bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolite Damage and Damage-Control in a Minimal Genome
Authors: Haas Drago , Thamm Antje M. , Sun Jiayi , Huang Lili , Sun Lijie , Beaudoin Guillaume A.W. , Wise Kim S. , Lerma-Ortiz Claudia , Bruner Steven D. , Breuer Marian , Luthey-Schulten Zaida , Lin Jiusheng , Wilson Mark A. , Brown Greg , Yakunin Alexander F. , Kurilyak Inna , Folz Jacob , Fiehn Oliver , Glass John I. , Hanson Andrew D. , Henry Christopher S. , de Crécy-Lagard Valérie 
Published: December 2021

AbstractAnalysis of the genes retained in the minimized Mycoplasma JCVI-Syn3A genome established that systems that repair or preempt metabolite damage are essential to life. Several genes with known metabolite damage repair or preemption functions were identified and experimentally validated, including 5-formyltetrahydrofolate cyclo-ligase, CoA disulfide reductase, and certain hydrolases. Furthermore, we discovered that an enigmatic YqeK hydrolase domain fused to NadD has a novel proofreading function in NAD synthesis and could double as a MutT-like sanitizing enzyme for the nucleotide pool. Finally, we combined metabolomics and cheminformatics approaches to extend the core metabolic map of JCVI-Syn3A to include promiscuous enzymatic reactions and spontaneous side reactions. This extension revealed that several key metabolite damage-control systems remain to be identified in JCVI-Syn3A, such as that for methylglyoxal.
AraC binds the p75NTRtransmembrane domain to induce neurodegeneration in mature neurons
Authors: Lopes-Rodrigues Vanessa , Boxy Pia , Sim Eunice , Park Dong Ik , Carbonell Josep , Andersson Annika , Fernández-Suárez Diana , Nykjær Anders , Kisiswa Lilian 
Published: December 2021

AbstractBackgroundCytosine arabinoside (AraC) is one of the main therapeutic treatments for several types of cancer including acute myeloid leukaemia. However, after high dose AraC chemotherapy regime, patients develop severe neurotoxicity and neurodegeneration in the central nervous system leading to cerebellar ataxia, dysarthria, nystagmus, somnolence and drowsiness. AraC induces apoptosis in dividing cells, however, the mechanism by which it leads to neurite degeneration and cell death in mature neurons remains unclear. We hypothesized that the upregulation of the death receptor p75NTRis responsible for AraC-mediated neurodegeneration and cell death in leukemia patients undergoing AraC treatment.MethodsTo determine the role of AraC-p75NTRsignalling in degeneration of mature cerebellar granule neurons, we used primary cultures from p75NTRknockout andp75NTRCys259mice. Evaluation of neurodegeneration, cell death and p75NTRsignalling was done by immunohistochemistry and immunoblotting. To assess the direct interaction between AraC and p75NTR, we performed isothermal dose response-cellular thermal shift and AraTM assays as well as Homo-FRET anisotropy imaging.ResultsWe show that AraC induces neurite degeneration and programmed cell death of mature cerebellar granule neurons in a p75NTR-dependent manner. Mechanistically, AraC binds to Proline 252 and Cysteine 256 of the p75NTRtransmembrane domain and selectively uncouples p75NTRfrom the NFκB survival pathway. This in turn, exacerbates the activation of the cell death/JNK pathway by recruitment of TRAF6 to p75NTR.ConclusionOur findings identify p75NTRas a novel molecular target to develop treatments to counteract AraC-mediated neurodegeneration.
Dual role of strigolactone receptor signaling partner in inhibiting substrate hydrolysis
Authors: Sobecks Briana L. , Chen Jiming , Shukla Diwakar 
Published: December 2021

AbstractPlant branch and root growth relies on metabolism of the strigolactone (SL) hormone. The interaction between the SL molecule, Oryza sativa DWARF14 (D14) SL receptor, and D3 F-box protein has been shown to play a critical role in SL perception. Previously, it was believed that D3 only interacts with the closed form of D14 to induce downstream signaling, but recent experiments indicate that D3, as well as its C-terminal helix (CTH), can interact with the open form as well to inhibit strigolactone signaling. Two hypotheses for the CTH induced inhibition are that either the CTH affects the conformational ensemble of D14 by stabilizing catalytically inactive states, or the CTH interacts with SLs in a way that prevents them from entering the binding pocket. In this study, we have performed molecular dynamics (MD) simulations to assess the validity of these hypotheses. We used an apo system with only D14 and the CTH to test the active site conformational stability and a holo system with D14, the CTH, and an SL molecule to test the interaction between the SL and CTH. Our simulations show that the CTH affects both active site conformation and the ability of SLs to move into the binding pocket. In the apo system, the CTH allosterically stabilized catalytic residues into their inactive conformation. In the holo system, significant interactions between SLs and the CTH hindered the ability of SLs to enter the D14 binding pocket. These two mechanisms account for the observed decrease in SL binding to D14 and subsequent ligand hydrolysis in the presence of the CTH.
Rapid, Reference-Free Human Genotype Imputation with Denoising Autoencoders
Authors: Dias Raquel , Evans Doug , Chen Shang-Fu , Chen Kai-Yu , Chan Leslie , Torkamani Ali 
Published: December 2021

AbstractGenotype imputation is a foundational tool for population genetics. Standard statistical imputation approaches rely on the co-location of large whole-genome sequencing-based reference panels, powerful computing environments, and potentially sensitive genetic study data. This results in computational resource and privacy-risk barriers to access to cutting-edge imputation techniques. Moreover, the accuracy of current statistical approaches is known to degrade in regions of low and complex linkage disequilibrium.Artificial neural network-based imputation approaches may overcome these limitations by encoding complex genotype relationships in easily portable inference models. Here we demonstrate an autoencoder-based approach for genotype imputation, using a large, commonly-used reference panel, and spanning the entirety of human chromosome 22. Our autoencoder-based genotype imputation strategy achieved superior imputation accuracy across the allele-frequency spectrum and across genomes of diverse ancestry, while delivering at least 4-fold faster inference run time relative to standard imputation tools.
Age-related changes in microRNAs expression in cruciate ligaments of wild-stock house mice
Authors: Kharaz Yalda A. , Goljanek-Whysall Katarzyna , Nye Gareth , Hurst Jane , McArdle Anne , Comerford Eithne J. 
Published: December 2021

AbstractAimCruciate ligaments (CLs) of the knee joint are commonly injured following trauma or ageing. MicroRNAs (miRs) are potential therapeutic targets in musculoskeletal disorders. This study aimed to 1) identify if wild-stock house (WSH) mice are an appropriate model to study age-related changes of the knee joint and 2) investigate expression of miRs in ageing murine CLs.MethodsKnee joints were collected from 6 and 24 months old C57BL/6 and WSH mice (Mus musculus domesticus) for histological analysis. RNA extraction and qPCR gene expression were performed on CLs in 6, 12, 24, and 30 month WSH old mice. Expression of miR targets in CLs was determined, followed by analysis of predicted mRNA target genes and Ingenuity Pathway Analysis.ResultsHigher CL and knee OARSI histological scores were found in 24 month old WSH mice compared to 6 and 12 month old C57BL/6 and 6 month old WSH mice (p< 0.05). miR-29a and miR-34a were upregulated in 30 month-old WSH mice in comparison to 6, 12 and 24-month-old WSH mice (p<0.05). Ingenuity Pathway Analysis on miR-29a and 34a targets was associated with inflammation through interleukins, TGFβ and Notch genes and p53 signalling. Collagen type I alpha 1 chain (COL1A1) correlated negatively with both miR-29a (r= -0.35) and miR-34a (r= -0.33).ConclusionThe findings of this study support WSH house mice as an accelerated ageing model of the murine knee joint. This study also indicated that miR-29a and 34a may be important regulators of COL1A1 gene expression in murine CLs.
Physics Augmented U-Net: A High-Frequency Aware Generative Prior for Microscopy
Authors: Pradeepkumar Jathurshan , Anandakumar Mithunjha , Kugathasan Vinith , Seeber Andrew , Wadduwage Dushan N. 
Published: December 2021

AbstractA key challenge in optical microscopy is to image fast at high-resolution. To address this problem, we propose “Physics Augmented U-Net”, which combines deep learning and structured illumination microscopy (SIM). In SIM, the structured illumination aliases out-of-band high-frequencies to the passband of the microscope; thus SIM captures some high-frequencies even when the image is sampled at low-resolution. To utilize these features, we propose a three-element method: 1) a modified U-Net model, 2) a physics-based forward model of SIM 3) an inference algorithm combining the two models. The modified U-Net architecture is similar to the seminal work, but the bottleneck is modified by concatenating two latent vectors, one encoding low-frequencies (LFLV), and the other encoding high-frequencies (HFLV). LFLV is learned by U-Net contracting path, and HFLV is learned by a second encoding path. In the inference mode, the high-frequency encoder is removed; HFLV is then optimized to fit the measured microscopy images to the output of the forward model for the generated image by the U-Net. We validated our method on two different datasets under different experimental conditions. Since a latent vector is optimized instead of a 2D image, the inference mode is less computationally complex. The proposed model is also more stable compared to other generative prior-based methods. Finally, as the forward model is independent of the U-Net, Physics Augmented U-Net can enhance resolution on any variation of SIM without further retraining.
Community Composition of Bacteria Isolated from Swiss Banknotes Varies Depending on Collection Environment
Authors: Bischofberger Anna M. , Hall Alex R. 
Published: December 2021

AbstractHumans interact constantly with surfaces and associated microbial communities in the environment. The factors shaping the composition of these communities are poorly understood: some proposed explanations emphasize the influence of local habitat conditions (niche-based explanations), while others point to geographic structure and the distance among sampled locations (dispersal-based explanations). However, the relative roles of these different drivers for microbial community assembly on human-associated surfaces are not clear. Here, we used a combination of sampling, sequencing (16S rRNA) and culturing to show that the composition of banknote-associated bacterial communities varies depending on the local collection environment. Using banknotes collected from various locations and types of shops across Switzerland, we found taxonomic diversity dominated by families such asPseudomonadaceaeandStaphylococcaceae, but with banknote samples from particular types of shops (especially butcher shops) having distinct community structure. By contrast, we found no evidence of geographic structure: similarity of community composition did not decrease with increasing distance among sampled locations. These results show that microbial communities associated with banknotes, one of the most commonly encountered and exchanged human-associated surfaces, can reflect the local environmental conditions (in this case, the type of shop), and the signal for this type of variation was stronger than that for geographic structure among the locations sampled here.
Overexpression of NDR1 Leads to Pathogen Resistance at Elevated Temperatures
Authors: Samaradivakara Saroopa P. , Chen Huan , Lu Yi-Ju , Li Pai , Kim Yongsig , Tsuda Kenichi , Mine Akira , Day Brad 
Published: December 2021

ABSTRACTAbiotic and biotic environments influence a myriad of plant-related processes, including growth, development, and the establishment and maintenance of interaction(s) with microbes. As a driver of this signaling between plants and microbes, the role of plant hormones in both surveillance and signaling has emerged as a point of intersection between plant-abiotic and -biotic responses. In the current study, we elucidate a role for NON-RACE-SPECIFIC DISEASE RESISTANCE1 (NDR1) by exploiting effector-triggered immunity (ETI) to define the regulation of plant host immunity in response to both pathogen infection and elevated temperature. We generated time-series RNA sequencing data of WT Col-0, a NDR1 overexpression line, as well as ndr1 and ics1-2 mutant plants under elevated temperature. Not surprisingly, the NDR1-overexpression line showed genotype-specific gene expression changes related to defense response and immune system function. Interestingly, overexpression of NDR1 revealed a role for NDR1 in immune system function; specifically, we describe a mechanism that intersects with Pseudomonas syringae, type-III effector translocation, R-protein signaling complex stabilization, and sustained levels of SA at elevated temperature during ETI. The results described herein support a role for NDR1 in maintaining cell signaling during simultaneous exposure to elevated temperature and avirulent pathogen stressors.One-sentence summaryNDR1 is required for Pst-AvrRpt2 triggered ETI at elevated temperature.
CURT1A and CURT1C mediate distinct stages of plastid conversion inArabidopsis
Authors: Liang Zizhen , Yeung Wai Tsun , Ki Mai Keith Ka , Ma Juncai , Liu Zhongyuan , Chong Yau-Lun Felix , Kang Byung-Ho 
Published: December 2021

AbstractThe crystalline structure of prolamellar bodies (PLBs) and light-induced etioplasts-to-chloroplasts transformation have been investigated with electron microscopy methods. However, these studies suffer from chemical fixation artifacts and limited volumes of tomographic reconstruction. We have examinedArabidopsis thalianacotyledon samples preserved by high-pressure freezing with scanning transmission electron tomography to visualize larger volumes in etioplasts and their conversion into chloroplasts. PLB tubules were arranged in a zinc blende-type lattice like carbon atoms in diamonds. Within 2 hours after illumination, the lattice collapsed from the PLB exterior and the disorganized tubules merged to form fenestrated sheets that eventually matured into lamellar thylakoids. These planar thylakoids emerging from PLBs overlapped or folded into grana stacks in PLBs’ vicinity. Since the nascent lamellae had curved membrane at their tips, we examined the localization of CURT1 proteins.CURT1Atranscript was most abundant in de-etiolating cotyledon samples, and CURT1A concentrated at the peripheral PLB. Incurt1amutant etioplasts, thylakoid sheets were swollen and failed to develop stacks. Incurt1cmutant, however, PLBs had cracks in their lattices, indicating that CURT1C contributes to cubic crystal growth under darkness. Our data provide evidence that CURT1A and CURT1C play distinct roles in the etioplast and chloroplast biogenesis.
Demographic feedbacks can hamper the spatial spread of a gene drive
Authors: Girardin Léo , Débarre Florence 
Published: December 2021

AbstractThis paper is concerned with a reaction–diffusion system modeling the fixation and the invasion in a population of a gene drive (an allele biasing inheritance, increasing its own transmission to offspring). In our model, the gene drive has a negative effect on the fitness of individuals carrying it, and is therefore susceptible of decreasing the total carrying capacity of the population locally in space. This tends to generate an opposing demographic advection that the gene drive has to overcome in order to invade. While previous reaction–diffusion models neglected this aspect, here we focus on it and try to predict the sign of the traveling wave speed. It turns out to be an analytical challenge, only partial results being within reach, and we complete our theoretical analysis by numerical simulations. Our results indicate that taking into account the interplay between population dynamics and population genetics might actually be crucial, as it can effectively reverse the direction of the invasion and lead to failure. Our findings can be extended to other bistable systems, such as the spread of cytoplasmic incompatibilities caused by Wolbachia.
iDEP-assisted isolation of insulin secretory vesicles
Authors: Barekatain Mahta , Liu Yameng , Wang Zhongying , Cherezov Vadim , Fraser Scott E. , White Kate L , Hayes Mark A. 
Published: December 2021

ABSTRACTOrganelle heterogeneity and inter-organelle associations within a single cell contribute to the limited sensitivity of current organelle separation techniques, thus hindering organelle subpopulation characterization. Here we use direct current insulator-based dielectrophoresis (DC-iDEP) as an unbiased separation method and demonstrate its capability by identifying distinct distribution patterns of insulin vesicles from pancreatic β-cells. A multiple voltage DC-iDEP strategy with increased range and sensitivity has been applied, and a differentiation factor (ratio of electrokinetic to dielectrophoretic mobility) has been used to characterize features of insulin vesicle distribution patterns. We observed a significant difference in the distribution pattern of insulin vesicles isolated from glucose-stimulated cells relative to unstimulated cells, in accordance with functional maturation of vesicles upon glucose stimulation, and interpret this to be indicative of high-resolution separation of vesicle subpopulation. DC-iDEP provides a path for future characterization of subtle biochemical differences of organelle subpopulations within any biological system.
Distinct ribosome states trigger diverse mRNA quality control pathways
Authors: Veltri Anthony J. , D’Orazio Karole N. , Lessen Laura N. , Loll-Krippleber Raphael , Brown Grant W. , Green Rachel 
Published: December 2021

AbstractKey protein adapters couple translation to mRNA decay on specific classes of problematic mRNAs in eukaryotes. Slow decoding on non-optimal codons leads to codon-optimality-mediated decay (COMD) and prolonged arrest at stall sites leads to no-go decay (NGD). The identities of the decay factors underlying these processes and the mechanisms by which they respond to translational distress remain open areas of investigation. We use carefully-designed reporter mRNAs to perform genetic screens and functional assays inS. cerevisiae. We characterize the roles of Hel2 and Syh1 in coordinating translational repression and mRNA decay on NGD reporter mRNAs, finding that Syh1 acts as the primary link to mRNA decay in NGD. Importantly, we observe that these NGD factors are not involved in the degradation of mRNAs enriched in non-optimal codons. Further, we establish that a key factor previously implicated in COMD, Not5, contributes modestly to the degradation of an NGD-targeted mRNA. Finally, we use ribosome profiling to reveal distinct ribosomal states associated with each reporter mRNA that readily rationalize the contributions of NGD and COMD factors to degradation of these reporters. Taken together, these results provide new mechanistic insight into the role of Syh1 in NGD and define the molecular triggers that determine how distinct pathways target mRNAs for degradation in yeast.
Allosteric Regulation of Human Plastins
Authors: Schwebach Christopher L. , Kudryashova Elena , Agrawal Richa , Zheng Weili , Egelman Edward H. , Kudryashov Dmitri S. 
Published: December 2021

ABSTRACTPlastins/fimbrins are conserved actin-bundling proteins contributing to motility, cytokinesis, and other cellular processes by organizing actin assemblies of strikingly different geometries as in aligned bundles and branched networks. We propose that this unique ability stems from an allosteric communication between plastins’ two actin-binding domains (ABD1/2) engaged in a tight spatial association. We found that although ABD1 binds actin first, ABD2 can bind to actin three orders of magnitude stronger if not inhibited by an equally strong allosteric engagement with ABD1. Binding of ABD1 to actin lessened the inhibition, enabling weak bundling within aligned bundles. A mutation mimicking physiologically relevant phosphorylation at the ABD1-ABD2 interface strongly reduced their association, dramatically potentiating actin cross-linking. Cryo-EM reconstruction revealed the ABD1-actin interface and enabled modeling of the plastin bridge to confirm domain separation in parallel bundles. The characteristic domain organization with a strong allosteric inhibition imposed by ABD1 on ABD2 allows plastins to tune cross-linking, contributing to the assembly and remodeling of actin assemblies with different morphological and functional properties defining the unique place of plastins in actin organization.
Ikaros family proteins regulate developmental windows in the mouse retina through convergent and divergent transcriptional programs
Authors: Javed Awais , Mattar Pierre , Cui Allie , Cayouette Michel 
Published: December 2021

ABSTRACTTemporal identity factors regulate the competence of neural progenitors to generate specific cell types in a time-dependent manner, but how they operate remains poorly defined. In the developing mouse retina, the Ikaros zinc finger transcription factor Ikzf1 regulates the production of early-born cell types, except cone photoreceptors. In this study we show that Ikzf4, another Ikaros family protein, cooperates with Ikzf1 to control cone photoreceptor production during early stages of retinal development, whereas at late stages, when Ikzf1 is no longer expressed in progenitors, Ikzf4 is instead required for Müller glia production. Using CUT&RUN sequencing, we find that both Ikzf1 and Ikzf4 generally bind to the same genes involved in cone development and other early-born fates, but at different cis-regulatory elements. In late-stage progenitors, Ikzf4 re-localizes to bind target genes involved in Müller glia development and regulate their expression. Specifically, we show that Ikzf4 maintains Hes1 expression in differentiating cells using two Ikzf GGAA binding sites at the Hes1 promoter, thereby favouring Müller glia fate commitment. These results uncover a combinatorial role for Ikaros family members in nervous system development and provide mechanistic insights on how they temporally regulate cell fate output.