023

Sustained attention, the ability to focus on an activity or stimulus over time, is significantly impaired in many psychiatric disorders, and there remains a major unmet need in treating impaired attention. Continuous performance tests (CPTs) were developed to measure sustained attention in humans, non-human primates, rats, and mice, and similar neural circuits are engaged across species during CPT performance, supporting their use in translational studies to identify novel therapeutics. Here, we identified electrophysiological correlates of attentional performance in a touchscreen-based rodent CPT (rCPT) in the locus coeruleus (LC) and anterior cingulate cortex (ACC), two inter-connected regions that are implicated in attentional processes. We used viral labeling and molecular techniques to demonstrate that neural activity is recruited in LC-ACC projections during the rCPT, and that this recruitment increases with cognitive demand. We implanted male mice with depth electrodes within the LC and ACC for local field potential (LFP) recordings during rCPT training, and identified an increase in ACC delta and theta power, and an increase in LC delta power during correct responses in the rCPT. We also found that the LC leads the ACC in theta frequencies during correct responses while the ACC leads the LC in gamma frequencies during incorrect responses. These findings may represent translational biomarkers that can be used to screen novel therapeutics for drug discovery in attention.
Reversing protonation of weakly basic drugs greatly enhances intracellular diffusion and decreases lysosomal sequestration
Authors: Dey Debabrata , Marciano Shir , Poryvai Anna , Groborz Ondřej , Wohlrábová Lucie , Slanina Tomás , Schreiber Gideon
Published: April 2023

For drugs to be active they have to reach their targets. Within cells this requires crossing the cell membrane, and then free diffusion, distribution, and availability. Here, we explored the in-cell diffusion rates and distribution of a series of small molecular fluorescent drugs, in comparison to proteins, by microscopy and fluorescence recovery after photobleaching (FRAP). While all proteins diffused freely, we found a strong correlation between pKaand the intracellular diffusion and distribution of small molecule drugs. Weakly basic, small-molecule drugs displayed lower fractional recovery after photobleaching and 10-to-20-fold slower diffusion rates in cells than in aqueous solutions. As, more than half of pharmaceutical drugs are weakly basic, they, are protonated in the cell cytoplasm. Protonation, facilitates the formation of membrane impermeable ionic form of the weak base small molecules. This results in ion trapping, further reducing diffusion rates of weakly basic small molecule drugs under macromolecular crowding conditions where other nonspecific interactions become more relevant and dominant. Our imaging studies showed that acidic organelles, particularly the lysosome, captured these molecules. Surprisingly, blocking lysosomal import only slightly increased diffusion rates and fractional recovery. Conversely, blocking protonation byN-acetylated analogues, greatly enhanced their diffusion and fractional recovery after FRAP. Based on these results,N-acetylation of small molecule drugs may improve the intracellular availability and distribution of weakly basic, small molecule drugs within cells.
Impact of water models on structure and dynamics of enzyme tunnels
Authors: Sethi Aaftaab , Agrawal Nikhil , Brezovsky Jan
Published: April 2023

Protein hydration plays a vital role in many biological functions and molecular simulations are frequently used to study the effect of protein hydration at the atomic level. However, the accuracy of these simulations has often been highly sensitive to the water model used, a phenomenon best known in the case of intrinsically disordered proteins. In the present study, we investigated the extent to which the choice of water model alters the behavior of complex networks of transport tunnels. Tunnels are essential because they allow substrates and products to access and exit the active sites of enzymes that are otherwise deeply embedded within the protein structure. The ability of these tunnels to regulate access directly affects enzyme efficiency and selectivity, making their study crucial for understanding enzyme function and inhibition at a mechanistic level. By performing all-atom molecular dynamics simulations of the wild-type haloalkane dehalogenase LinBWT and its two variants, LinB32 and LinB86, with synthetically engineered tunnel networks in TIP3P and OPC water models, we investigated the effects of these models on the overall tunnel topology. We also analyzed the properties of the main tunnels, such as their conformation, bottleneck dimensions, sampling efficiency, and duration of the tunnel opening. Our data demonstrate that all three proteins exhibited similar conformational behavior in both water models and differed in the geometrical characteristics of their auxiliary tunnels, in line with experimental observations. Interestingly, the results indicate that the stability of the open tunnels is sensitive to the water model and the system under question. Our findings suggest that the 3-point TIP3P model can provide comparable inference on the overall topology of the networks of primary tunnels and their geometry, and thus may be a desirable choice when computational resources are limited or when compatibility issues impede usage of OPC with certain protein force fields. However, when a more thorough investigation is performed, such as the calculation of ligand unbinding rates via such tunnel networks, where precision and intricate details are paramount, the more costly 4-point OPC model would be more suited.

Graphical Abstract
Multiparametric domain insertional profiling of Adeno-Associated Virus VP1
Authors: Hoffmann Mareike D. , Zdechlik Alina C. , He Yungui , Nedrud David , Aslanidi George , Gordon Wendy , Schmidt Daniel
Published: April 2023

Evolved properties of Adeno-Associated Virus (AAV), such as broad tropism and immunogenicity in humans, are barriers to AAV-based gene therapy. Previous efforts to re-engineer these properties have focused on variable regions near AAV’s 3-fold protrusions and capsid protein termini. To comprehensively survey AAV capsids for engineerable hotspots, we determined multiple AAV fitness phenotypes upon insertion of large, structured protein domains into the entire AAV-DJ capsid protein VP1. This is the largest and most comprehensive AAV domain insertion dataset to date. Our data revealed a surprising robustness of AAV capsids to accommodate large domain insertions. There was strong positional, domain-type, and fitness phenotype dependence of insertion permissibility, which clustered into correlated structural units that we could link to distinct roles in AAV assembly, stability, and infectivity. We also identified new engineerable hotspots of AAV that facilitate the covalent attachment of binding scaffolds, which may represent an alternative approach to re-direct AAV tropism.
Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin
Authors: Thore Stéphane , Raoelijaona Finaritra , Talenton Vincent , Fribourg Sébastien , Mackereth Cameron D.
Published: April 2023

Eukaryotic pre-mRNA is processed by a large multiprotein complex to accurately cleave the 3’ end, and to catalyze the addition of the poly(A) tail. Within this cleavage and polyadenylation specificity factor (CPSF) machinery, the CPSF73 endonuclease subunit directly contacts both CPSF100 and the scaffold protein Symplekin to form a subcomplex known as the core cleavage complex (CCC) or mammalian cleavage factor (mCF). Here we have taken advantage of a stable CPSF73-CPSF100 minimal heterodimer from E. cuniculi to determine the solution structure formed by the first and second C-terminal domain (CTD1 and CTD2) of both proteins. We find a large number of contacts between both proteins in the complex, and notably in the region between CTD1 and CTD2. A similarity is also observed between CTD2 and the TATA-box binding protein (TBP) domains. Separately, we have determined the structure of the terminal CTD3 domain of CPSF73, which also belongs to the TBP domain family and is connected by a flexible linker to the rest of CPSF73. Biochemical assays demonstrate a key role for the CTD3 of CPSF73 in binding Symplekin, and structural models of the trimeric complex from other species allow for comparative analysis and support an overall conserved architecture.
Self-referencing rates in biological disciplines
Authors: Cascarina Sean M.
Published: April 2023

The use of citation counts (among other bibliometrics) as a facet of academic research evaluation can influence citation behavior in scientific publications. One possible unintended consequence of this bibliometric is excessive self-referencing, where an author favors referencing their own publications over related publications from different research groups. Peer reviewers are often prompted by journals to examine whether references listed in the manuscript under review are unbiased, but there is no consensus on what is considered “excessive” self-referencing. Here, self-referencing rates are estimated across multiple journals in the fields of biology, genetics, computational biology, medicine, pathology, and cell biology. Median self-referencing rates are between 8-13% across a range of journals within these subdisciplines. However, self-referencing rates vary as a function of total number of references, number of authors, author status/rank, author position, and total number publications for each author. These results may serve as useful statistical guidelines for authors, editors, reviewers, and journals when considering referencing practices for individual publications.
Decision Considerations and Strategies for Lip Surgery in Patients with Cleft lip/Palate: A Qualitative Study
Authors: Trotman Carroll Ann , Faraway Julian , Bennett M. Elizabeth , Garson G. David , Phillips Ceib , Bruun Richard , Daniel Renie , David Lisa Renee , Ganske Ingrid , Leeper Lauren K , Rogers-Vizena Carolyn R. , Runyan Christopher , Scott Andrew R. , Wood Jeyhan
Published: April 2023

Objective

To qualitatively assess surgeons decision making for lip surgery in patients with cleft lip/palate (CL/P).

Design

Prospective, non-randomized, clinical trial.

Setting

Clinical data institutional laboratory setting.

Patients, Participants

The study included both patient and surgeon participants recruited from four craniofacial centers. The patient participants were babies with a CL/P requiring primary lip repair surgery (n=16) and adolescents with repaired CL/P who may require secondary lip revision surgery (n=32). The surgeon participants (n=8) were experienced in cleft care. Facial imaging data that included 2D images, 3D images, videos, and objective 3D visual modelling of facial movements were collected from each patient, and compiled as a collage termed the Standardized Assessment for Facial Surgery (SAFS) for systematic viewing by the surgeons.

Interventions

The SAFS served as the intervention. Each surgeon viewed the SAFS for six distinct patients (two babies and four adolescents) and provided a list of surgical problems and goals. Then an in-depth-interview (IDI) was conducted with each surgeon to explore their decision-making processes. IDIs were conducted either in person or virtually, recorded, and then transcribed for qualitative statistical analyses using the Grounded Theory Method.

Results

Rich narratives/themes emerged that included timing of the surgery; risks/limitations and benefits of surgery; patient/family goals; planning for muscle repair and scarring; multiplicity of surgeries and their impact; and availability of resources. For diagnoses/treatments, surgeons agreed, and level of surgical experience was not a factor.

Conclusions

The themes provided important information to populate a checklist of considerations to serve as a guide for clinicians.
Designing a brief and simple intervention to help young people with type 1 diabetes to live well: protocol for developing a novel intervention with participation from young people
Authors: Howland Samantha , Huber Jörg , Aicken Catherine
Published: April 2023

Young people living with type 1 diabetes (T1D) navigate daily complex diabetes related tasks as they take on increasing (and eventually full) responsibility for managing their condition, in addition to developing their lives as independent adults. Alongside the need for careful day-to-day diabetes management, the psychosocial burden and mental health impact and stigma are well recognised. Despite advances in psychological care, many young people with diabetes still experience a greater mental health burden than those without diabetes. This study aims to develop a brief and simple intervention for young people with T1D that will support their wellbeing day to day, as required, and grow their ability to live confidently with their condition that requires lifelong meticulous management. This study will consist of qualitative research and collaboration with young people with T1D and their siblings, friends, and peers to co-create a testable intervention. In Part 1, research interviews will be conducted with young people (16-24 years old) with T1D and, where possible, their siblings/peers to understand the day-to-day challenges of type 1 and what a novel intervention should address. Thematic analysis of interviews will inform the generation of a prototype intervention to take into part two, focus group discussions. Focus groups with (i) young people with T1D and, separately (ii) carers (comprising parents, carers, teachers, specialist nurses). Collaborative principles will be used to review, redesign and evolve the intervention to meet user needs. A blend of narrative and thematic analysis will inform the findings and report.

Insights from Parts 1 and 2 will shape a user-defined and formatively analysed brief and simple intervention and future study design ready for pilot testing. The aim of this part of the research is to maximise acceptability and usability of a testable intervention by the target population. To aim of the future intervention will be to demonstrate effectiveness in helping young adults to live well with T1D.

METADATA

This research is funded by a studentship to the first author, provided by University of Brighton as part of its partnership activities with the National Institute for Health Research (NIHR) Applied Research Collaboration Kent, Surrey, Sussex. The funders did not and will not have a role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. The views expressed are those of the authors and not necessarily those of the NHS, the NIHR or the Department of Health and Social Care.

Ethical approval for this study was provided by Cornwall and Plymouth Research Ethics Committee on behalf of the Health Research Authority and Health and Care Research Wales on 22 Aug 2022 (22/SW/0097). The University of Brighton is the Sponsor (protocol number 2022-9871).
Sialoglycan binding triggers spike opening in a human coronavirus
Authors: Pronker Matti F. , Creutznacher Robert , Drulyte Ieva , Hulswit Ruben J.G. , Li Zeshi , van Kuppeveld Frank J.M. , Snijder Joost , Lang Yifei , Bosch Berend-Jan , Boons Geert-Jan , Frank Martin , Groot Raoul J. de , Hurdiss Daniel L.
Published: April 2023

Coronavirus (CoV) spikes mediate receptor binding and membrane fusion, making them prime targets for neutralising antibodies. In the cases of SARS-CoV, SARS-CoV-2, and MERS-CoV, spikes transition freely between open and closed conformations to balance host cell attachment and immune evasion. The open conformation exposes domain S1B, allowing it to bind to proteinaceous cell surface receptors. It also facilitates protein refolding during spike-mediated membrane fusion. However, with a single exception, the pre-fusion spikes of all other CoVs studied so far have been observed exclusively in the closed state. This raises the possibility of regulation, where spikes more commonly transition to open states in response to specific cues, rather than spontaneously. In our study, using cryo-EM and molecular dynamics simulations, we show that the spike protein of the common cold human coronavirus HKU1 undergoes local and long-range conformational changes upon binding a sialoglycan-based primary receptor to domain S1A. This binding triggers the transition of S1Bdomains to the open state via allosteric inter-domain cross-talk. Our findings paint a more elaborate picture of CoV attachment, with possibilities of dual receptor usage and priming of entry as a means of immune escape.
Exploring the Landscape of Spatial Transcriptome Analysis: Introducing STASH, a Database of Spatial Transcriptome Tools
Authors: Chu Han , Wang Kun , Cheng Hansen , Ma Wenhao , Dong Liting , Gou Yixiong , Yang Jian , Cai Haoyang
Published: April 2023

Spatial transcriptomics (ST) has emerged as a powerful tool for unravelling tissue structure and function. However, the continuous development of ST has made it challenging to select and effectively use appropriate analysis tools. To address this issue, we have developed the Spatial Transcriptome Analysis Hub (STASH,http://cailab.labshare.cn:7004), a comprehensive, systematic, and user-friendly database of ST analysis tools. STASH collects and categorizes most of the tools currently available and provides insight into their current status and trends. This can help researchers quickly locate the appropriate tool for their needs, or even guide researchers in the development of better tools.
Efficient multiple gene knock-out inColletotrichum higginsianumvia CRISPR-Cas9 ribonucleoprotein andURA3-based marker recycling
Authors: Yonehara Katsuma , Kumakura Naoyoshi , Motoyama Takayuki , Ishihama Nobuaki , Dallery Jean-Félix , O’Connell Richard , Shirasu Ken
Published: April 2023

Colletotrichum higginsianum is a hemibiotrophic pathogen that causes anthracnose disease on crucifer hosts, including Arabidopsis thaliana. Despite the availability of genomic and transcriptomic information and the ability to transform both organisms, identifying C. higginsianum genes involved in virulence has been challenging due to their recalcitrance to gene targeting and redundancy of virulence factors. To overcome these obstacles, we developed an efficient method for multiple gene disruption in C. higginsianum by combining CRISPR-Cas9 and URA3-based marker recycling systems. Our method significantly increased the efficiency of gene knock-out via homologous recombination by introducing genomic DNA double-strand breaks. We demonstrated the applicability of the URA3-based marker recycling system for multiple gene targeting in the same strain. Using our technology, we successfully targeted two melanin biosynthetic genes, SCD1 and PKS1, which resulted in deficiency in melanisation and pathogenicity in the mutants. Our findings demonstrate the effectiveness of our developments in analysing virulence factors in C. higginsianum, thus accelerating research on plant-fungus interactions.
Cooperation and deception through stigmergic interactions in human groups
Authors: Bassanetti Thomas , Cezera Stéphane , Delacroix Maxime , Escobedo Ramón , Blanchet Adrien , Sire Clément , Theraulaz Guy
Published: April 2023

Stigmergy is a generic coordination mechanism widely used by animal societies, in which traces left by individuals in a medium guide and stimulate their subsequent actions. In humans, new forms of stigmergic processes have emerged through the development of online services that extensively use the digital traces left by their users. Here we combine interactive experiments with faithful data-based modeling to investigate how groups of individuals exploit a simple rating system and the resulting traces in an information search task in competitive or non-competitive conditions. We find that stigmergic interactions can help groups to collectively find the cells with the highest values in a table of hidden numbers. We show that individuals can be classified into three behavioral profiles that differ in their degree of cooperation. Moreover, the competitive situation prompts individuals to give deceptive ratings and reinforces the weight of private information versus social information in their decisions.
A novel injectable radiopaque hydrogel with potent properties for multicolor CT imaging in the context of brain and cartilage regenerative therapy
Authors: Said Moustoifa , Tavakoli Clément , Dumot Chloé , Toupet Karine , Dong Yuxi Clara , Collomb Nora , Auxenfans Céline , Moisan Anaïck , Favier Bertrand , Chovelon Benoit , Barbier Emmanuel Luc , Jorgensen Christian , Cormode David Peter , Noël Danièle , Brun Emmanuel , Elleaume Hélène , Wiart Marlène , Detante Olivier , Rome Claire , Auzély-Velty Rachel
Published: April 2023

Cell therapy is promising to treat many conditions, including neurological and osteoarticular diseases. Encapsulation of cells within hydrogels facilitates cell delivery and can improve therapeutic effects. However, much work remains to be done to align treatment strategies with specific diseases. The development of imaging tools that enable monitoring cells and hydrogel independently is key to achieving this goal. Our objective herein is to longitudinally study an iodine-labeled hydrogel, incorporating gold-labeled stem cells, by bicolor CT imaging afterin vivoinjection in rodent brains or knees. To this aim, an injectable self-healing hyaluronic acid (HA) hydrogel with long-persistent radiopacity was formed by the covalent grafting of a clinical contrast agent on HA. The labeling conditions were tuned to achieve sufficient X-ray signal and to maintain the mechanical and self-healing properties as well as injectability of the original HA scaffold. The efficient delivery of both cells and hydrogel at the targeted sites was demonstrated by synchrotron K-edge subtraction-CT. The iodine labeling enabled to monitor the hydrogel biodistributionin vivoup to 3 days post-administration, which represents a technological first in the field of molecular CT imaging agents. This tool may foster the translation of combined cell-hydrogel therapies into the clinics.
Genistein enhances NAD+biosynthesis by binding to Prohibitin 1 and upregulating nicotinamide phosphoribosyltransferase in adipocytes
Authors: Watanabe Shun , Haruyama Riki , Umezawa Koji , Tomioka Ikuo , Nakamura Soichiro , Katayama Shigeru , Mitani Takakazu
Published: April 2023

Decreased NAD+levels in adipocytes cause adipose-tissue dysfunction, leading to systemic glucose and lipid metabolism failure. Therefore, developing small molecules and nutraceuticals that can increase NAD+levels in adipocytes is necessary. Genistein, a nutraceutical derived from soybeans, has various physiological activities and improves glucose and lipid metabolism. In this study, we aimed to unravel the effects of genistein on the intracellular NAD+levels in adipocytes and the underlying molecular mechanisms. We showed that genistein enhanced NAD+biosynthesis by increasing the expression of nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in NAD+biosynthesis. A pull-down assay using genistein-immobilized beads identified prohibitin 1 (PHB1) as a target protein of genistein. The knockdown of PHB1 suppressed the genistein-induced increase in NAMPT expression and NAD+levels in adipocytes. Genistein-bound PHB1 contributed to the stabilization of the transcription factor CCAAT/enhancer-binding protein β through activation of extracellular signal-regulated kinase, resulting in increased NAMPT expression at the transcriptional level. Genistein induced dephosphorylation of peroxisome proliferator-activated receptor at serine 273 and increased the insulin-sensitizing adipokine, adiponectin, in adipocytes, whereas the knockdown of NAMPT and PHB1 abolished these genistein-mediated effects. Our results proved the potential efficacy of nutraceuticals in promoting NAD+levels and restoring metabolic function in adipocytes. Furthermore, we identified PHB1, localized to the plasma membrane, as a candidate target protein for increased expression of NAMPT in adipocytes. Overall, these findings will assist in developing NAD+boosting strategies to alleviate the metabolic dysfunctions in adipose tissues.

Significance Statement

Increasing NAD+levels is an important preventive strategy for maintaining metabolic function. Here, we showed that genistein, a nutraceutical, which increases NAD+levels in adipocytes, increased NAD+biosynthesis by upregulating nicotinamide phosphoribosyltransferase (NAMPT), a rate-limiting enzyme in the NAD+biosynthesis pathway. Our findings also showed that genistein increased NAMPT expression by binding to prohibitin 1 in the plasma membrane. Genistein-induced increase in NAD+levels promoted adiponectin expression, an insulin-sensitizing adipokine, in adipocytes. This study provides evidence that nutraceuticals, such as genistein, are effective in enhancing NAD+biosynthesis in adipocytes and that PHB1 is a candidate target protein for increased expression of NAMPT to maintain metabolic functions in adipose tissues.
AbFold -- an AlphaFold Based Transfer Learning Model for Accurate Antibody Structure Prediction
Authors: Peng Chao , Wang Zelong , Zhao Peize , Ge Weifeng , Huang Charles
Published: April 2023

Motivation

Antibodies are a group of proteins generated by B cells, which are crucial for the immune system. The importance of antibodies is ever-growing in pharmaceutics and biotherapeutics. Despite recent advancements pioneered by AlphaFold in general protein 3D structure prediction, accurate structure prediction of antibodies still lags behind, primarily due to the difficulty in modeling the Complementarity-determining regions (CDRs), especially the most variable CDR-H3 loop.

Results

This paper presents AbFold, a transfer learning antibody structure prediction model with 3D point cloud refinement and unsupervised learning techniques. AbFold consistently produces state-of-the-art results on the prediction accuracy of the six CDR loops. The predictions of AbFold achieve an average RMSD of 1.51 Å for both heavy and light chains and an average RMSD of 3.04 Å for CDR-H3, bettering current models AlphaFold and IgFold. AbFold will contribute to antibody structure prediction and design processes.
Pathfinder: protein folding pathway prediction based on conformational sampling
Authors: Huang Zhaohong , Cui Xinyue , Xia Yuhao , Zhao Kailong , Zhang Guijun
Published: April 2023

The study of protein folding mechanism is a challenge in molecular biology, which is of great significance for revealing the movement rules of biological macromolecules, understanding the pathogenic mechanism of folding diseases, and designing protein engineering materials. Based on the hypothesis that the conformational sampling trajectory contain the information of folding pathway, we propose a protein folding pathway prediction algorithm named Pathfinder. Firstly, Pathfinder performs large-scale sampling of the conformational space and clusters the decoys obtained in the sampling. The heterogeneous conformations obtained by clustering are named seed states. Then, a resampling algorithm that is not constrained by the local energy basin is designed to obtain the transition probabilities of seed states. Finally, protein folding pathways are inferred from the maximum transition probabilities of seed states. The proposed Pathfinder is tested on our developed test set (34 proteins). For 5 widely studied proteins, we correctly predicted their folding pathways. For 25 partial biological experiments proteins, we predicted folding pathways could be further verified. For the other 4 proteins without biological experiment results, potential folding pathways were predicted to provide new insights into protein folding mechanism. The results reveal that structural analogs may have different folding pathways to express different biological functions, homologous proteins may contain common folding pathways, and α-helices may be more prone to early protein folding than β-strands.
Endogenous epitope tagging of eEF1A2 in mice reveals early embryonic expression of eEF1A2 and subcellular compartmentalisation of neuronal eEF1A1 and eEF1A2
Authors: Davies Faith C.J. , Marshall Grant F. , Gadd Danni , Abbott Catherine M.
Published: April 2023

All vertebrate species express two independently-encoded forms of translation elongation factor eEF1A. In humans and mice eEF1A1 and eEF1A2 are 92% identical at the amino acid level, but the well conserved developmental switch between the two variants in specific tissues suggests the existence of important functional differences. Heterozygous mutations in eEF1A2 result in neurodevelopmental disorders in humans; the mechanism of pathogenicity is unclear, but one hypothesis is that there is a dominant negative effect on eEF1A1 during development. The high degree of similarity between the eEF1A proteins has complicated expression analysis in the past; here we describe a gene edited mouse line in which we have introduced a V5 tag in the gene encoding eEF1A2. Expression analysis using anti-V5 and anti-eEF1A1 antibodies demonstrates that, in contrast to the prevailing view that eEF1A2 is only expressed postnatally, it is expressed from as early as E11.5 in the developing neural tube. Two colour immunofluorescence also reveals coordinated switching between eEF1A1 and eEF1A2 in different regions of postnatal brain. Completely reciprocal expression of the two variants is seen in post-weaning mouse brain with eEF1A1 expressed in oligodendrocytes and astrocytes and eEF1A2 in neuronal soma. Although eEF1A1 is absent from neuronal cell bodies after development, it is widely expressed in axons. This expression does not appear to coincide with myelin sheaths originating from oligodendrocytes but rather results from localised translation within the axon, suggesting that both variants are transcribed in neurons but show completely distinct subcellular localisation at the protein level. These findings will form an underlying framework for understanding how missense mutations in eEF1A2 result in neurodevelopmental disorders.
Epidermal tyrosine catabolism is critical for metabolic homeostasis and survival against high-protein diets inDrosophila
Authors: Kosakamoto Hina , Miura Masayuki , Obata Fumiaki
Published: April 2023

The insect epidermis that forms the exoskeleton and determines the body size of an organism has the potential to respond and adapt to the changing nutritional environment. However, the extent to which the tissue contributes to adaptation to varying dietary protein availability, as well as its role as a metabolic regulator, remains incompletely understood. Here, we show that theDrosophilaepidermis promptly reacts to dietary protein intake, promoting tyrosine (Tyr) catabolism. Among the enzymes involved in Tyr degradation, 4- hydroxyphenylpyruvate dioxygenase (Hpd) is particularly induced under high-protein regimens. We found that AMP-activated protein kinase (AMPK) pathway and forkhead box O subfamily (FoxO) induce Hpd expression. Impaired Hpd function in the epidermis leads to aberrant increases in internal Tyr levels and its metabolites, disrupting larval development under high-protein diets. Taken together, our findings uncover the critical role of epidermal metabolism in adapting to imbalanced protein environments and hence in promoting animal survival.

Summary statement

Tyrosine degradation is upregulated inDrosophilaepidermal tissue via the AMPK-FoxO axis upon dietary high-protein stress.
Regression models for partially localized fMRI connectivity analyses
Authors: Smith Bonnie B. , Zhao Yi , Lindquist Martin A. , Caffo Brian
Published: April 2023

Brain functional connectivity analysis of resting-state functional magnetic resonance imaging (fMRI) data is typically performed in a standardized template space assuming consistency of connections across subjects. This can come in the form of one-edge-at-a-time analyses or dimension reduction/decomposition methods. Common to these approaches is the assumption of complete localization (or spatial alignment) of brain regions across subjects. Alternative approaches completely eschew localization assumptions by treating connections as statistically exchangeable (for example, using the density of connectivity between nodes). Yet other approaches, such as hyperalignment, attempt to align subjects on function as well as structure, thereby achieving a different sort of template-based localization. In this paper, we propose the use of simple regression models to characterize connectivity. To that end, we build regression models on subject-level Fisher transformed regional connection matrices using geographic distance, homotopic distance, network labels, and region indicators as covariates to explain variation in connections. While we perform our analysis in template-space in this paper, we envision the method being useful in multi-atlas registration settings, where subject data remains in its own geometry and templates are warped instead. A byproduct of this style of analysis is the ability to characterize the fraction of variation in subject-level connections explained by each type of covariate. Using Human Connectome Project data, we found that network labels and regional characteristics contribute far more than geographic or homotopic relationships (considered non-parametrically). In addition, visual regions had the highest explanatory power (i.e., largest regression coefficients). We also considered subject repeatability and found that the degree of repeatability seen in fully localized models is largely recovered using our proposed subject-level regression models. Further, even fully exchangeable models retain a sizeable amount of repeatability information, despite discarding all localization information. These results suggest the tantalizing possibility that fMRI connectivity analysis can be performed in subject-space, using less aggressive registration, such as simple affine transformations, multi-atlas subject-space registration, or perhaps even no registration whatsoever.
Unisensory visual and auditory objects are processed in olfactory cortex, independently of odor association
Authors: Thunell Evelina , Peter Moa , Iravani Behzad , Porada Danja K. , Prenner Katharina , Darki Fahimeh , Lundström Johan N.
Published: April 2023

Primary sensory cortices have been demonstrated to process sensory input from non-preferred sensory modalities, e.g. primary visual cortex reacting to auditory stimulation, bringing their presumed sensory specificity into question. Whether this reflects processing of the non-preferred stimulus per se or originates from cross-modal associations is debated. Visual/auditory objects typically have strong reciprocal associations; hence, it is difficult to address this question in these modalities. Here, we attempt to dissociate between the two competing hypotheses of whether this form of activation in primary cortices is caused by unisensory processing or cross-modal associations by turning to the olfactory system where cross-modal associations are generally weaker. Using unisensory visual and auditory objects with odor associations ranging from none to strong, we show that the posterior piriform cortex, an area known to process odor objects, is activated by both sounds and pictures of objects. Critically, this activation is independent of the objects’ odor associations, thereby demonstrating that the activity is not due to cross-modal associations. Using a Floyd–Warshall algorithm, we further show that the amygdala mediate condition-relevant information between the posterior piriform cortex and both the auditory and visual object-oriented cortices. Importantly, we replicate past findings of clear crossmodal processing in the visual and auditory systems. Our study demonstrates processing of non-olfactory input in olfactory cortices that is independent of cross-modal associations and contributes to a more nuanced view of modality specificity in olfactory, auditory, and visual cortices.
Alterations in cortical excitability during pain: A combined TMS-EEG Study
Authors: Chowdhury Nahian S , Chiang Alan KI , Millard Samantha K , Skippen Patrick , Chang Wei-Ju , Seminowicz David A , Schabrun Siobhan M
Published: April 2023

Transcranial magnetic stimulation (TMS) has been used to examine inhibitory and facilitatory circuits during experimental pain and in chronic pain populations. However, current applications of TMS to pain have been restricted to measurements of motor evoked potentials (MEPs) from peripheral muscles. Here, TMS was combined with electroencephalography (EEG) to determine whether experimental pain could induce alterations in cortical inhibitory/facilitatory activity observed in TMS-evoked potentials (TEPs). In Experiment 1 (n = 29), multiple sustained thermal stimuli were administered to the forearm, with the first, second and third block of thermal stimuli consisting of warm but non-painful (pre-pain block), painful (pain block) and warm but non-painful (post-pain block) temperatures respectively. During each stimulus, TMS pulses were delivered while EEG (64 channels) was simultaneously recorded. Verbal pain ratings were collected between TMS pulses. Relative to pre-pain warm stimuli, painful stimuli led to an increase in the amplitude of the frontocentral negative peak ∼45ms post-TMS (N45), with a larger increase associated with higher pain ratings. Experiments 2 and 3 (n = 10 in each) showed that the increase in the N45 in response to pain was not due to changes in sensory potentials associated with TMS, or a result of stronger reafferent muscle feedback during pain. This is the first study to use combined TMS-EEG to examine alterations in cortical excitability in response to pain. These results suggest that the N45 TEP peak, which indexes GABAergic neurotransmission, is implicated in pain perception and is a potential marker of individual differences in pain sensitivity.
A quasi-analytic solution for real-time multi-exposure speckle imaging of tissue perfusion
Authors: Rivera Daniel A. , Schaffer Chris B.
Published: April 2023

Laser speckle contrast imaging (LSCI) is a widefield imaging technique that enables high spatiotemporal resolution measurement of blood flow. Laser coherence, optical aberrations, and static scattering effects restrict LSCI to relative and qualitative measurements. Multi-exposure speckle imaging (MESI) is a quantitative extension of LSCI that accounts for these factors but has been limited to post-acquisition analysis due to long data processing times. Here we propose and test a real-time quasi-analytic solution to fitting MESI data, using both simulated and real-world data from a mouse model of photothrombotic stroke. This rapid estimation of multi-exposure imaging (REMI) enables processing of full-frame MESI images at up to 8 Hz with negligible errors relative to time-intensive least-squares methods. REMI opens the door to real-time, quantitative measures of perfusion change using simple optical systems.
Complex Conformational Space of RNA Polymerase II C-Terminal Domain upon Phosphorylation
Authors: Amith Weththasinghage D. , Dutagaci Bercem
Published: April 2023

Intrinsically disordered proteins (IDPs) have been closely studied during the past decade due to their importance for many biological processes. The disordered nature of this group of proteins makes it difficult to observe its full span of the conformational space either using experimental or computational studies. In this article, we explored the conformational space of the C-terminal domain (CTD) of RNA polymerase II (Pol II), which is also an intrinsically disordered low complexity domain, using enhanced sampling methods. We provided a detailed conformational analysis of model systems of CTD with different lengths; first with the last 44 residues of the human CTD sequence and finally the CTD model with two heptapeptide repeating units. We then investigated the effects of phosphorylation on CTD conformations by performing simulations at different phosphorylated states. We obtained broad conformational spaces in non-phosphorylated CTD models and phosphorylation has complex effects on the conformations of the CTD. These complex effects depend on the length of the CTD, spacing between the multiple phosphorylation sites, ion coordination and interactions with the nearby residues.
Unified understanding of nonparametric causality detection in time series
Authors: Osada Yutaka , Ushio Masayuki , Kondoh Michio
Published: April 2023

Most complex systems in the real world are driven by multiple interactions among components. Identifying these interactions is critical for understanding, forecasting, and controlling system-level phenomena. Transfer entropy (TE) and convergent cross mapping (CCM) are two widely-used approaches for nonparametric causality detection based on time-series data. However, the theoretical relationship between TE and CCM has not been formally explained. Here, we provide a theoretical formulation that links TE and CCM in an information-theoretic framework, showing that they have different definitions of causal influence. Furthermore, from the formulation, we propose a novel nonparametric causality test, named unified information-theoretic causality (UIC), which has lower data requirements than those of TE (due to robustness to noise) and lower false-positive rates than those of CCM. Numerical experiments confirmed that UIC outperforms TE and CCM in terms of the performance of causality detection for both linear and nonlinear dynamical systems. Finally, we demonstrate the practical importance of the conditional test based on UIC using numerical simulations with indirect causality and empirical data for microbial communities in irrigated water samples from rice fields. Our results contribute to a unified understanding of nonparametric causality tests in time series and the accurate reconstruction of complex real-world systems.
Vascular Endothelial Cells Perform Distinct Sensing and Signaling of Laminar and Disturbed Flows across Plasma Membranes and Mitochondria
Authors: Yamamoto Kimiko , Maeno Ryohei , Kawabe Kenshiroh , Shimogonya Yuji , Ando Joji
Published: April 2023

BACKGROUND

Vascular endothelial cells (ECs) experience two different blood flow patterns: laminar and disturbed flows. Their responses to laminar flow contribute to vascular homeostasis, whereas their responses to disturbed flow result in EC dysfunction and vascular diseases. However, it remains unclear how ECs differentially sense laminar and disturbed flows and trigger signalings that elicit different EC responses. We aimed to investigate EC flow-sensing and signaling mechanisms, focusing on the role of the plasma membrane and mitochondria.

METHODS

We exposed cultured human aortic ECs to laminar flow and disturbed flow in flow-loading devices and used real-time imaging with optical probes to examine changes in the lipid order of the plasma and mitochondria membranes and the mitochondrial adenosine triphosphate (ATP) production and hydrogen peroxide (H2O2) release.

RESULTS

The lipid order of EC plasma membranes immediately decreased in response to laminar flow, while it increased in response to disturbed flow. Laminar flow also decreased the lipid order of mitochondrial membranes and increased mitochondrial ATP production. In contrast, disturbed flow increased the lipid order of mitochondrial membranes and increased the release of H2O2from mitochondria. Addition of cholesterol to the cells increased the lipid order of both membranes and abrogated the laminar flow-induced ATP production, while treatment of the cells with a cholesterol-depleting reagent, methyl-β cyclodextrin, decreased the lipid order of both membranes and abolished the disturbed flow-induced H2O2release, indicating that the changes in the membrane lipid order are closely linked to the flow-induced changes in the mitochondrial functions.

CONCLUSIONS

ECs differentially sense laminar and disturbed flows by altering the lipid order of their plasma and mitochondrial membranes in opposite directions, which result in distinct changes in the mitochondrial functions, namely, increased ATP production for laminar flow and increased H2O2release for disturbed flow, leading to ATP- and H2O2-mediated signalings, respectively.