bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phosphoproteomics of ATR Signaling in Prophase I of Mouse Meiosis
Authors: Sims Jennie R. , Faça Vitor M. , Pereira Catalina , Arroyo-Martinez Gerardo A. , Freire Raimundo , Cohen Paula E. , Weiss Robert S. , Smolka Marcus B. 
Published: April 2021

AbstractDuring mammalian meiosis, the ATR kinase plays crucial roles in the coordination of DNA repair, meiotic sex chromosome inactivation and checkpoint signaling. Despite the importance of ATR in meiosis, the meiotic ATR signaling network remains largely unknown. Here we defined ATR signaling during prophase I in mice. Quantitative analysis of phosphoproteomes obtained after genetic ablation of the ATR-activating 9-1-1 complex or chemical inhibition of ATR revealed over 12,000 phosphorylation sites, of which 863 phosphorylation sites were dependent on both 9-1-1 and ATR. ATR and 9-1-1-dependent signaling was enriched for S/T-Q and S/T-X-X-K motifs and included proteins involved in DNA damage signaling, DNA repair, and piRNA and mRNA metabolism. We find that ATR targets the RNA processing factors SETX and RANBP3 and regulate their localization to the sex body. Overall, our analysis establishes a comprehensive map of ATR signaling in spermatocytes and highlights potential meiotic-specific actions of ATR during prophase I.
MLL1 Methyltransferase Activity is Regulated by Distinct Nucleosome Binding Modes
Authors: Ayoub Alex , Park Sang Ho , Lee Young-Tae , Cho Uhn-Soo , Dou Yali 
Published: April 2021

AbstractHere we solve the single particle cryoEM structure for the MLL1 complex with nucleosome core particle (NCP) carrying histone H3 lysine 4 to methionine mutation. The MLL1 complex displays significant rotational dynamics on the NCP, a feature distinct from the yeast SET1 complex. We identified two major binding modes of the MLL1 complex on the NCP. Both binding modes anchor on the NCP through ASH2L, but they differ drastically with regard to where the MLL1 SET domain and RbBP5 bind. We show that one of the binding modes is catalytically inactive since disrupting interactions unique to this binding mode does not affect overall MLL1 activity in an NCP-specific manner. Interestingly, the inactive binding mode is in a configuration similar to that of the ySET1- NCP complex, which is intrinsically inactive on an unmodified NCP. The high rotational dynamics of the MLL1 complex as well as distinction between MLL and yeast SET1 complexes may reflect the necessity for loci-specific regulation of H3K4 methylation states in higher eukaryotes.
Conformational landscape of full-length Smad proteins
Authors: Gomes Tiago , Martin-Malpartida Pau , Ruiz Lidia , Aragón Eric , Cordeiro Tiago N. , Macias Maria J. 
Published: April 2021

AbstractSmad transcription factors, the main effectors of the TGFβ (transforming growth factor β) network, have been shaped along the evolution of multicellular animals to regulate essential processes. Smad proteins have a mixed architecture of globular domains and flexible linkers and adopt distinct quaternary structures depending on their activation state and cellular context. Here we studied the structures of full-length Smad4 and Smad2 proteins through an integrative approach combining small-angle X-ray scattering and detailed atomic information obtained from Nuclear Magnetic Resonance spectroscopy, X-ray and molecular dynamic simulations. Both Smad4 and Smad2 populate ensembles of expanded/compact conformations, with the MH1 and MH2 domains tethered by intrinsically disordered linkers that provide conformational freedom to the proteins. In solution, Smad4 is monomeric, whereas Smad2 coexists as monomer-dimer-trimer association states, even without activation. Smad2 dimers, which were previously overlooked, are proposed as key building blocks that define the functional quaternary structures of Smad proteins.HighlightsSolution ensembles of full-length Smad2 and Smad4 proteinsSmad4 populates dynamic extended and compact monomeric conformationsSmad2 dimers may be the intermediate state to form heterotrimers with Smad4New integrative methodological strategy for examining multi-domain and flexible proteins
Post-encoding reactivation promotes one-shot learning of episodes in humans
Authors: Wu Xiongbo , Viñals Xavier , Ben-Yakov Aya , Staresina Bernhard P. , Fuentemilla Lluís 
Published: April 2021

AbstractPrior animal and human work have shown that post-encoding reinstatement plays an important role in organizing the temporal sequence of unfolding episodes in memory. Here, we investigated whether post-encoding reinstatement serves to promote the encoding of ‘one-shot’ episodic learning beyond the temporal structure in humans. In experiment 1, participants encoded sequences of pictures depicting unique and meaningful episodic-like events. We used representational similarity analysis on scalp electroencephalography recordings during encoding and found evidence of rapid picture elicited EEG patterns reinstatement at episodic offset (around 500ms post-episode). Memory reinstatement was not observed between successive elements within an episode and the degree of memory reinstatement at episodic offset predicted later recall for that episode. In experiment 2, participants encoded a shuffled version of the picture sequences from experiment 1, rendering each episode meaningless to the participant but temporally structured as in experiment 1, and we found no evidence of memory reinstatement at episodic offset. These results suggest that post-encoding memory reinstatement is akin to the rapid formation of unique and meaningful episodes that unfold over time.
Echoes of the late Pleistocene in a novel trophic cascade between cougars and feral donkeys
Authors: Lundgren Erick J. , Ramp Daniel , Middleton Owen M. , Balisi Mairin , Ripple William J. , Hasselerharm Chris D. , Sanchez Jessica N. , Wooster Eamonn I. F. , Mills Mystyn , Wallach Arian D. 
Published: April 2021

AbstractIntroduced large herbivores have partly filled ecological gaps formed in the late Pleistocene, when many of the Earth’s megafauna were driven extinct. However, surviving predators are widely considered unable to influence introduced megafauna, leading them to exert unusually strong herbivory and disturbance-related effects. We report on a behaviorally-mediated trophic cascade between cougars (Puma concolor) and feral donkeys (Equus africanus asinus) at desert wetlands in North America. In response to predation of juveniles, donkeys shifted from nocturnal to almost exclusively diurnal, thereby avoiding peaks in cougar activity. Furthermore, donkeys reduced the time they spent at desert wetlands by 87%: from 5.5 hours a day to 0.7 hours at sites with predation. These shifts in activity were associated with increased activity and richness of other mammal species and reduced disturbance and herbivory-related effects on these ecologically-distinct wetland ecosystems, including 49% fewer trails, 35% less trampled bare ground, and 227% more canopy cover. Cougar predation on introduced donkeys rewires an ancient food web, with diverse implications for modern ecosystems.
Chemoproteomic study uncovers HemK2/KMT9 as a new target for NTMT1 bisubstrate inhibitors
Authors: Chen Dongxing , Meng Ying , Yu Dan , Noinaj Nicholas , Cheng Xiaodong , Huang Rong 
Published: April 2021

AbstractUnderstanding the selectivity of methyltransferase inhibitors is important to dissect the functions of each methyltransferase target. From this perspective, here we report a chemoproteomic study to profile the selectivity of a potent protein N-terminal methyltransferase 1 (NTMT1) bisubstrate inhibitor NAH-C3-GPKK (Ki, app= 7±1 nM) in endogenous proteomes. First, we describe the rational design, synthesis, and biochemical characterization of a new chemical probe6, a biotinylated analogue of NAH-C3-GPKK. Next, we systematically analyze protein networks that may selectively interact with the biotinylated probe6in concert with the competitor NAH-C3-GPKK. Besides NTMT1, the designated NTMT1 bisubstrate inhibitor NAH-C3-GPKK was found to also potently inhibit a methyltransferase complex HemK2-Trm112 (also known as KMT9-Trm112), highlighting the importance of systematic selectivity profiling. Furthermore, this is the first potent inhibitor for HemK2/KMT9 reported to date. Thus, our studies lay the foundation for future efforts towards the development of selective inhibitors for NTMT1 and HemK2/KMT9.TOC
Correcting artifacts in ratiometric biosensor imaging; an improved approach for dividing noisy signals
Authors: Marston Daniel J. , Slattery Scott , Hahn Klaus M. , Tsygankov Denis 
Published: April 2021

AbstractThe accuracy of biosensor ratio imaging is limited by signal/noise. Signals can be weak when biosensor concentrations must be limited to avoid cell perturbation. This can be especially problematic in imaging of low volume regions, e.g., along the cell edge. The cell edge is an important imaging target in studies of cell motility. We show how the division of fluorescence intensities with low signal-to-noise at the cell edge creates specific artifacts due to background subtraction and division by small numbers, and that simply improving the accuracy of background subtraction cannot address these issues. We propose a new approach where, rather than simply subtracting background from the numerator and denominator, we subtract a noise correction factor (NCF) from the numerator only. This NCF can be derived from the analysis of noise distribution in the background near the cell edge or from ratio measurements in the cell regions where signal-to-noise is high. We test the performance of the method first by examining two noninteracting fluorophores distributed evenly in cells. This generated a uniform ratio that could provide a ground truth. We then analyzed actual protein activities reported by a single chain biosensor for the guanine exchange factor Asef, and a dual chain biosensor for the GTPase Cdc42. The reduction of edge artifacts revealed persistent Asef activity in a narrow band (∼640 nm wide) immediately adjacent to the cell edge. For Cdc42, the NCF method revealed an artefact that would have been obscured by traditional background subtraction approaches.
Inhibition of gibberellin accumulation by water deficiency promotes fast and long-term ‘drought avoidance’ responses in tomato
Authors: Shohat Hagai , Cheriker Hadar , Vasuki Himabindu , Illouz-Eliaz Natanella , Blum Shula , Amsellem Ziva , Tarkowská Danuše , Aharoni Asaph , Eshed Yuval , Weiss David 
Published: April 2021

ABSTRACTPlants reduce transpiration to avoid dehydration during drought episodes by stomatal closure and inhibition of canopy growth. While abscisic acid (ABA) has a primary role in ‘drought avoidance’, previous studies suggest that gibberellin (GA), might also be involved. Here we show in tomato (Solanum lycopersicum) that shortage of water inhibited the expression of the GA biosynthesis genesGA20 oxidase1(GA20ox1) andGA20ox2and induced the GA-deactivating geneGA2ox7in leaves and guard cells, resulting in reduced bioactive GA levels. Drought regulation of GA metabolism was mediated by ABA-dependent and independent pathways, and by the transcription factorDEHYDRATION RESPONSIVE ELEMENT BINDING (DREB), TINY1. Mutations inGA20ox1andGA20ox2reduced water loss due to the smaller canopy area. On the other hand, loss ofGA2ox7did not affect leaf size, but attenuated stomatal response to water deficiency; during soil dehydration,ga2ox7plants closed their stomata and reduced transpiration later than WT, suggesting thatga2ox7stomata are hyposensitive to soil dehydration. Together, the results suggest that drought-induced GA deactivation in guard cells contributes to stomatal closure at the early stages of soil dehydration, whereas inhibition of GA synthesis in leaves promotes mainly the long-term reduction in canopy growth to reduce transpiration area.
Accelerated electron transfer in nanostructured electrodes improves the sensitivity of electrochemical biosensors
Authors: Fu Kaiyu , Seo Ji-Won , Kesler Vladimir , Maganzini Nicolo , Wilson Brandon D. , Eisenstein Michael , Soh H. Tom 
Published: April 2021

ABSTRACTElectrochemical biosensors hold the exciting potential to integrate molecular detection with signal processing and wireless communication in a miniaturized, low-cost system. However, as electrochemical biosensors are miniaturized to the micron scale, their detection sensitivity degrades precipitously, thereby greatly reducing their utility in the context of molecular diagnostic applications. Studies have reported that nanostructured electrodes can greatly improve electrochemical biosensor sensitivity, but the underlying mechanism remains poorly understood, thus making it difficult to fully exploit this phenomenon to improve biosensor performance. In this work, we propose and experimentally validate a novel mechanism in which electron transfer is physically accelerated within nanostructured electrodes due to reduced charge screening, resulting in enhanced sensitivity. We show that this mechanism can be exploited to achieve up to 24-fold increase in signal and nearly four-fold lower limit-of-detection relative conventional planar electrodes. This accelerated electron transfer mechanism should prove broadly applicable for improving the performance of electrochemical biosensors.
Divergent Acyl Carrier Protein Decouples Mitochondrial Fe-S Cluster Biogenesis from Fatty Acid Synthesis in Malaria Parasites
Authors: Falekun Seyi , Sepulveda Jaime , Jami-Alahmadi Yasaman , Park Hahnbeom , Wohlschlegel James A. , Sigala Paul A. 
Published: April 2021

AbstractPlasmodium falciparummalaria parasites are early-diverging eukaryotes with many unusual metabolic adaptations. Understanding these adaptations will give insight into parasite evolution and unveil new parasite-specific drug targets. Most eukaryotic cells retain a mitochondrial fatty acid synthesis (FASII) pathway whose acyl carrier protein (mACP) and 4-phosphopantetheine (Ppant) prosthetic group provide a soluble scaffold for acyl chain synthesis. In yeast and humans, mACP also functions to biochemically couple FASII activity to electron transport chain (ETC) assembly and Fe-S cluster biogenesis. In contrast to most eukaryotes, thePlasmodiummitochondrion lacks FASII enzymes yet curiously retains a divergent mACP lacking a Ppant group. We report that ligand-dependent knockdown of mACP is lethal to parasites, indicating an essential FASII-independent function. Decyl-ubiquinone rescues parasites temporarily from death, suggesting a dominant dysfunction of the mitochondrial ETC followed by broader cellular defects. Biochemical studies reveal thatPlasmodiummACP binds and stabilizes the Isd11-Nfs1 complex required for Fe-S cluster biosynthesis, despite lacking the Ppant group required for this association in other eukaryotes, and knockdown of parasite mACP causes loss of both Nfs1 and the Rieske Fe-S protein in ETC Complex III. This work reveals thatPlasmodiumparasites have evolved to decouple mitochondrial Fe-S cluster biogenesis from FASII activity, and this adaptation is a shared metabolic feature of otherApicomplexanpathogens, includingToxoplasmaandBabesia. This discovery also highlights the ancient, fundamental role of ACP in mitochondrial Fe-S cluster biogenesis and unveils an evolutionary driving force to retain this interaction with ACP independent of its eponymous function in FASII.Significance StatementPlasmodiummalaria parasites are single-celled eukaryotes that evolved unusual metabolic adaptations. Parasites require a mitochondrion for blood-stage viability, but essential functions beyond the electron transport chain are sparsely understood. Unlike yeast and human cells, thePlasmodiummitochondrion lacks fatty acid synthesis enzymes but retains a divergent acyl carrier protein (mACP) incapable of tethering acyl groups. Nevertheless, mACP is essential for parasite viability by binding and stabilizing the core mitochondrial Fe-S cluster biogenesis complex via a divergent molecular interface lacking an acyl-pantetheine group that contrasts with other eukaryotes. This discovery unveils an essential metabolic adaptation inPlasmodiumand other human parasites that decouples mitochondrial Fe-S cluster biogenesis from fatty acid synthesis and evolved at or near the emergence ofApicomplexanparasitism.
Limitations of the ABEGO representation: ambiguity between αα-corner and αα-hairpin
Authors: Sakuma Koya 
Published: April 2021

SummaryABEGO is a coarse-grained representation for polypeptide backbone dihedral angles. The Ramachandran map is divided into four segments denoted as A, B, E, and G to represent the local conformation of polypeptide chains in the character strings. Although the ABEGO representation is widely used in structural informatics and protein design, it cannot capture minor differences in backbone dihedral angles, which potentially leads to ambiguity between two structurally distinct fragments. Here, we show a nontrivial example of two local motifs that could not be distinguished by their ABEGO representations. We found that two well-known local motifs αα-hairpins and αα-corners are both represented as α-GBB-α and thus indistinguishable in the ABEGO representation, although they show distinct arrangements of the flanking α-helices. We also found that α-GBB-α motifs caused a loss of efficiency in the ABEGO-based fragment-assembly simulations for protein backbone design. Nevertheless, we designed amino-acid sequences that were predicted to fold into the target topologies that contained these α-GBB-α motifs. Our finding that certain local motifs bottleneck the ABEGO-based fragment-assembly simulations for construction of backbone structures suggests that finer representations of backbone torsion angles are required for efficiently generating diverse topologies containing such indistinguishable local motifs.
Changes in regional white matter volumetry and microstructure during the post-adolescence period: a cross-sectional study of a cohort of 1,713 university students
Authors: Tsuchida Ami , Laurent Alexandre , Crivello Fabrice , Petit Laurent , Pepe Antonietta , Beguedou Naka , Debette Stephanie , Tzourio Christophe , Mazoyer Bernard 
Published: April 2021

AbstractHuman brain white matter undergoes a protracted maturation that continues well into adulthood. Recent advances in diffusion-weighted imaging (DWI) methods allow detailed characterizations of the microstructural architecture of white matter, and they are increasingly utilised to study white matter changes during development and ageing. However, relatively little is known about the late maturational changes in the microstructural architecture of white matter during post-adolescence. Here we report on regional changes in white matter volume and microstructure in young adults undergoing university-level education. As part of the MRi-Share multi-modal brain MRI database, multi-shell, high angular resolution DWI data were acquired in a unique sample of 1,713 university students aged 18 to 26. We assessed the age and sex dependence, as well as hemispheric asymmetry of diffusion metrics derived from diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI), in the white matter regions as defined in the John Hopkins University (JHU) white matter labels atlas. We demonstrate that while regional white matter volume is relatively stable over the age range of our sample, the white matter microstructural properties show clear age-related variations. Globally, it is characterised by a robust increase in neurite density index (NDI), and to a lesser extent, orientation dispersion index (ODI). These changes are accompanied by a decrease in diffusivity. In contrast, there is minimal age-related variation in fractional anisotropy. There are regional variations in these microstructural changes: some tracts, most notably cingulum bundles, show a strong age-related increase in NDI coupled with decreases in radial and mean diffusivity, while others, mainly cortico-spinal projection tracts, primarily show an ODI increase and axial diffusivity decrease. These age-related variations are not different between males and females, but males show higher NDI and ODI and lower diffusivity than females across many tracts. We also report a robust hemispheric asymmetry in both the volume and microstructural properties in many regions. These findings emphasise the complexity of changes in white matter structure occurring in this critical period of late maturation in early adulthood.
Quantification and image-derived phenotyping of retinal ganglion cell nuclei in theneemouse model of congenital glaucoma
Authors: van der Heide Carly J. , Meyer Kacie J. , Hedberg-Buenz Adam , Pellack Danielle , Pomernackas Nicholas , Mercer Hannah E. , Anderson Michael G. 
Published: April 2021

ABSTRACTTheneemouse model exhibits characteristic features of congenital glaucoma, a common cause of childhood blindness. The current study ofneemice had two components. First, the time course of neurodegeneration inneeretinal flat-mounts was studied over time using a retinal ganglion cell (RGC)-marker, BRN3A; a pan-nuclear marker, TO-PRO-3; and H&E staining. Based on segmentation of nuclei using ImageJ and RetFM-J, this analysis identified a rapid loss of BRN3A+nuclei from 4–15 weeks of age, with the first statistically significant difference in average density compared to age-matched controls detected in 8-week-old cohorts (49% reduction innee). Consistent with a model of glaucoma, no reductions in BRN3A−nuclei were detected, but the combined analysis indicated that some RGCs lost BRN3A marker expression prior to actual cell loss. These results have a practical application in the design of experiments usingneemice to study mechanisms or potential therapies for congenital glaucoma. The second component of the study pertains to a discovery-based analysis of the large amount of image data with 748,782 segmented retinal nuclei. Using the automatedly collected region of interest feature data captured by ImageJ, we tested whether RGC density of glaucomatous mice was significantly correlated to average nuclear area, perimeter, Feret diameter, or MinFeret diameter. These results pointed to two events influencing nuclear size. For variations in RGC density above approximately 3,000 nuclei/mm2apparent spreading was observed, in which BRN3A−nuclei—regardless of genotype—became slightly larger as RGC density decreased. This same spreading occurred in BRN3A+nuclei of wild-type mice. For variation in RGC density below 3,000 nuclei/mm2, which only occurred in glaucomatousneemutants, BRN3A+nuclei became smaller as disease was progressively severe. These observations have relevance to defining RGCs of relatively higher sensitivity to glaucomatous cell death and the nuclear dynamics occurring during their demise.
The TRRAP transcription cofactor represses interferon-stimulated genes in colorectal cancer cells
Authors: Detilleux Dylane , Raynaud Peggy , Pradet-Balade Bérengère , Helmlinger Dominique 
Published: April 2021

ABSTRACTTranscription is essential for cells to respond to signaling cues and involves factors with multiple distinct activities. One such factor, TRRAP, functions as part of two large complexes, SAGA and TIP60, which have crucial roles during transcription activation. Structurally, TRRAP belongs to the PIKK family but is the only member classified as a pseudokinase. Recent studies established that a dedicated HSP90 co-chaperone, the TTT complex, is essential for PIKK stabilization and activity. Here, using endogenous auxin- inducible degron alleles, we show that the TTT subunit TELO2 promotes TRRAP assembly into SAGA and TIP60 in human colorectal cancer cells (CRC). Transcriptomic analysis revealed that TELO2 contributes to TRRAP regulatory roles in CRC cells, most notably of MYC target genes. Surprisingly, TELO2 and TRRAP depletion also induced the expression of type I interferon genes. Using a combination of nascent RNA, antibody-targeted chromatin profiling (CUT&RUN) and kinetic analyses, we show that TRRAP directly represses the expression of IRF9, which is a master regulator of interferon stimulated genes. We have therefore uncovered a new, unexpected transcriptional repressor role for TRRAP, which may contribute to its tumorigenic activity.