bluuebunny/crossref_metadata_2025_split huggingface dataset:
Hyperactivation of L-lactate oxidase by liquid-liquid phase separation
Authors: Ura Tomoto , Kagawa Ako , Yagi Hiromasa , Tochio Naoya , Kigawa Takanori , Mikawa Tsutomu , Shiraki Kentaro 
Published: December 2020

ABSTRACTLiquid droplets formed by liquid-liquid phase separation are attracting attention as functional states of proteins in living cells. Liquid droplets are thought to activate enzymatic reactions by assembling the required molecules. Thus, liquid droplets usually increase the affinity of an enzyme to its substrates, leading to decreasedKMvalues. In this study, we demonstrate a new mechanism of enzyme activation in the droplets using Llactate oxidase (LOX). In the presence of poly-L-lysine (PLL), LOX formed droplets with diameters of hundreds of nanometers to tens of micrometers, stabilized by electro-static interaction. The enzyme activity of LOX in the droplets was significantly enhanced by a fourfold decrease inKMand a tenfold increase inkcat. To our knowledge, this represents the first report for increasingkcatby the formation of the liquid droplet. Interestingly, the conformation of LOX changed in the liquid droplet, probably leading to increasedkcatvalue. Understanding enzyme activation in the droplets provides essential information about enzyme function in living cells in addition to biotechnology applications.
A molecular mechanism for the generation of ligand-dependent differential outputs by the epidermal growth factor receptor
Authors: Huang Yongjian , Ognjenović Jana , Karandur Deepti , Miller Kate , Merk Alan , Subramaniam Sriram , Kuriyan John 
Published: December 2020

AbstractThe epidermal growth factor receptor (EGFR) is a receptor tyrosine kinase that couples the binding of extracellular ligands, such as EGF and transforming growth factor-α(TGF-α), to the initiation of intracellular signaling pathways. EGFR binds to EGF and TGF-αwith similar affinity but generates different signals from these ligands. To address the mechanistic basis of this phenomenon, we have carried out cryo-EM analyses of human EGFR bound to EGF and TGF-α. We show that the extracellular module adopts an ensemble of dimeric conformations when bound to either EGF or TGF-α. The two extreme states of this ensemble represent distinct ligand-bound quaternary structures in which the membrane-proximal tips of the extracellular module are either juxtaposed or separated. EGF and TGF-αdiffer in their ability to maintain the conformation with the membrane-proximal tips of the extracellular module separated, and this conformation is stabilized preferentially by an oncogenic EGFR mutation. Close proximity of the transmembrane helices at the junction with the extracellular module has been associated previously with increased EGFR activity. Our results show how EGFR can couple the binding of different ligands to differential modulation of this proximity, thereby suggesting a molecular mechanism for the generation of ligand-sensitive differential outputs in this receptor family.
microRNAs slow translating ribosomes to prevent protein misfolding
Authors: Sako Hiroaki , Akimoto Takayuki , Suzuki Katsuhiko , Ushida Takashi , Yamamoto Tadashi 
Published: December 2020

AbstractAn evolutionarily conserved mechanism, use of non-optimal codons, slows ribosomes during translation to allow proper folding of nascent polypeptides. However, until now, it was unknown whether any eukaryote-specific mechanisms exist for this purpose. Here, we propose that miRNAs slow translating ribosomes to prevent protein misfolding, with little negative effect on protein abundance. To prove this, we bioinformatically analyze ribosome profiling and miRNA binding sites and biochemically confirm that miRNA deficiency causes severe misfolding, which is rescued by slowing translating ribosomes. We demonstrate that non-cleaving shRNAs, targeting regions where elongation rates become faster in miRNA-deficient cells, improve protein folding with minimal effects on protein abundance. These results reveal broader functionality of miRNAs and a previously unknown mechanism to prevent protein misfolding.One Sentence SummaryEukaryote use of miRNAs prevents protein misfolding in a target-specific manner.
Spatial rearrangement of theStreptomyces venezuelaelinear chromosome during sporogenic development
Authors: Szafran MJ. , Małecki T. , Strzałka A. , Pawlikiewicz K. , Duława J. , Zarek A. , Kois-Ostrowska A. , Findlay K. , Le TBK. , Jakimowicz D. 
Published: December 2020

ABSTRACTDepending on the species, bacteria organize their chromosomes with either spatially separated or closely juxtaposed replichores. However, in contrast to eukaryotes, significant changes in bacterial chromosome conformation during the cell cycle have not been demonstrated to date.Streptomycesare unique among bacteria due to their linear chromosomes and complex life cycle. These bacteria develop multigenomic hyphae that differentiate into chains of unigenomic exospores. Only during sporulation-associated cell division, chromosomes are segregated and compacted. In this study, we show that at entry to sporulation, arms ofS. venezuelaechromosomes are spatially separated, but they are closely aligned within the core region during sporogenic cell division. Arm juxtaposition is imposed by the segregation protein ParB and condensin SMC. Moreover, we disclose that the chromosomal terminal regions are organized into domains by theStreptomyces-specific protein - HupS. Thus, we demonstrate chromosomal rearrangement from open to close conformation duringStreptomyceslife cycle.
MBGC: Multiple Bacteria Genome Compressor
Authors: Grabowski Szymon , Kowalski Tomasz M. 
Published: December 2020

AbstractSummaryGenomes within the same species reveal large similarity, exploited by specialized multiple genome compressors. The existing algorithms and tools are however targeted at large, e.g., mammalian, genomes, and their performance on bacteria strains is mediocre. In this work, we propose MBGC, a specialized genome compressor making use of specific redundancy of bacterial genomes. Our tool is not only compression efficient, but also fast. On a collection of 168,311 bacterial genomes, totalling 587 GB, we achieve the compression ratio around the factor of 730, and the compression (resp. decompression) speed around 1070 MB/s (resp. 740 MB/s) using 8 hardware threads, on a computer with a 6-core / 12-thread CPU and a fast SSD, being about 4 times more succinct and more than an order of magnitude faster in the compression than our main competitors.Availability and implementationMBGC is freely available at github.com/kowallus/mbgc.
Prediction of Eye, Hair and Skin Color in Admixed Populations of Latin America
Authors: Palmal Sagnik , Adhikari Kaustubh , Mendoza-Revilla Javier , Fuentes-Guajardo Macarena , de Cerqueira Caio C. Silva , Chacón-Duque Juan Camilo , Sohail Anood , Hurtado Malena , Villegas Valeria , Granja Vanessa , Jaramillo Claudia , Arias William , Lozano Rodrigo Barquera , Everardo-Martínez Paola , Gómez-Valdés Jorge , Villamil-Ramírez Hugo , Hünemeier Tábita , Ramallo Virginia , Gonzalez-José Rolando , Schüler-Faccini Lavinia , Bortolini Maria-Cátira , Acuña-Alonzo Victor , Canizales-Quinteros Samuel , Gallo Carla , Poletti Giovanni , Bedoya Gabriel , Rothhammer Francisco , Balding David , Faux Pierre , Ruiz-Linares Andrés 
Published: December 2020

AbstractWe report an evaluation of prediction accuracy for eye, hair and skin pigmentation based on genomic and phenotypic data for over 6,500 admixed Latin Americans (the CANDELA dataset). We examined the impact on prediction accuracy of three main factors: (i) The methods of prediction, including classical statistical methods and machine learning approaches, (ii) The inclusion of non-genetic predictors, continental genetic ancestry and pigmentation SNPs in the prediction models, and (iii) Compared two sets of pigmentation SNPs: the commonly-used HIrisPlex-S set (developed in Europeans) and novel SNP sets we defined here based on genome-wide association results in the CANDELA sample. We find that Random Forest or regression are globally the best performing methods. Although continental genetic ancestry has substantial power for prediction of pigmentation in Latin Americans, the inclusion of pigmentation SNPs increases prediction accuracy considerably, particularly for skin color. For hair and eye color, HIrisPlex-S has a similar performance to the CANDELA-specific prediction SNP sets. However, for skin pigmentation the performance of HIrisPlex-S is markedly lower than the SNP set defined here, including predictions in an independent dataset of Native American data. These results reflect the relatively high variation in hair and eye color among Europeans for whom HIrisPlex-S was developed, whereas their variation in skin pigmentation is comparatively lower. Furthermore, we show that the dataset used in the training of prediction models strongly impacts on the portability of these models across Europeans and Native Americans.
Dynamics of the compartmentalizedStreptomyceschromosome during metabolic differentiation
Authors: Lioy Virginia , Lorenzi Jean-Noël , Najah Soumaya , Poinsignon Thibault , Leh Hervé , Saulnier Corinne , Aigle Bertrand , Lautru Sylvie , Thibessard Annabelle , Lespinet Olivier , Leblond Pierre , Jaszczyszyn Yan , Gorrichon Kevin , Varoquaux Nelle , Junier Ivan , Boccard Frédéric , Pernodet Jean-Luc , Bury-Moné Stéphanie 
Published: December 2020

AbstractStreptomycesare among the most prolific bacterial producers of specialized metabolites, including antibiotics. The linear chromosome is partitioned into a central region harboring core genes and two extremities enriched in specialized metabolite biosynthetic gene clusters (SMBGCs). The molecular mechanisms governing structure and function of these compartmentalized genomes remain mostly unknown. Here we show that in exponential phase, chromosome structure correlates with genetic compartmentalization: conserved, large and highly transcribed genes form boundaries that segment the central part of the chromosome into domains, whereas the terminal ends are transcriptionally, largely quiescent compartments with different structural features. Onset of metabolic differentiation is accompanied by remodeling of chromosome architecture from an ‘open’ to a rather ‘closed’ conformation, in which the SMBGCs are expressed forming new boundaries. Altogether, our results reveal thatS. ambofaciens’linear chromosome is partitioned into structurally distinct entities, indicating a link between chromosome folding, gene expression and genome evolution.
Skeletal muscle mitochondrial dysfunction in mice is linked to bone loss via the bone marrow immune microenvironment
Authors: Tian Jingwen , Moon Ji Sun , Nga Ha Thi , Chung Hyo Kyun , Lee Ho Yeop , Kim Jung Tae , Chang Joon Young , Kang Seul Gi , Ryu Dongryeol , Che Xiangguo , Choi Je-Yong , Tsukasaki Masayuki , Sasako Takayoshi , Lee Sang-Hee , Shong Minho , Yi Hyon-Seung 
Published: December 2020

AbstractMitochondrial oxidative phosphorylation (OxPhos) is a critical regulator of skeletal muscle mass and function. Although muscle atrophy due to mitochondrial dysfunction is closely associated with bone loss caused by reduction of mechanical loading, questions remain about the biological characteristics in the relationship between muscle and bone. Here, we have shown that muscle atrophy caused by skeletal muscle-specificCrif1knockout (MKO) modulates the bone marrow inflammatory response, leading to bone loss. Transcriptome analysis of the extensor digitorum longus revealed that local mitochondrial stress increased serum levels of fibroblast growth factor 21 (FGF21) in mice. However, we have shown byFgf21knockout in MKO mice that FGF21 is dispensable for muscle atrophy-mediated bone loss. RNA sequencing in MKO mice indicated that mitochondrial stress response in skeletal muscles induces an inflammatory response and adipogenesis in the bone marrow. We also found, using transcriptomic analysis of bone marrow, that the CXCL12–CXCR4 axis is important for T-cell homing to the bone marrow, which is an immunological mediator of muscle-bone communication. CXCR4 antagonism attenuated bone marrow inflammation and bone loss in MKO mice. Together, these data highlight the role that muscle mitochondrial dysfunction plays in triggering bone marrow inflammation via the CXCL12–CXCR4 signaling axis, which is critical for inducing bone loss.
Deletion of the Clock GenePeriod2 (Per2)in Glial Cells Alters Mood-Related Behavior in Mice
Authors: Martini Tomaz , Ripperger Jürgen A. , Stalin Jimmy , Kores Andrej , Stumpe Michael , Albrecht Urs 
Published: December 2020

AbstractThe circadian clock regulates many biochemical and physiological pathways, and lack of clock genes, such asPeriod(Per) 2, do not only affect circadian activity rhythms, but can also modulate food-anticipatory and mood-related behaviors. However, it is not known how cell-type specific expression ofPer2contributes to these behaviors. In this study, we find thatPer2in glial cells is important for balancing mood-related behaviors. Genetic and adeno-associated virus-mediated deletion ofPer2in glial cells of mice leads to a depression-resistant phenotype, as manifested in reduced despair and anxiety. This is paralleled by an increase of theGABA transporter 3(Gat3) mRNA and a reduction of glutamate levels in the nucleus accumbens (NAc). Exclusive deletion ofPer2in glia of the NAc reduced despair, but had no influence on anxiety. Our data provide strong evidence for an important role of glialPer2in regulating mood-related behavior.
Notch signaling is a critical initiator of roof plate formation as revealed by the use of RNA profiling of the dorsal neural tube
Authors: Ofek Shai , Wiszniak Sophie , Kagan Sarah , Tondl Markus , Schwarz Quenten , Kalcheim Chaya 
Published: December 2020

AbstractThe factors underlying establishment of the definitive roof plate (RP) and its segregation from neural crest (NC) and interneurons are unknown. We performed transcriptome analysis at trunk levels of quail embryos comparing the dorsal neural tube at premigratory NC and RP stages. This unraveled molecular heterogeneity between NC and RP stages, and within the RP itself. By implementing these genes, we asked whether Notch signaling is involved in RP development. First, we observed that Notch is active at the RP-interneuron interface. Furthermore, gain and loss of Notch function in quail and mouse embryos, respectively, revealed no effect on early NC behavior. Constitutive Notch activation caused a local downregulation of RP markers with a concomitant development of dI1 interneurons, as well as an ectopic upregulation of RP markers in the interneuron domain. Reciprocally, in mice lacking Notch activity both the RP and dI1 interneurons failed to form and this was associated with expansion of the dI2 population. Collectively, our results offer a new resource for defining specific cell types, and provide evidence that Notch is required to establish the definitive RP, and to determine the choice between RP and interneuron fates, but not the segregation of RP from NC.Summary statementA new set of genes involved in Notch-dependent roof plate formation is unraveled by transcriptome analysis.
Ovarian carcinoma immunoreactive antigen-like protein 2 (OCIAD2) is a novel metazoan specific complex III assembly factor
Authors: Chojnacka Katarzyna Justyna , Mohanraj Karthik , Callegari Sylvie , Marins Mussulini Ben Hur , Elanchelyan Praveenraj , Gosk Aleksandra , Banach Tomasz , Góral Tomasz , Rehling Peter , Serwa Remigiusz Adam , Chacińska Agnieszka 
Published: December 2020

ABSTRACTAssembly of the dimeric complex III (CIII2) in the mitochondrial inner membrane is an intricate process in which many factors are involved. Despite many studies this process is yet to be completely understood. Here we report the identification of human OCIAD2 (Ovarian Carcinoma Immunoreactive Antigen domain containing protein 2) protein as an assembly factor for CIII2. OCIAD2 was found deregulated in several carcinomas and in some neurodegenerative disorders; however its non-pathological role was not elucidated to date. We have shown that OCIAD2 localizes to mitochondria and interacts with electron transport chain (ETC) proteins. Complete loss of OCIAD2 using gene editing in HEK293 cells resulted in abnormal mitochondrial morphology, decrease assembly of both CIII2and supercomplex III2+IV and decreased activities of complex I and III. Identification of OCIAD2 as a protein required for assembly of functional CIII2provides a new insight into the biogenesis and architecture of the ETC. Elucidating the mechanism of OCIAD2 action is important both for the understanding of cellular metabolism and for understanding of its role in the malignant transformation.
Genome-wide CRISPR and small-molecule screens uncover targetable dependencies in ATRT
Authors: Merk Daniel J. , Hirsch Sophie , Tsiami Foteini , Walter Bianca , Haeusser Lara A. , Babaei Sepideh , Admar Jakob , Casadei Nicolas , Roggia Cristiana , Spohn Michael , Schittenhelm Jens , Singer Stephan , Schüller Ulrich , Piccioni Federica , Persky Nicole S. , Root David E. , Claassen Manfred , Tatagiba Marcos , Tabatabai Ghazaleh 
Published: December 2020

SummaryAtypical teratoid rhabdoid tumors (ATRT) are incurable high-grade pediatric brain tumors. Concepts for molecular-driven therapies in ATRTs lag behind, mainly due to the absence of actionable genetic alterations. We performed genome-wide CRISPR/Cas9 knockout screens in six human ATRT cell lines and identified a total of 671 context-specific essential genes. Based on these genetic dependencies, we constructed a library of small-molecule inhibitors that we found to preferentially inhibit growth of ATRT cells. CDK4/6 inhibitors, among the most potent drugs in our library, are capable of inhibiting tumor growth due to mutual exclusive dependency of ATRTs onCDK4orCDK6. These distinct dependencies drive heterogeneity in response to CDK4/6 inhibitors in ATRTs. Our approach might serve as a blueprint for fostering the identification of functionally-instructed therapeutic strategies in other incurable diseases beyond ATRT, whose genomic profiles also lack actionable alterations so far.
An Rshiny app for modelling environmental DNA data: accounting for false positive and false negative observation error
Authors: Diana Alex , Matechou Eleni , Griffin Jim E. , Buxton Andrew S. , Griffiths Richard A. 
Published: December 2020

AbstractEnvironmental DNA (eDNA) surveys have become a popular tool for assessing the distribution of species. However, it is known that false positive and false negative observation error can occur at both stages of eDNA surveys, namely the field sampling stage and laboratory analysis stage.We present an RShiny app that implements the Griffin et al. (2019) statistical method, which accounts for false positive and false negative errors in both stages of eDNA surveys. Following Griffin et al. (2019), we employ a Bayesian approach and perform efficient Bayesian variable selection to identify important predictors for the probability of species presence as well as the probabilities of observation error at either stage.We demonstrate the RShiny app using a data set on great crested newts collected by Natural England in 2018 and we identify water quality, pond area, fish presence, macrophyte cover, frequency of drying as important predictors for species presence at a site.The state-of-the-art statistical method that we have implemented is the only one that has specifically been developed for the purposes of modelling false negatives and false positives in eDNA data. Our RShiny app is user-friendly, requires no prior knowledge of R and fits the models very efficiently. Therefore, it should be part of the tool-kit of any researcher or practitioner who is collecting or analysing eDNA data.
In vitroevaluation of antifungal activity ofAgeratum conyzoides,Basella albaandMitracarpus villosuson the strain ofLasiodiplodia theobromaein the Kisangani Region / D R Congo
Authors: Kwembe J.T.K. , Asumani M.K. , Onautshu O. , Mpiana P.T. , Haesaert G. 
Published: December 2020

ABSTRACTFollowing our previous investigations relating to the in vitro evaluation of antifungal activity, this study focused on the demonstration of the inhibitory power of extracts of fresh and dry leaves of Ageratum conyzoides, Basella alba and Mitracarpus villosus on the strain of Lasiodiplodia theobromae, fungus responsible for brown rot of cocoa pod in the Kisangani region. In six repetitions on the Patato dextrose agar medium, the strain of L. theobromae was inhibited up to 68.1% by the aqueous extract of B. alba; 60.0% by the ethanolic extract of A. conyzoides and 55.2% by the ethanolic extract of M. villosus (all obtained from dry leaves). Only the fresh leaves of the aqueous (56.7%) and ethereal (51.1%) extracts of A. conyzoides showed high inhibition percentages compared to those of the extracts of the fresh leaves of B. alba and M. villosus. The extracts of the dry leaves showed high inhibition percentages followed by those of the fresh leaves and finally those of crude extracts after two days of incubation. Thus, in addition to the expected results, the plants studied are all active. These inhibitory powers could be very high for the secondary metabolites of the respective plants.
The role of mechanical interactions in EMT
Authors: Murphy Ryan J. , Buenzli Pascal R. , Tambyah Tamara A. , Thompson Erik W. , Hugo Honor J. , Baker Ruth E. , Simpson Matthew J. 
Published: December 2020

AbstractThe detachment of cells from the boundary of an epithelial tissue and the subsequent invasion of these cells into surrounding tissues is important for cancer development and wound healing, and is strongly associated with the epithelial-mesenchymal transition (EMT). Chemical signals, such as TGF-β, produced by surrounding tissue can be up-taken by cells and induce EMT. In this work, we present a novel cell-based discrete mathematical model of mechanical cellular relaxation, cell proliferation, and cell detachment driven by chemically-dependent EMT in an epithelial tissue. A continuum description of the model is then derived in the form of a novel nonlinear free boundary problem. Using the discrete and continuum models we explore how the coupling of chemical transport and mechanical interactions influences EMT, and postulate how this could be used to help control EMT in pathological situations.
Coiled-coil heterodimers with increased stability for cellular regulation and sensing SARS-CoV-2 spike protein-mediated cell fusion
Authors: Plaper Tjaša , Aupič Jana , Dekleva Petra , Lapenta Fabio , Manček Keber Mateja , Jerala Roman , Benčina Mojca 
Published: December 2020

AbstractCoiled-coil (CC) dimer-forming peptides are attractive designable modules for mediating protein association. Highly stable CCs are desired for biological activity regulation and assay. Here, we report the design and versatile applications of orthogonal CC dimer-forming peptides with a dissociation constant in the low nanomolar range.In vitrostability and specificity was confirmed in mammalian cells by enzyme reconstitution, transcriptional activation using a combination of DNA-binding and a transcriptional activation domain, and cellular-enzyme-activity regulation based on externally-added peptides. In addition to cellular regulation, coiled-coil-mediated reporter reconstitution was used for the detection of cell fusion mediated by the interaction between the spike protein of pandemic SARS-CoV2 and the ACE2 receptor. This assay can be used to investigate the mechanism and screen inhibition of viral spike protein-mediated fusion under the biosafety level 1conditions.