bluuebunny/crossref_metadata_2025 huggingface dataset:
An RNAi screen for conserved kinases that enhance microRNA activity after dauer inC. elegans
Authors: Pun Himal Roka , Karp Xantha
Published: October 2023

Gene regulation in changing environments is critical for maintaining homeostasis. Some animals undergo a stress-resistant diapause stage to withstand harsh environmental conditions encountered during development. MicroRNAs (miRNAs) are one mechanism for regulating gene expression during and after diapause. MicroRNAs downregulate target genes post-transcriptionally through the activity of the miRNA-Induced Silencing Complex (miRISC). Argonaute is the core miRISC protein that binds to both the miRNA and to other miRISC proteins. The two major miRNA Argonautes in theC. eleganssoma are ALG-1 and ALG-2, which function partially redundantly. Loss ofalg-1 (alg-1(0))causes penetrant developmental phenotypes including vulval defects and the reiteration of larval cell programs in hypodermal cells. However, these phenotypes are essentially absent ifalg-1(0)animals undergo a diapause stage called dauer. Levels of the relevant miRNAs are not higher during or after dauer, suggesting that activity of the miRISC may be enhanced in this context. To identify genes that are required foralg-1(0)mutants to develop without vulval defects after dauer, we performed an RNAi screen of genes encoding conserved kinases. We focused on kinases because of their known role in modulating miRISC activity. We found RNAi knockdown of four kinase-encoding genes,air-2,bub-1,chk-1,andnekl-3, caused vulval defects and reiterative phenotypes inalg-1(0)mutants after dauer, and that these defects were more penetrant in analg-1(0)background than in wild type. Our results implicate these kinases as potential regulators of miRISC activity during post-dauer development inC. elegans.
Eukaryotic chemotaxis under periodic stimulation shows temporal gradient dependence
Authors: Karmakar Richa , Karanam Aravind , Tang Man-Ho , Rappel Wouter-Jan
Published: October 2023

When cells of the social amoebaDictyostelium discoideumare starved of nutrients they start to synthesize and secrete the chemical messenger and chemoattractant cyclic Adenosine Mono Phosphate (cAMP). This signal is relayed by other cells, resulting in the establishment of periodic waves. The cells aggregate through chemotaxis towards the center of these waves. We investigated the chemotactic response of individual cells to repeated exposure to waves of cAMP generated by a microfluidic device. When the period of the waves is short, the chemotactic ability of the cells was found to increase upon exposure to more waves, suggesting the development of a longer-term memory. This effect was not significant for longer wave periods. We show that the experimental results are consistent with a model that includes a slowly rising and decaying component that is activated by the temporal gradient of cAMP concentration. The observed enhancement in chemotaxis is relevant to populations in the wild: once sustained, periodic waves of the chemoattractant are established, it is beneficial to cells to improve their chemotactic ability in order to reach the aggregation center sooner.
Preventing extinction in an age of species migration and planetary change
Authors: Lundgren Erick J. , Wallach Arian D. , Svenning Jens-Christian , Schlaepfer Martin A. , Andersson Astrid L.A. , Ramp Daniel
Published: October 2023

International and national conservation policies almost exclusively focus on conserving species in their historic native ranges, thus excluding species that have dispersed on their own accord or have been introduced by people. Given that many of these ‘migrant’ species are threatened in their native ranges, conservation goals that explicitly exclude these migrant populations may overlook opportunities to prevent extinctions and respond dynamically to rapidly changing environmental and climatic conditions. Focusing on terrestrial mammals, we quantified the extent to which migration, in this case via introductions, has provided new homes for threatened mammal species. We then devised alternative scenarios for the inclusion of migrant populations in mainstream conservation policy with the aim of preventing global species extinctions and used spatial prioritization algorithms to simulate how these scenarios could change global spatial conservation priorities. We found that 22% of all identified migrant mammals (70 species) are threatened in their native ranges, mirroring the 25% of all mammals that are threatened. Reassessing global threat statuses by combining native and migrant ranges reduced the threat status of 23 species (∼33% of threatened migrants). Thus, including migrant populations in threat assessments provides a more accurate assessment of actual global extinction risk among species. Spatial prioritization simulations showed that reimagining the role of migrant populations to prevent global species extinction could increase the importance of overlooked landscapes, particularly in central Australia. Our results indicate that these various and non-exhaustive ways to consider migrant populations, with due consideration for potential conservation conflicts with resident taxa, may provide unprecedented opportunities to prevent species extinctions. We present these alternatives and spatial simulations to stimulate discussion on how conservation ought to respond, both pragmatically and ethically, to rapid environmental change in order to best prevent extinctions.
Disinhibitory signaling enables flexible coding of top-down information
Authors: Aquino Tomas G , Kim Robert , Rungratsameetaweemana Nuttida
Published: October 2023

Recent studies have proposed employing biologically plausible recurrent neural networks (RNNs) to investigate flexible decision-making in the brain. However, the mechanisms underlying the integration of bottom-up sensory inputs and temporally varying top-down factors (such as task instructions and selective attention) remain poorly understood, both within the context of these models and the brain. To address this knowledge gap, we trained biologically inspired RNNs on complex cognitive tasks that require adaptive integration of these factors. Through comprehensive analyses of RNNs and neural activity from mouse primary visual cortex, we show that sensory neurons in low-level areas possess the remarkable ability to multiplex and dynamically combine both bottom-up and top-down information via local inhibitory-to-inhibitory connections. Our results shed light on the role of disinhibitory circuits in the intricate interplay between bottom-up and top-down factors to enable flexible decision processes.
Defining the Cell Surface Cysteinome using Two-step Enrichment Proteomics
Authors: Yan Tianyang , Boatner Lisa M. , Cui Liujuan , Tontonoz Peter , Backus Keriann M.
Published: October 2023

The plasma membrane proteome is a rich resource of functional and therapeutically relevant protein targets. Distinguished by high hydrophobicity, heavy glycosylation, disulfide-rich sequences, and low overall abundance, the cell surface proteome remains undersampled in established proteomic pipelines, including our own cysteine chemoproteomics platforms. Here we paired cell surface glycoprotein capture with cysteine chemoproteomics to establish a two-stage enrichment method that enables chemoproteomic profiling of cellSurfaceCysteinome. Our “Cys-Surf” platform captures >2,800 total membrane protein cysteines in 1,046 proteins, including 1,907 residues not previously captured by bulk proteomic analysis. By pairing Cys-Surf with an isotopic chemoproteomic readout, we uncovered 821 total ligandable cysteines, including known and novel sites. Cys-Surf also robustly delineates redox-sensitive cysteines, including cysteines prone to activation-dependent changes to cysteine oxidation state and residues sensitive to addition of exogenous reductants. Exemplifying the capacity of Cys-Surf to delineate functionally important cysteines, we identified a redox sensitive cysteine in the low-density lipoprotein receptor (LDLR) that impacts both the protein localization and uptake of LDL particles. Taken together, the Cys-Surf platform, distinguished by its two-stage enrichment paradigm, represents a tailored approach to delineate the functional and therapeutic potential of the plasma membrane cysteinome.
Accurate model and ensemble refinement using cryo-electron microscopy maps and Bayesian inference
Authors: Hoff S. E. , Thomasen F. E. , Lindorff-Larsen K. , Bonomi M.
Published: October 2023

Converting cryo-electron microscopy (cryo-EM) data into high-quality structural models is a challenging problem of outstanding importance. Current refinement methods often generate unbalanced models in which physico-chemical quality is sacrificed for excellent fit to the data. Furthermore, these techniques struggle to represent the conformational heterogeneity averaged out in low-resolution regions of density maps. Here we introduce EMMIVox, a Bayesian inference approach to determine single-structure models as well as structural ensembles from cryo-EM maps. EMMIVox automatically balances experimental information with accurate physico-chemical models of the system and the surrounding environment, including waters, lipids, and ions. Explicit treatment of data correlation and noise as well as inference of accurate B-factors enable determination of structural models and ensembles with both excellent fit to the data and high stereochemical quality, thus outperforming state-of-the-art refinement techniques. EMMIVox represents a flexible approach to determine high-quality structural models that will contribute to advancing our understanding of the molecular mechanisms underlying biological functions.
Local structural flexibility drives oligomorphism in computationally designed protein assemblies
Authors: Khmelinskaia Alena , Bethel Neville P. , Fatehi Farzad , Antanasijevic Aleksandar , Borst Andrew J. , Lai Szu-Hsueh , Wang Jing Yang (John) , Mallik Bhoomika Basu , Miranda Marcos C. , Watkins Andrew M. , Ogohara Cassandra , Caldwell Shane , Wu Mengyu , Heck Albert J.R. , Veesler David , Ward Andrew B. , Baker David , Twarock Reidun , King Neil P.
Published: October 2023

Many naturally occurring protein assemblies have dynamic structures that allow them to perform specialized functions. For example, clathrin coats adopt a wide variety of architectures to adapt to vesicular cargos of various sizes. Although computational methods for designing novel self-assembling proteins have advanced substantially over the past decade, most existing methods focus on designing static structures with high accuracy. Here we characterize the structures of three distinct computationally designed protein assemblies that each form multiple unanticipated architectures, and identify flexibility in specific regions of the subunits of each assembly as the source of structural diversity. Cryo-EM single-particle reconstructions and native mass spectrometry showed that only two distinct architectures were observed in two of the three cases, while we obtained six cryo-EM reconstructions that likely represent a subset of the architectures present in solution in the third case. Structural modeling and molecular dynamics simulations indicated that the surprising observation of a defined range of architectures, instead of non-specific aggregation, can be explained by constrained flexibility within the building blocks. Our results suggest that deliberate use of structural flexibility as a design principle will allow exploration of previously inaccessible structural and functional space in designed protein assemblies.
Vertebral level specific modulation of paraspinal muscle activity based on vestibular signals during walking
Authors: Li Yiyuan C. , Bruijn Sjoerd M. , Lemaire Koen K. , Brumagne Simon , van Dieën Jaap H.
Published: October 2023

Evoking muscle responses by electrical vestibular stimulation (EVS) may help to understand the contribution of the vestibular system to postural control. Although paraspinal muscles play a role in postural stability, the vestibulo-muscular coupling of these muscles during walking has rarely been studied. This study aimed to investigate how vestibular signals affect paraspinal muscle activity at different vertebral levels during walking with preferred and narrow step width. Sixteen healthy participants were recruited. Participants walked on a treadmill for 8 minutes at 78 steps/min and 2.8 km/h, at two different step width, either with or without EVS. Bipolar electromyography was recorded bilaterally from the paraspinal muscles at eight vertebral levels from cervical to lumbar. Coherence, gain, and delay of EVS and EMG responses were determined. Significant EVS-EMG coupling (p<0.01) was found at ipsilateral and/or contralateral heel strikes. This coupling was mirrored between left and right relative to the midline of the trunk and between the higher and lower vertebral levels, i.e., a peak occurred at ipsilateral heel strike at lower levels, whereas it occurred at contralateral heel strike at higher levels. EVS-EMG coupling only partially coincided with peak muscle activity. EVS-EMG coherence slightly, but not significantly, increased when walking with narrow steps. No significant differences were found in gain and phase between the vertebral levels or step width conditions. In summary, vertebral level specific modulation of paraspinal muscle activity based on vestibular signals might allow a fast, synchronized, and spatially co-ordinated response along the trunk during walking.

Key Points Summary

Mediolateral stabilization of gait requires an estimate of the state of the body, which is affected by vestibular afference.

During gait, the heavy trunk segment is controlled by phasic paraspinal muscle activity and in rodents the medial and lateral vestibulospinal tracts activate these muscles.

To gain insight in vestibulospinal connections in humans and their role in gait, we recorded paraspinal surface EMG of cervical to lumbar paraspinal muscles, and characterized coherence, gain and delay between EMG and electrical vestibular stimulation, during slow walking.

Vestibular stimulation caused phasic, vertebral level specific modulation of paraspinal muscle activity at delays of around 40 milliseconds, which was mirrored between left, lower and right, upper vertebral levels.

Our results indicate that vestibular afference causes fast, synchronized, and spatially co-ordinated responses of the paraspinal muscles along the trunk, that simultaneously contribute to stabilizing the centre of mass trajectory and to keeping the head upright.
Ataxia-telangiectasia mutated(Atm) disruption sensitizes spatially-directed H3.3K27M/TP53 diffuse midline gliomas to radiation therapy
Authors: Mangoli Avani , Wu Sophie , Liu Harrison Q. , Aksu Michael , Jain Vaibhav , Foreman Bronwen E. , Regal Joshua A. , Weidenhammer Loren B. , Stewart Connor E. , Guerra Garcia Maria E. , Hocke Emily , Abramson Karen , Williams Nerissa T. , Luo Lixia , Deland Katherine , Attardi Laura , Abe Kouki , Hashizume Rintaro , Ashley David M. , Becher Oren J. , Kirsch David G. , Gregory Simon G. , Reitman Zachary J.
Published: October 2023

Diffuse midline gliomas (DMGs) are lethal brain tumors characterized by p53-inactivating mutations and oncohistone H3.3K27M mutations that rewire the cellular response to genotoxic stress, which presents therapeutic opportunities. We used RCAS/tv-a retroviruses and Cre recombinase to inactivate p53 and induce K27M in the nativeH3f3aallele in a lineage- and spatially-directed manner, yielding primary mouse DMGs. Genetic or pharmacologic disruption of the DNA damage response kinase Ataxia-telangiectasia mutated (ATM) enhanced the efficacy of focal brain irradiation, extending mouse survival. This finding suggests that targeting ATM will enhance the efficacy of radiation therapy for p53-mutant DMG but not p53-wildtype DMG. We used spatialin situtranscriptomics and an allelic series of primary murine DMG models with different p53 mutations to identify transactivation-independent p53 activity as a key mediator of such radiosensitivity. These studies deeply profile a genetically faithful and versatile model of a lethal brain tumor to identify resistance mechanisms for a therapeutic strategy currently in clinical trials.
Improved Inter-Subject Alignment of the Lumbosacral Cord for Group-Level In Vivo Gray and White Matter Assessments: A Scan-Rescan MRI Study at 3T
Authors: Büeler Silvan , Freund Patrick , Kessler Thomas M. , Liechti Martina D. , David Gergely
Published: October 2023

Introduction

Magnetic resonance imaging (MRI) enables the investigation of pathological changes in gray and white matter at the lumbosacral enlargement (LSE) and conus medullaris (CM). However, conducting group-level analyses of MRI metrics in the lumbosacral spinal cord is challenging due to variability in CM size, lack of established image-based landmarks, and unknown scan-rescan reliability. This study aimed to improve inter-subject alignment of the lumbosacral cord to facilitate group-level analyses of MRI metrics. Additionally, we evaluated the scan-rescan reliability of MRI-based cross-sectional area (CSA) measurements and diffusion tensor imaging (DTI) metrics.

Methods

Fifteen participants (10 healthy volunteers and 5 patients with spinal cord injury) underwent axial T2*-weighted and diffusion MRI at 3T. We assessed (i) the reliability of spinal cord and gray matter based landmarks for consistent inter-subject alignment of the lumbosacral cord, (ii) the inter-subject variability of MRI metrics before and after adjusting for the CM length, (iii) the intra- and inter-rater reliability of CSA measurements, and (iv) the scan-rescan reliability of CSA measurements and DTI metrics.

Results

The slice with the largest gray matter CSA as an LSE landmark exhibited the highest reliability, both within and across raters. Adjusting for the CM length greatly reduced the inter-subject variability of MRI metrics. The intra-rater, inter-rater, and scan-rescan reliability of MRI metrics were the highest at and around the LSE (scan-rescan coefficient of variation <3% for CSA measurements and <7% for DTI metrics within the white matter) and decreased considerably caudal to it.

Conclusion

To facilitate group-level analysis of corresponding spinal cord levels, we recommend using the slice with the largest gray matter CSA as a reliable LSE landmark, along with an adjustment for the CM length. We also stress the significance of the anatomical location within the lumbosacral cord in relation to the reliability of MRI metrics. The scan-rescan reliability values serve as valuable guides for power and sample size calculations in future longitudinal studies.
Multivariate Age-related Analysis of Variance in quantitative MRI maps: Widespread age-related differences revisited
Authors: Moallemian Soodeh , Bastin Christine , Callaghan Martina F. , Phillips Christophe
Published: October 2023

This study utilized multivariate ANOVA analysis to investigate age-related microstructural changes in the brain tissues driven primarily by myelin, iron, and water content. Voxel-wise analyses were performed on gray matter (GM) and white matter (WM), in addition to region of interest (ROI) analyses. The multivariate approach identified brain regions showing coordinated alterations in multiple tissue properties and demonstrated bidirectional correlations between age and all examined modalities in various brain regions, including the caudate nucleus, putamen, insula, cerebellum, lingual gyri, hippocampus, and olfactory bulb. The multivariate model was more sensitive than univariate analyses as evidenced by detecting a larger number of significant voxels within clusters in the supplementary motor area, frontal cortex, hippocampus, amygdala, occipital cortex, and cerebellum bilaterally. The examination of normalized, smoothed, and z-transformed maps within the ROIs revealed age-dependent differences in myelin, iron, and water content. These findings contribute to our understanding of age-related brain differences and provide insights into the underlying mechanisms of aging. The study emphasizes the importance of multivariate analysis for detecting subtle microstructural changes associated with aging that may motivate interventions to mitigate cognitive decline in older adults.
Common and Distinct Drug Cue Reactivity Patterns Associated with Cocaine and Heroin: An fMRI Meta-Analysis
Authors: Dejoie Jordan M , Senia Nicole , Konova Anna , Smith David , Fareri Dominic
Published: October 2023

Substance use and substance use disorders represent ongoing major public health crises. Specifically, the use of substances such as cocaine and heroin are responsible for over 50,000 drug related deaths combined annually. We used a comparative meta-analysis procedure to contrast activation patterns associated with cocaine and heroin cue reactivity, which may reflect substance use risk for these substances. PubMed and Google Scholar were searched for studies with within-subject whole brain analyses comparing drug to neutral cues for users of cocaine and heroin published between 1995 and 2022. A total of 18 studies were included, 9 in each subgroup. Voxel-based meta-analyses were performed using seed-based d mapping with permuted subject images (SDM-PSI) for subgroup mean analyses and a contrast meta-regression comparing the two substances. Results from our mean analysis indicated that users of heroin showed more widespread activation in the nucleus accumbens, right inferior and left middle temporal gyrus, right thalamus, and right cerebellum. Cocaine use was associated with recruitment of dorsolateral prefrontal cortex during cue reactivity. Direct comparison of cue reactivity studies in heroin relative to cocaine users revealed greater activation in dopaminergic targets for users of heroin compared to users of cocaine. Differential activation patterns between substances may underlie differences in the clinical characteristics observed in users of cocaine and heroin, including seeking emotional blunting in users of heroin. More consistent research methodology is needed to provide adequate studies for stringent meta-analyses examining common and distinct neural activation patterns across substances and moderation by clinically relevant factors.
ER procollagen storage defect without coupled unfolded protein response drives precocious arthritis
Authors: Yammine Kathryn M. , Abularach Sophia Mirda , Kim Seo-yeon , Bikovtseva Agata A. , Lilianty Jinia , Butty Vincent L. , Schiavoni Richard P. , Bateman John F. , Lamandé Shireen R. , Shoulders Matthew D.
Published: October 2023

Collagenopathies are a group of clinically diverse disorders caused by defects in collagen folding and secretion. For example, mutations in the gene encoding collagen type-II, the primary collagen in cartilage, can lead to diverse chondrodysplasias. One example is the Gly1170Ser substitution in procollagen-II, which causes precocious osteoarthritis. Here, we biochemically and mechanistically characterize an induced pluripotent stem cell-based cartilage model of this disease, including both hetero- and homozygous genotypes. We show that Gly1170Ser procollagen-II is notably slow to fold and secrete. Instead, procollagen-II accumulates intracellularly, consistent with an endoplasmic reticulum (ER) storage disorder. Owing to unique features of the collagen triple helix, this accumulation is not recognized by the unfolded protein response. Gly1170Ser procollagen-II interacts to a greater extent than wild-type with specific proteostasis network components, consistent with its slow folding. These findings provide mechanistic elucidation into the etiology of this disease. Moreover, the cartilage model will enable rapid testing of therapeutic strategies to restore proteostasis in the collagenopathies.
HDL regulates TGFß-receptor lipid raft partitioning, restoring contractile features of cholesterol-loaded vascular smooth muscle cells
Authors: Thevkar Nagesh Prashanth , Nishi Hitoo , Rawal Shruti , Zahr Tarik , Miano Joseph M. , Sorci-Thomas Mary , Xu Hao , Akbar Naveed , Choudhury Robin P , Misra Ashish , Fisher Edward A
Published: October 2023

Background

Cholesterol-loading of mouse aortic vascular smooth muscle cells (mVSMCs) downregulatesmiR-143/145, a master regulator of the contractile state downstream of TGFβ signaling.In vitro,this results in transitioning from a contractile mVSMC to a macrophage-like state. This process likely occursin vivobased on studies in mouse and human atherosclerotic plaques.

Objectives

To test whether cholesterol-loading reduces VSMC TGFβ signaling and if cholesterol efflux will restore signaling and the contractile statein vitroandin vivo.

Methods

Human coronary artery (h)VSMCs were cholesterol-loaded, then treated with HDL (to promote cholesterol efflux). Forin vivostudies, partial conditional deletion ofTgfβr2in lineage-traced VSMC mice was induced. Mice wild-type for VSMCTgfβr2or partially deficient (Tgfβr2+/-) were made hypercholesterolemic to establish atherosclerosis. Mice were then treated with apoA1 (which forms HDL).

Results

Cholesterol-loading of hVSMCs downregulated TGFβ signaling and contractile gene expression; macrophage markers were induced. TGFβ signaling positively regulatedmiR-143/145expression, increasingActa2expression and suppressing KLF4. Cholesterol-loading localized TGFβ receptors into lipid rafts, with consequent TGFβ signaling downregulation. Notably, in cholesterol-loaded hVSMCs HDL particles displaced receptors from lipid rafts and increased TGFβ signaling, resulting in enhancedmiR-145expression and decreased KLF4-dependent macrophage features. ApoA1 infusion intoTgfβr2+/-mice restoredActa2expression and decreased macrophage-marker expression in plaque VSMCs, with evidence of increased TGFβ signaling.

Conclusions

Cholesterol suppresses TGFβ signaling and the contractile state in hVSMC through partitioning of TGFβ receptors into lipid rafts. These changes can be reversed by promotion of cholesterol efflux, consistent with evidencein vivo.

Condensed abstract

Many cells identified as macrophage-like in human and mouse atherosclerotic plaques are thought to be of VSMC origin. We identified cholesterol-mediated downregulation of TGFβ signalingin vitroin human (h)VSMCs by localization of TGFβ receptors in membrane lipid rafts, which was reversed by HDL-mediated cholesterol efflux. This restored VSMC contractile marker (Acta2) and suppressed macrophage marker (CD68) expression by promoting TGFβ enhancement ofmiR-145expression.In vivo, administration of apoA1 (which forms HDL) to atherosclerotic mice also promoted VSMCActa2expression and reduced CD68 expression. Because macrophage-like VSMC are thought to have adverse properties, our studies not only show mechanistically how cholesterol causes their transition, but also suggest that efflux-competent HDL particles may have a therapeutic role by restoring a more favorable phenotypic state of VSMC in atherosclerotic plaques.
3D Bioprinting Using Poly(ethylene-glycol)-dimethacrylate (PEGDMA) Composite
Authors: Chang Shu-Yung , Lee Joseph Zhi Wei , Ranganath Anupama Sargur , Ching Terry , Hashimoto Michinao
Published: October 2023

Recent progress in additive manufacturing has enabled rapid printing of bioinspired structures such as vasculature and alveoli using stereolithography (SLA) bioprinting. Bioinks for SLA often require synthetic polymers as additives to ensure the structural integrity of the printed cell-laden constructs. To this end, high molecular weight (MW) poly(ethylene-glycol)- diacrylate (PEGDA) (MW = 3400) is commonly used to enhance the mechanical property of crosslinked hydrogels, which requires in-house polymer synthesis or the acquisition of costly reagents. This research investigated the use of poly(ethylene-glycol)-dimethacrylate (PEGDMA) (MW = 1000) as a component of a composite bioink to enhance the mechanical properties of the SLA-printed constructs. We successfully demonstrated the fabrication of three-dimensional (3D) constructs with overhang and complex architecture, while human colorectal cancer cells (Caco-2) embedded in the crosslinked bioink exhibited the capability to proliferate on Day 6 ofin vitrocell culture. Our study suggested PEGDMA as a viable alternative to high MW PEGDA used in SLA bioprinting. The accessibility to PEGDMA will facilitate the advance in 3D bioprinting to fabricate complex bioinspired structures and tissue surrogates for biomedical applications.

Article Highlights

Poly(ethylene-glycol)-dimethacrylate (PEGDMA) can be used in cell-laden bioprinting to enhance the mechanical property of bioinks.

PEGDMA-based bioink was non-cytotoxic and conducive to cell proliferation.

The facile preparation of PEGDMA composite ink will help to accelerate the research in tissue engineering via bioprinting.
Increased stromal densities of B cells, CD103+ cells, and CD163+ M2-like macrophages associate with poor clinical outcomes in BCG treated non-muscle invasive bladder cancer
Authors: Ravenscroft Benjamin , Yolmo Priyanka , Chenard Stephen , Rahimi Sadaf , Pace Keiran , Sachdeva Kartik , Jamaspishvilli Tamara , Ghaedi Hamid , Garven Andrew , Tyryshkin Kathrin , Berman David M. , Jackson Chelsea , Robert D. Siemens , Koti Madhuri
Published: October 2023

Non-muscle invasive bladder cancer (NMIBC) constitutes a significant clinical challenge, with over 50% of patients experiencing poor clinical outcomes in the form of early recurrence or progression following treatment with Bacillus Calmette-Guerin (BCG) immunotherapy. The pre-treatment tumor immune microenvironment (TIME) is an established determinant of response to BCG. This study explores the spatial profiles of CD79a+ B cells, CD163+ M2-like macrophages, proliferating and tissue-resident phenotypes of T cells, along with PD-1/PD-L1 checkpoint expression in pre-BCG treatment tumors of 173 patients (139 males, 34 females). Multiplex immunofluorescence staining of a tumor tissue microarray, revealed elevated infiltration of CD79a+ B cells, CD163+ M2-like macrophages, CD103+ cells, and CD8+ T cells at the tumor invasive margins. Increased epithelial PD-L1 immune-checkpoint expression in tumors was observed in female and male patients who exhibited significantly shorter recurrence-free survival (RFS). Importantly, high CD79a+ B cell density in BCG-treated females in both stromal and epithelial compartments exhibited significantly shorter RFS and progression-free survival compared to males. Stromal CD79a+ B cell density was positively correlated with M2-like macrophages, CD8+ T cells, CD103+ cells and PD-1 expressing cells. CD79a+ B cells, CD103+ cells, and M2-like macrophage density were associated with higher grade and enriched in basal subtype tumor. This study highlights the significance of an understudied role of B cells and their cellular neighborhoods in the pre-treatment TIME and BCG-therapy response. Overall, findings from this study underscore the importance of considering sex-related immunobiological differences in the stromal compartments of bladder tumors towards the development of optimal therapeutic targeting strategies.
Evolution of microRNAs in Amoebozoa and implications for the origin of multicellularity
Authors: Edelbroek Bart , Kjellin Jonas , Biryukova Inna , Liao Zhen , Lundberg Torgny , Noegel Angelika A. , Eichinger Ludwig , Friedländer Marc R. , Söderbom Fredrik
Published: October 2023

MicroRNAs (miRNAs) are important and ubiquitous regulators of gene expression in both plants and animals. They are thought to have evolved convergently in these lineages and hypothesized to have played a role in the evolution of multicellularity. In line with this hypothesis, miRNAs have so far only been described in few unicellular eukaryotes. Here, we investigate the presence and evolution of miRNAs in Amoebozoa, focusing on species belonging toAcanthamoeba,Physarum, and dictyostelid taxonomic groups, representing a range of unicellular and multicellular lifestyles. miRNAs that adhere to both the stringent plant and animal miRNA criteria were identified in all examined amoebae, greatly expanding the total number of protists harbouring miRNAs. We found conserved miRNAs between closely related species, but the majority of species feature only unique miRNAs. Our results show that miRNAs are rapidly lost and gained in Amoebozoa, and that miRNAs were not required for transition from uni- to multicellular life.
Growth inhibitory factor/metallothionein-3 is a sulfane sulfur-binding protein
Authors: Shinkai Yasuhiro , Ding Yunjie , Matsui Toru , Devitt George , Akiyama Masahiro , Shen Tang-Long , Nishida Motohiro , Ida Tomoaki , Akaike Takaaki , Mahajan Sumeet , Fukuto Jon M. , Shigeta Yasuteru , Kumagai Yoshito
Published: October 2023

Cysteine-bound sulfane sulfur atoms in proteins have received much attention as key factors in cellular redox homeostasis. However, the role of sulfane sulfur in zinc regulation has been underinvestigated. We report here that cysteine-bound sulfane sulfur atoms serve as ligands to hold and release zinc ions in growth inhibitory factor (GIF)/metallothionein-3 (MT-3) with an unexpected C– S–S–Zn structure. Oxidation of such a zinc/persulfide cluster in Zn7GIF/MT-3 results in the release of zinc ions, and intramolecular tetrasulfide bridges in apo-GIF/MT-3 efficiently undergo S–S bond cleavage by thioredoxin to regenerate Zn7GIF/MT-3. Three-dimensional molecular modeling confirmed the critical role of the persulfide group in the thermostability and Zn-binding affinity of GIF/MT-3. The present discovery raises the fascinating possibility that the function of other Zn-binding proteins is controlled by sulfane sulfur.
An Antibiotic Degrading Engineered Living Material Platform to Combat Environmental Antibiotic Resistance
Authors: Özkul Gökçe , Kehribar Ebru Şahin , Şeker Urartu Özgür Şafak
Published: October 2023

Presence of antibiotics in natural water bodies is a growing problem regarding the occurrence of antibiotic resistance among various species. This is mainly caused due to excessive use of medical and veterinary antibiotics as well as the lack of effective treatment processes for eliminating residual antibiotic from wastewaters. In this study, we introduce a genetically engineered biomaterial as a solution for effective degradation of one of the dominantly found antibiotics in natural water bodies. Our biomaterial harnesses laccase type enzymes which are known to attack specific type of antibiotics, i.e. fluoroquinolone type synthetic antibiotics, and as a result degradation occurs. The engineered biomaterial is built usingEscherichia colibiofilm protein CsgA as a scaffold, which is fused separately to two different laccase enzymes with the SpyTag – SpyCatcher peptide-protein duo. The final material is implemented as a part of a living material system. Our proposed system can be integrated as living antibiotic degrading materials to help the combat with antibiotic resistance.
FAKHRAVAC and BBIBP-CorV vaccine seeds’ binding to angiotensin-converting enzyme 2: A comparative molecular dynamics study
Authors: Setareh Soroush , Rad Iman , Meghdadi Jafar , Khodayari Kaveh , Karimi Rahjerdi Ahmad
Published: October 2023

Background

Safety and efficacy of the SARS-CoV-2 inactivated vaccines have been question since the emergence of SARS-CoV-2 variants of concern (VOCs). Using residue fluctuations and statistically comparing RMSF values, have escalated the understanding of the binding dynamics of the viral proteins to their receptors and here in this study, we compared the interaction between inactivated spike proteins (representing FAKHRAVAC and BBIBP-CorV vaccines seed) and the human Angiotensin-Converting Enzyme 2 (hACE2) receptor.

Methodology

Through 100 set of accelerated 1 ns comparative molecular dynamics simulations, we analyze the binding dynamics and energy components of these interactions and compared residue backbone fluctuations using entropy and statistics including KL-Divergence and KS-test.

Principal Findings

Our results reveal that FAKHRAVAC and Sinopharm exhibit similar binding dynamics and affinity to hACE2. Further examination of residue-wise fluctuations highlights the common behavior of binding key residues and mutation sites between the two vaccines. However, subtle differences in residue fluctuations, especially at critical sites like Q24, Y435, L455, S477, Y505, and F486, raise the possibility of distinct efficacy profiles.

Conclusion

These variations may influence vaccine immunogenicity and safety in response to evolving SARS-CoV-2 variants. The study underscores the importance of considering residue-wise fluctuations for understanding vaccine-pathogen interactions and their implications for vaccine design.

Author summary

It is fundamentally important to ensure the safety and efficacy of the FAKHRAVAC, as an inactivated vaccine candidate for SARS-CoV-2. Considering the previously published pre-clinical and clinical findings about the similarity of the FAKHRAVAC’s safety and efficacy in comparison to the BBIBP-CorV vaccine seed (which is recalled as Sinopharm), it is necessary to gain more insights into structure and function of this vaccine at the molecular level, as well. Since the binding dynamics of the viral proteins to their receptor can imply the vaccine’s immunogenicity and mechanism-of-action, binding dynamics of a vaccine candidate must be studied comprehensively. Hereby, we have compared binding dynamics of the FAKHRAVAC and Sinopharm vaccine seeds to the SARS-CoV-2 spike protein’s receptor, the ACE2. We took advantage of a comparative molecular dynamics simulation approach to effectively compare binding dynamics using atom fluctuations and at the residue level to ensure the resolution of this study. We have found similar binding dynamics and binding mechanics between these two vaccines, validating the pre-clinical and clinical findings computationally, as well as highlighting residues with different fluctuations and discussed their potential roles.
Folding correctors can restore CFTR posttranslational folding landscape by allosteric domain-domain coupling
Authors: Soya Naoto , Xu Haijin , Roldan Ariel , Yang Zhengrong , Ye Haoxin , Jiang Fan , Premchandar Aiswarya , Veit Guido , Cole Susan P.C. , Kappes John , Hegedus Tamas , Lukacs Gergely L.
Published: October 2023

Abstract

The folding/misfolding and pharmacological rescue of multidomain ATP-binding cassette (ABC) C-subfamily transporters, essential for organismal health, remain incompletely understood. The ABCC transporters core consists of two nucleotide binding domains (NBD1,2) and transmembrane domains (TMD1,2). Using molecular dynamic simulations, biochemical and hydrogen deuterium exchange approaches, we show that the mutational uncoupling or stabilization of NBD1-TMD1/2 interfaces can compromise or facilitate the CFTR(ABCC7)-, MRP1(ABCC1)-, and ABCC6-transporters posttranslational coupled domain-folding in the endoplasmic reticulum. Allosteric or orthosteric binding of VX-809 and/or VX-445 folding correctors to TMD1/2 can rescue kinetically trapped CFTR post-translational folding intermediates of cystic fibrosis (CF) mutants of NBD1 or TMD1 by global rewiring inter-domain allosteric-networks. We propose that dynamic allosteric domain-domain communications not only regulate ABCC-transporters function but are indispensable to tune the folding landscape of their post-translational intermediates. These allosteric networks can be compromised by CF-mutations, and reinstated by correctors, offering a framework for mechanistic understanding of ABCC-transporters (mis)folding.

One-Sentence Summary

Allosteric interdomain communication and its modulation are critical determinants of ABCC-transporters post-translational conformational biogenesis, misfolding, and pharmacological rescue.
CENP-E initiates chromosome congression by opposing Aurora kinases to promote end-on attachments
Authors: Vukušić Kruno , Tolić Iva M.
Published: October 2023

Chromosome congression to the spindle equator is crucial for accurate cell division. The kinetochore motor protein CENP-E/kinesin-7 is uniquely required for the rapid congression of chromosomes near centrosomes. Current models suggest that CENP-E drives congression by gliding kinetochores along microtubules independently of chromosome biorientation. Here, by studying chromosome movement under different levels of CENP-E activity, we propose an alternative model in which CENP-E initiates congression by promoting the formation or stabilization of end-on attachments at kinetochores, rather than by directly propelling the chromosomes. CENP-E accelerates congression initiation by opposing Aurora kinase activity, but subsequent chromosome movement toward the equator does not depend on CENP-E. Without CENP-E, stabilization of end-on attachments is delayed due to Aurora kinase-mediated phosphorylation of microtubule-binding proteins on kinetochores and the expansion of the fibrous corona. We propose that CENP-E counters this inhibition by reducing Aurora B-mediated phosphorylation of outer kinetochore proteins in a BubR1-dependent manner, thereby stabilizing end-on attachments, facilitating the removal of the fibrous corona, and initiating biorientation-dependent chromosome movement.
Machine learning approach to assess the pathogenicity of BRCA1/2 genetic variants : brca-NOVUS
Authors: Vatsyayan Aastha , Scaria Vinod
Published: October 2023

Breast cancer is globally the leading type of cancer in terms of both incidence and mortality. BRCA1 and BRCA2 gene variants have long been linked to and studied in context of the disease. Rapid variant discovery has further been made freely accessible by advances in Next-generation sequencing, making it a demanding task to accurately interpret these variants for clinical and research applications. To establish the nature of these variants, the American College of Medical Genetics and Genomics and the Association of Molecular Pathologists (ACMG-AMP) have issued a set of guidelines for variant classification. However, given the huge number of variants associated with the two large and well-studied genes, functional studies or ACMG-AMP classification is a mountainous challenge. Here we describe brca-NOVUS, a machine learning approach trained on a gold-standard ACMG-qualified dataset for the accurate interpretation of variants at large scale. Using two independent test and validation datasets of ACMG-qualified variants, we show that brca-NOVUS can be used to for the classification of variants in clinical as well as research settings.
Understanding the prevalence of germline oncogenic biomarker variants across the Indian population
Authors: Vatsyayan Aastha , Scaria Vinod
Published: October 2023

Background

Germline variants have traditionally been used for determining carrier status in heritable cancer families. However, studies are increasingly finding use of germline variants as therapeutic, diagnostic and prognostic biomarkers used to guide therapy decisions in cancer treatment.

Objectives

To study the prevalence of mutation specific oncogenic biomarkers in the Indian population and analyze their presence across disease cohorts

Materials and Methods

We annotate the IndiGen data obtained from whole genome sequencing of 1029 self-declared healthy Indian individuals with biomarker information obtained from the OncoKB knowledgebase, a repository of evidence-based information about somatic biomarkers and structural alterations in patient tumors.

Results

In our study we have discovered 34 biomarker variants of therapeutic actionability across 16 genes linked with 23 unique drugs or drug combinations in 23 unique types of cancer disease in the Indian population. In all, we have found 52 biomarker variants with 172 different biomarker types including therapeutic, resistance, diagnostic, and prognostic. We establish that 4.3% of the Indian population are carriers of therapeutic, and 2.13% are carriers of both diagnostic as well as prognostic germline biomarkers. Finally, we also establish the prevalence of 42 biomarker variants across the 23 genes in both AD and AR modes of inheritance in the Indian population.
Mapping axon diameters and conduction velocity in the rat brain – different methods tell different stories of the structure-function relationship
Authors: Skoven Christian S. , Andersson Mariam , Pizzolato Marco , Siebner Hartwig R. , Dyrby Tim B.
Published: October 2023

The structure-function relationship of nerve fibers describes an empirically determined linear relationship between axon diameter, myelin thickness (i.e., g-ratio), and conduction velocity. We investigated the structure-function relationship with different modalities in axons projecting through the corpus callosum of the rodent brain. We measured transcallosal conduction times using optogenetically evoked local field potentials (LFP) and estimated conduction velocity after measuring the callosal length with diffusion magnetic resonance imaging (dMRI) based tractography. Tractography followed the same projection as the fluorescently labeled axons in the corpus callosum. In the same animal, axon diameters were quantified using transmission electron microscopy (TEM) and dMRI. Axon distributions of TEM indicated a bimodal population, where the larger axons shrink more than the smaller ones, when comparing the modes with cryo-TEM. When applying shrinkage-correction to axon diameters from TEM of dehydrated tissue, they were better aligned with estimates from dMRI obtained in the same animal. Measured LFPs predicted axon diameters that agree with the primary mode of the axon distribution, whereas the large axons estimated by dMRI predicted latencies too short to be measured by LFPs. Different modalities show different degrees of variations, being low between animals, suggesting that the variation is methodologically dominated - not anatomically. Our results show that modalities have different sensitivity profiles to the whole axon diameter distribution. Therefore, caution must be taken when interpreting a method’s prediction of a metric, as it may not represent the full but only a sub-part of the structure-function relationship of an axonal projection.

Significance Statement

We acquire both functional and structural metrics, namely conduction velocity, pathway length, axon diameter, and g-ratio in the same cohort of animals. The transcallosal conduction time was obtained from electrophysiological measurements after contralateral optogenetic stimulation in the rat motor cortex. Cryo-fixation of the tissue reveals different shrinkages for different sub-populations in the diameter distribution. Measured latencies correspond to the small axonal subpopulation with diameters extending up to the mode of the distribution obtained with electron microscopy. Diffusion-MRI primarily appears sensitive to the larger axons, obtained with histology, after correcting for diameter weighting and shrinkage. Different modalities can have very different sensitivities to the structure-function relationship of an axonal projection which must be accounted for in the interpretation.