bluuebunny/crossref_metadata_2025_split huggingface dataset:
PDX models reflect the proteome landscape of pediatric acute lymphoblastic leukemia but divert in select pathways
Authors: Uzozie Anuli C. , Ergin Enes K. , Rolf Nina , Tsui Janice , Lorentzian Amanda , Weng Samuel S. , Nierves Lorenz , Smith Theodore G. , Lim C. James , Maxwell Christopher A. , Reid Gregor S.D. , Lange Philipp F. 
Published: December 2019

AbstractMurine xenografts of pediatric leukemia are known to accurately recapitulate genomic aberrations. How this translates to the functional capacity of the proteome is unknown. Here, we studied global protein abundance, phosphorylation, and proteolytic processing in 11 pediatric B- and T-cell acute lymphoblastic leukemia patients and 19 corresponding xenografts. Protein level differences that stratified pediatric disease subtypes at diagnostic and relapse stages were largely recapitulated in xenograft models. Patient xenografts lacked multiple human leukocyte antigens, and complement proteins, and presented incomplete response mechanisms to the host immune system which is absent in the murine model. The dominant expression of MKI67 and cell cycle proteins indicated a high proliferative capacity of xenografted cells residing in the spleen. Structural genomic changes and mutations found in patients were reflected at the protein level. The post-translational modification landscape is shaped by leukemia type and host and only to a limited degree by the patient of origin. This study portrays how genomic and host factors shape protein and post-translational modification landscapes differently, and confirms murine patient-derived xenograft as competent model system while highlighting important areas of diverging biology.
Theory of transcription bursting: Stochasticity in the transcription rates
Authors: Murugan Rajamanickam 
Published: December 2019

ABSTRACTTranscription bursting creates variation among the individuals of a given population. Bursting emerges as the consequence of turning on and off the transcription process randomly. There are at least three sub-processes involved in the bursting phenomenon with different timescale regimes viz. flipping across the on-off state channels, microscopic transcription elongation events and the mesoscopic transcription dynamics along with the mRNA recycling. We demonstrate that when the flipping dynamics is coupled with the microscopic elongation events, then the distribution of the resultant transcription rates will be over-dispersed. This in turn reflects as the transcription bursting with over-dispersed non-Poisson type distribution of mRNA numbers. We further show that there exist optimum flipping rates (αC,βC) at which the stationary state Fano factor and variance associated with the mRNA numbers attain maxima. These optimum points are connected via. Hereαis the rate of flipping from the on-state to the off-state,βis the rate of flipping from the off-state to the on-state andγris the decay rate of mRNA. Whenα=β=χwith zero rate in the off-state channel, then there exist optimum flipping rates at which the non-stationary Fano factor and variance attain maxima. Here(hereis the rate of transcription purely through the on-state elongation channel) is the optimum flipping rate at which the variance of mRNA attains a maximum andχC,κ≃ 1.72/tis the optimum flipping rate at which the Fano factor attains a maximum. Close observation of the transcription mechanism reveals that the RNA polymerase performs several rounds of stall-continue type dynamics before generating a complete mRNA. Based on this observation, we model the transcription event as a stochastic trajectory of the transcription machinery across these on-off state elongation channels. Each mRNA transcript follows different trajectory. The total time taken by a given trajectory is the first passage time (FPT). Inverse of this FPT is the resultant transcription rate associated with the particular mRNA. Therefore, the time required to generate a given mRNA transcript will be a random variable. For a stall-continue type dynamics of RNA polymerase, we show that the overall average transcription rate can be expressed aswhereis the microscopic transcription elongation rate in the on-state channel andLis the length of a complete mRNA transcript andis the stationary state probability of finding the transcription machinery in the on-state.
Cryo-EM Structure of the Fork Protection Complex Bound to CMG at a Replication Fork
Authors: Baretić Domagoj , Jenkyn-Bedford Michael , Aria Valentina , Cannone Giuseppe , Skehel Mark , Yeeles Joseph T.P. 
Published: December 2019

AbstractThe eukaryotic replisome, organized around the Cdc45-MCM-GINS (CMG) helicase, orchestrates chromosome replication. Multiple factors associate directly with CMG including Ctf4 and the heterotrimeric fork protection complex (Csm3/Tof1 and Mrc1), that have important roles including aiding normal replication rates and stabilizing stalled forks. How these proteins interface with CMG to execute these functions is poorly understood. Here we present 3-3.5 Å resolution cryo-EM structures comprising CMG, Ctf4, Csm3/Tof1 and Mrc1 at a replication fork. The structures provide high-resolution views of CMG:DNA interactions, revealing the mechanism of strand separation. Furthermore, they illustrate the topology of Mrc1 in the replisome and show Csm3/Tof1 ‘grips’ duplex DNA ahead of CMG via a network of interactions that are important for efficient replication fork pausing. Our work reveals how four highly conserved replisome components collaborate with CMG to facilitate replisome progression and maintain genome stability.
Two distinct HIRA-dependent pathways handle H3.3de novodeposition and recycling during transcription
Authors: Torné Júlia , Ray-Gallet Dominique , Boyarchuk Ekaterina , Garnier Mickaël , Coulon Antoine , Orsi Guillermo A. , Almouzni Geneviève 
Published: December 2019

ABSTRACTThe packaging of DNA into nucleosomes represents a challenge for transcription. Nucleosome disruption and histone eviction enables RNA Polymerase II progression through DNA, a process that compromises chromatin integrity and the maintenance of epigenetic information. Here, we used the imaging SNAP-tag system to distinguish new and old histones and monitor chromatin re-assembly coupled to transcription in cells. First, we uncovered a loss of both old variants H3.1 and H3.3 that depends on transcriptional activity, with a major effect on H3.3. Focusing on transcriptionally active domains, we revealed a local enrichment in H3.3 with dynamics involving both new H3.3 incorporation and old H3.3 retention. Mechanistically, we demonstrate that the HIRA chaperone is critical to handle both new and old H3.3, and showed that this implicates different pathways. The de novo H3.3 deposition depends strictly on HIRA trimerization as well as its partner UBN1 while ASF1 interaction with HIRA can be bypassed. In contrast, the recycling of H3.3 requires HIRA but proceeds independently of UBN1 or HIRA trimerization and shows an absolute dependency on ASF1-HIRA interaction. Therefore, we propose a model where HIRA can coordinate these distinct pathways for old H3.3 recycling and new H3.3 deposition during transcription to fine-tune chromatin states.
Inclusion of Oxford Nanopore long reads improves all microbial and phage metagenome-assembled genomes from a complex aquifer system
Authors: Overholt Will A. , Hölzer Martin , Geesink Patricia , Diezel Celia , Marz Manja , Küsel Kirsten 
Published: December 2019

AbstractAssembling microbial and phage genomes from metagenomes is a powerful and appealing method to understand structure-function relationships in complex environments. In order to compare the recovery of genomes from microorganisms and their phages from groundwater, we generated shotgun metagenomes with Illumina sequencing accompanied by long reads derived from the Oxford Nanopore sequencing platform. Assembly and metagenome-assembled genome (MAG) metrics for both microbes and viruses were determined from Illumina-only assemblies and a hybrid assembly approach. Strikingly, the hybrid approach more than doubled the number of mid to high-quality MAGs (> 50% completion, < 10% redundancy), generated nearly four-fold more phage genomes, and improved all associated genome metrics relative to the Illumina only method. The hybrid assemblies yielded MAGs that were on average 7.8% more complete, with 133 fewer contigs and a 14 kbp greater N50. Furthermore, the longer contigs from the hybrid approach generated microbial MAGs that had a higher proportion of rRNA genes. We demonstrate this usefulness by linking microbial MAGs containing 16S rRNA genes with extensive amplicon dataset. This work provides quantitative data to inform a cost-benefit analysis on the decision to supplement shotgun metagenomic projects with long reads towards the goal of recovering genomes from environmentally abundant groups.
LYS3encodes a prolamin-box-binding transcription factor that controls embryo growth in barley and wheat
Authors: Orman-Ligeza Beata , Borrill Philippa , Chia Tansy , Chirico Marcella , Doležel Jaroslav , Drea Sinead , Karafiátová Miroslava , Schatlowski Nicole , Solomon Charles U. , Steuernagel Burkhard , Wulff Brande B. H. , Uauy Cristobal , Trafford Kay 
Published: December 2019

ABSTRACTMutations at theLYS3locus in barley have multiple effects on grain development, including an increase in embryo size and a decrease in endosperm starch content. The gene underlyingLYS3was identified by genetic mapping and mutations in this gene were identified in all four barleylys3alleles.LYS3encodes a transcription factor called Prolamin Binding Factor (PBF). Its role in controlling embryo size was confirmed using wheat TILLING mutants. To understand howPBFcontrols embryo development, we studied its spatial and temporal patterns of expression in developing grains. ThePBFgene is expressed in both the endosperm and the embryos, but the timing of expression in these organs differs.PBFexpression in wild-type embryos precedes the onset of embryo enlargement inlys3mutants, suggesting thatPBFsuppresses embryo growth. We predicted the down-stream target genes ofPBFin wheat and found them to be involved in a wide range of biological processes, including organ development and starch metabolism. Our work suggests thatPBFmay influence embryo size and endosperm starch synthesis via separate gene control networks.HIGHLIGHTSLYS3encodes a transcription factor called Prolamin Binding Factor (PBF) that is expressed in grains only.Wheat and barleyLYS3/PBFmutants have enlarged embryos suggesting that this gene suppresses embryo growth.The down-stream target genes ofPBFin wheat are predicted to be involved in a wide range of biological processes including organ development and starch metabolism.
Revealing the impact of recurrent and rare structural variants in multiple myeloma
Authors: Rustad Even H , Yellapantula Venkata D , Glodzik Dominik , Maclachlan Kylee H , Diamond Benjamin , Boyle Eileen M , Ashby Cody , Blaney Patrick , Gundem Gunes , Hultcrantz Malin , Leongamornlert Daniel , Angelopoulos Nicos , Auclair Daniel , Zhang Yanming , Dogan Ahmet , Bolli Niccolò , Papaemmanuil Elli , Anderson Kenneth C. , Moreau Philippe , Avet-Loiseau Herve , Munshi Nikhil , Keats Jonathan , Campbell Peter J , Morgan Gareth J , Landgren Ola , Maura Francesco 
Published: December 2019

SummaryThe landscape of structural variants (SVs) in multiple myeloma remains poorly understood. Here, we performed comprehensive classification and analysis of SVs in multiple myeloma, interrogating a large cohort of 762 patients with whole genome and RNA sequencing. We identified 100 SV hotspots involving 31 new candidate driver genes, including drug targets BCMA (TNFRSF17) andSLAMF7. Complex SVs, including chromothripsis and templated insertions, were present in 61 % of patients and frequently resulted in the simultaneous acquisition of multiple drivers. After accounting for all recurrent events, 63 % of SVs remained unexplained. Intriguingly, these rare SVs were associated with up to 7-fold enrichment for outlier gene expression, indicating that many rare driver SVs remain unrecognized and are likely important in the biology of individual tumors.
Relationships between community composition, productivity and invasion resistance in semi-natural bacterial microcosms
Authors: Jones Matt Lloyd , Rivett Damian W. , Pascual-García Alberto , Bell Thomas 
Published: December 2019

AbstractExperiments with artificial communities have suggested that invasion resistance in microbial communities is often a side-effect of community members’ contribution towards overall community productivity (broadly defined as cumulative cell density and/or growth rate). However, few experiments have investigated this in natural microbial communities. We conducted experimental invasions of two bacterial species (Pseudomonas fluorescensandPseudomonas putida) into laboratory microcosms inoculated with 680 different mixtures of bacteria derived from naturally-occurring microbial communities collected in the field. Using 16S amplicon sequencing to characterise microcosm starting composition, and high-throughput assays of community phenotypes including productivity and invader survival, we determined that productivity is a key predictor of invasion resistance in natural microbial communities, substantially mediating the effect of composition on invasion resistance. The results suggest that similar general principles govern invasion in artificial and natural communities, and that factors affecting resident community productivity should be a focal point for future microbial invasion experiments.
Robust detection of oncometabolic aberrations by1H-13C heteronuclear single quantum correlation in live cells and intact tumorsex-vivo
Authors: Barekatain Yasaman , Yan Victoria C , Arthur Kenisha , Ackroyd Jeffrey J. , Khadka Sunada , De Groot John , Huse Jason T. , Muller Florian L. 
Published: December 2019

AbstractExtensive efforts have been made to use non-invasive1H magnetic resonance (MR) spectroscopy to quantify metabolites that are diagnostic of specific disease states. Within the realm of precision oncology, these efforts have largely centered on quantifying 2-hydroxyglutarate (2-HG) in tumors harboring isocitrate dehydrogenase 1 (IDH1) mutations. As many metabolites have similar chemical shifts, the resulting1H spectra of intact biological material are highly convoluted, limiting the application of1H MR to high abundance metabolites. Hydrogen-Carbon Heteronuclear single quantum correlation1H-13C HSQC is routinely employed in organic synthesis to resolve complex spectra but has received limited attention for biological studies. Here, we show that1H-13C HSQC offers a dramatic improvement in sensitivity compared to one-dimensional (1D)13C NMR and dramatic signal deconvolution compared to 1D1H spectra in an intact biological setting. Using a standard NMR spectroscope without specialized signal enhancements features such as magic angle spinning, metabolite extractions or13C-isotopic enrichment, we obtain well-resolved 2D1H-13C HSQC spectra in live cancer cells, inex-vivofreshly dissected xenografted tumors and resected primary tumors. We demonstrate that this method can readily identify tumors with specific genetic-driven oncometabolite alterations such asIDHmutations with elevation of 2-HG as well asPGD-homozygously deleted tumors with elevation of gluconate. These data support the potential of1H-13C HSQC as a non-invasive diagnostic tool for metabolic precision oncology.
Ca2+ions promote fusion of Middle East Respiratory Syndrome coronavirus with host cells and increase infectivity
Authors: Straus Marco R. , Tang Tiffany , Lai Alex L. , Flegel Annkatrin , Bidon Miya , Freed Jack H. , Daniel Susan , Whittaker Gary R. 
Published: December 2019

AbstractMiddle East respiratory syndrome coronavirus (MERS-CoV) is a major emerging zoonotic infectious disease. Since its first outbreak in 2012, the virus has repeatedly transmitted from camels to humans with 2,468 confirmed cases, causing 851 deaths. To date, there are no efficacious drugs and vaccines against MERS-CoV, increasing its potential to cause a public health emergency. A critical step in the life cycle of MERS-CoV is the fusion with the host cell with its spike (S) protein as main determinant of viral entry. Proteolytic cleavage of S exposes its fusion peptide (FP), which initiates membrane fusion. Previous studies on the related severe acute respiratory syndrome coronavirus (SARS-CoV) FP have shown that calcium (Ca2+) plays an important role for fusogenic activity via a Ca2+binding pocket with conserved glutamic acid (E) and aspartic acid (D) residues. SARS-CoV and MERS-CoV FP share a high sequence homology and here, we investigated whether Ca2+is required for MERS-CoV fusion by substituting E and D residues in the MERS-CoV FP with neutrally charged alanines. Upon verifying mutant cell surface expression and proteolytic cleavage, we tested the mutants ability to mediate infection of pseudo-particles (PPs) on host cells without and with Ca2+. Our results demonstrate that intracellular Ca2+enhances MERS-CoV WT PPs infection by approximately two-fold and that E891 is a crucial residue for Ca2+interaction. Electron spin resonance revealed that this enhancement could be attributed to Ca2+increasing MERS-CoV FP fusion-relevant membrane ordering. Intriguingly, isothermal calorimetry titration showed that MERS-CoV FP binds one Ca2+, as opposed to SARS-CoV FP which binds two. Our data suggests that there are significant differences in FP-Ca2+interactions of MERS-CoV and SARS-CoV FP despite their high sequence similarity and that the number of Ca2+ions interacting with the FP has implications on the fusion dynamics of the virus.
Integrase-RNA interactions underscore the critical role of integrase in HIV-1 virion morphogenesis
Authors: Elliott Jennifer , Eschbach Jenna E. , Koneru Pratibha C. , Li Wen , Chavez Maritza Puray , Townsend Dana , Lawson Dana , Engelman Alan N. , Kvaratskhelia Mamuka , Kutluay Sebla B. 
Published: December 2019

ABSTRACTA large number of HIV-1 integrase (IN) alterations, referred to as class II substitutions, exhibit pleotropic effects during virus replication. However, the underlying mechanism for the class II phenotype is not known. Here we demonstrate that all tested class II IN substitutions compromised IN-RNA binding in virions by one of three distinct mechanisms: i) markedly reducing IN levels thus precluding formation of IN complexes with viral RNA; ii) adversely affecting functional IN multimerization and consequently impairing IN binding to viral RNA; iii) directly compromising IN-RNA interactions without substantially affecting IN levels or functional IN multimerization. Inhibition of IN-RNA interactions resulted in mislocalization of the viral ribonucleoprotein complexes outside the capsid lattice, which led to premature degradation of the viral genome and IN in target cells. Collectively, our studies uncover causal mechanisms for the class II phenotype and highlight an essential role of IN-RNA interactions for accurate virion maturation.
Testing Hormone-specific Antibody Probes for Presumptive Detection and Separation of Contributor Cell Populations in Trace DNA Mixtures
Authors: Miller Jennifer M. , Brocato Emily R. , Yadavalli Vamsi K. , Greenspoon Susan A. , Ehrhardt Christopher J. 
Published: December 2019

Abstract“Touch” or trace DNA evidence represent a significant proportion of samples analyzed by forensic science laboratories. Because these samples frequently contain multiple contributors and are often challenging to analyze due to low DNA concentrations and frequent degradation, front end techniques to simplify the mixture prior to DNA profiling could significantly impact case processing and enhance success rates. The goal of this study was to investigate whether targeting hormone molecules within the cell with antibody probes could be used to selectively label and then physically isolate contributor cell populations in trace biological samples. The separation of male and female cells into distinct fractions could reduce the complexity of the mixture prior to DNA profiling. To accomplish this, we first tested the specificity of fluorescently labelled anti-testosterone and anti-dihydrotestosterone antibody probes to epidermal cells from both male and female individuals. Results show that male and female cell populations can be effectively labeled using anti-testosterone and anti-dihydrotestosterone antibody probes and that distinct differences in binding efficiency and resulting median fluorescence of cell populations were observed between several individuals. These differences were then used to design sorting criteria for physically isolating each cell population in two-person epidermal cell mixtures using fluorescence activated cell sorting (FACS). DNA profiling of separated fractions in combination with probabilistic modeling demonstrated that some cell mixtures could be enriched for one contributor in separated cell fractions and yielded statistically more discriminating profiles compared to those generated from the original mixtures. Other mixtures tested showed less evidence of effective cell separation possibly due to a number of factors including imbalance of contributor DNA ratio, intra-sex variation of antibody binding efficiency, and contributions of extracellular or cell-free DNA in the mixture sample. Screening and separation of trace DNA samples with this approach may be presumptive and ultimately constrained by specific parameters of the original mixture, however, antibody binding optimization may mitigate some of these influences.
Phase separation-mediated formation of condensed GIT/PIX enzyme complex module for compartmentalized signaling
Authors: Zhu Jinwei , Zhou Qingqing , Xia Yitian , Lin Lin , Li Jianchao , Peng Mengjuan , Zhang Rongguang , Zhang Mingjie 
Published: December 2019

AbstractCells compartmentalize enzymes for broad physiological functions such as efficient metabolic reactions and spatiotemporally controlled signaling. A given enzyme or enzyme complex can participate in multiple cellular processes in response to different signal inputs by forming different cellular compartments. Here, we demonstrate that association of GIT1 and β-Pix, a pair of GTPase regulatory enzymes involved in diverse cellular processes, leads to autonomous condensation of the complex via phase separation without additional scaffolding molecules. The atomic structure of the GIT/PIX complex reveals the molecular basis governing the phase separation-mediated condensation of the GIT1/β-Pix complex. Importantly, the GIT1/β-Pix condensates can function as a versatile modular membrane-less organelle- like structure for distinct cellular compartmentalization by binding to upstream proteins such as Paxillin in focal adhesions, Shank3 in neuronal synapses, and Scribble in cellular junctions. Thus, phase separation-mediated formation of condensed enzyme complexes provides a powerful way of dynamically concentrating limited amounts of cooperating enzymes to specific cellular compartments for optimal signaling.