bluuebunny/crossref_metadata_2025_split huggingface dataset:
The essentialPorphyromonas gingivalistype IX secretion system component PorZ delivers anionic-lipopolysaccharide to the PorU sortase for transpeptidase processing of cargos
Authors: Madej Mariusz , Nowakowska Zuzanna , Ksiazek Miroslaw , Lasica Anna M. , Mizgalska Danuta , Nowak Magdalena , Jacula Anna , Scavenius Carsten , Enghild Jan J. , Aduse-Opoku Joseph , Curtis Michael A. , Gomis-Rüth F. Xavier , Potempa Jan 
Published: July 2020

AbstractCargo proteins of the type IX secretion system (T9SS) in human pathogens from phylum Bacteroidetes invariably possess a conserved C-terminal domain (CTD) that functions as a signal for outer membrane (OM) translocation. InPorphyromonas gingivalis, the CTD of selected cargos is cleaved off after translocation, and anionic lipopolysaccharide (A-LPS) is attached. This transpeptidase reaction anchors secreted proteins to the OM. PorZ, a cell surface-associated protein, is an essential component of the T9SS whose function was previously unknown. We recently solved the crystal structure of PorZ, and found that it consists of two β-propeller moieties followed by a CTD. In this study, we performed structure-based modelling suggesting that PorZ is a carbohydrate-binding protein. We found that recombinant PorZ specifically binds A-LPS. Binding was blocked by monoclonal antibodies that specifically react with a phosphorylated branched mannan in the anionic polysaccharide (A-PS) component of the A-LPS, but not with the core oligosaccharide or the lipid A endotoxin. Examination of A-LPS derived from a cohort of mutants producing various truncations of A-PS confirmed that the phosphorylated branched mannan is indeed the PorZ ligand. Moreover, purified recombinant PorZ interacted with the PorU sortase in an A-LPS–dependent manner. This interaction on the cell surface is crucial for the function of the attachment complex composed of PorU, PorZ, and the integral OM β-barrel proteins PorV and PorQ, which is involved in post-translational modification and retention of T9SS cargos on the bacterial surface.Author summaryBacteria have evolved multiple systems to transport effector proteins to their surface or into the surrounding milieu. These proteins have a wide range of functions, including attachment, motility, nutrient acquisition, and toxicity in the host.Porphyromonas gingivalis, the human pathogen responsible for severe gum diseases (periodontitis), uses a recently characterized type IX secretion system (T9SS) to translocate and anchor secreted virulence effectors to the cell surface. Anchorage is facilitated by sortase, an enzyme that covalently attaches T9SS cargo proteins to a unique anionic lipopolysaccharide (A-LPS) moiety ofP. gingivalis. Here, we show that the T9SS component PorZ interacts with sortase and specifically binds A-LPS. Binding is mediated by a phosphorylated branched mannan repeat in A-LPS polysaccharide. A-LPS– bound PorZ interacts with sortase with significantly greater affinity, facilitating modification of cargo proteins by the cell-surface attachment complex of the T9SS.
Macroscopic digestive anatomy of ring-tailed lemurs (Lemur catta), including a comparison of frozen and formalin-stored specimens
Authors: Clauss Marcus , Trümpler Jelscha , Ackermans Nicole L. , Kitchener Andrew C. , Hantke Georg , Stagegaard Julia , Takano Tomo , Shintaku Yuta , Matsuda Ikki 
Published: July 2020

AbstractDigestive tract measurements are often considered species-specific, but little information exists on the degree to which they change during ontogeny within species. Additionally, access to anatomical material from nondomestic species is often limited, with fixed tissues possibly representing the only available source, though the degree at which this material is representative in terms of dimensions and weight is debatable. In the present study, the macroscopic digestive tract anatomy (length of intestinal portions, and tissue weights of stomach and intestines) ofn=58 Lemur catta(from neonates to 25 years of age) was quantified, of which 27 had been stored frozen and 31 fixed in formalin. Particular attention was paid to the caecum and the possible presence of an appendix. The intraspecific allometric scaling of body mass (BM)0.46[0.40;0.51]for total intestine length and BM0.48[0.41;0.54]for small intestine length was higher than the expected geometric scaling of BM0.33, similar to literature results on interspecific scaling. This difference in scaling is usually explained by the hypothesis that the diameter of the intestinal tube cannot increase geometrically, to maintain optimal absorption. Therefore, geometric volume gain of increasing body mass is accommodated by more-than-geometric length scaling. Literature describesL. cattaas being variable with respect to the presence of an appendix. No appendix was found in specimens of the present study. The proportions of length measurements did not change markedly during ontogeny, indicating that proportions developed in the foetus are already representative for the adult animal. By contrast, width and tissue-mass scaling of the caecum indicated a disproportionate growth of this organ during ontogeny that was not reflected in its length. Compared to overall intraspecific variation, the method of storage (frozen vs. formalin) had no relevant impact on length or weight measurements.
Spelling changes and fluorescent tagging with prime editing vectors for plants
Authors: Wang Li , Kaya Hilal Betul , Zhang Ning , Rai Rhitu , Willmann Matthew R. , Carpenter Sara C. D. , Read Andrew C. , Martin Federico , Fei Zhangjun , Leach Jan E. , Martin Gregory B. , Bogdanove Adam J. 
Published: July 2020

AbstractPrime editing (PE) is a recent adaptation of the CRISPR-Cas system that uses a Cas9(H840A)-reverse transcriptase (RT) fusion and a guide RNA (pegRNA) amended with template and primer binding site (PBS) sequences to achieve RNA-templated conversion of the target DNA, allowing specified substitutions, insertions, and deletions. In the first report of PE in plants, a variety of edits in rice and wheat were described, including insertions up to 15 bp. Several studies in rice quickly followed, but none reported a larger insertion. Here, we report easy-to-use vectors for PE in dicots and monocots, their validation inNicotiana benthamiana, rice and Arabidopsis, and an insertion of 66 bp that enabled split-GFP fluorescent tagging.
Cryo-EM reveals the complex architecture of dynactin’s shoulder and pointed end
Authors: Lau Clinton K. , O’Reilly Francis J. , Santhanam Balaji , Lacey Samuel E. , Rappsilber Juri , Carter Andrew P. 
Published: July 2020

AbstractDynactin is a 1.1 MDa complex that activates the molecular motor, dynein, for ultra-processive transport along microtubules. In order to do this it forms a tripartite complex with dynein and a coiled-coil adaptor. Dynactin consists of an actin-related filament whose length is defined by its flexible shoulder domain. Despite previous cryo-EM structures, the molecular architecture of the shoulder and pointed end of the filament is still poorly understood due to the lack of high-resolution information in these regions. Here we combine multiple cryo-EM datasets and define precise masking strategies for particle signal subtraction and 3D classification. This overcomes domain flexibility and results in high resolution maps into which we can build the shoulder and pointed end. The unique architecture of the shoulder positions the four identical p50 subunits in different conformations to bind dynactin’s filament and securely houses the p150 subunit. The pointed end map allows us to build the first structure of p62, and reveals the molecular basis for cargo adaptor binding to different sites at the pointed end.
Visual Search P300 Source Analysis Based On ERP-fMRI Integration
Authors: Zhang Qiuzhu , Luo Cimei , Zhang Junjun , Jin Zhenlan , Li Ling 
Published: July 2020

ABSTRACTAttention control can be achieved in two ways, stimulus-driven bottom-up attention and goal-driven top-down attention. Different visual search tasks involve different attention control. The pop-out task requires more bottom-up attention, whereas the search task involves more top-down attention. P300 which is the positive potential generated by the brain in the latency of 300-600 ms after the stimulus, reflects the processing of cognitive process and is an important component in visual attention. The P300 source is not consistent in the previous researches, our aim therefore, is to study the source location of P300 component based on visual search attention process. Here we use pop-out and search paradigm to get the ERP data of 13 subjects and the fMRI data of 25 subjects, and analyze the source location of P300 using the ERP-fMRI integration technology with high temporal resolution and high spatial resolution. The target differs from the distractor in color and orientation in the pop-out task, whereas the target and the distractor have different orientation and the same color in the search task. ERP results indicate that pop-out induces larger P300 concentrated in the parietal lobe, whereas search induced P300 is more distributed in the frontal lobe. Further ERP and fMRI integration analyses reveal that the left angular gyrus, right postcentral gyrus of parietal lobe and the left superior frontal gyrus (medial orbital) are the source of P300. Our study suggests the contribution of the frontal and parietal lobes to the P300 component.
An in-vivo study of BOLD laminar responses as a function of echo time and static magnetic field strength
Authors: Markuerkiaga Irati , Marques José P. , Bains Lauren J. , Norris David G. 
Published: July 2020

AbstractLayer specific functional MRI requires high spatial resolution data. An approach often used for compensating for the poor signal to noise ratio (SNR) associated with small voxel sizes consists of integrating the signal from voxels at a given cortical depth over a patch of cortex. After this integration, physiological noise is expected to be the dominant noise source in the signal. In this context, the sensitivity gain in moving to higher static field strengths is expected to be lower than when thermal noise dominates. In this work, activation profiles in response to the same visual stimulus are compared at 1.5 T, 3 T and 7 T using a multi-echo, gradient echo (GE) FLASH sequence, with a 0.75 mm isotropic voxel size and the cortical integration approach. The results show that after integrating over a patch of cortex between 40 and 100 mm3(at 7 T and 1.5 T, respectively), the signal is in the physiological noise dominated regime, and that the obtained activation profiles are similar at the three different field strengths for equivalent echo times. The evolution of the resting-state signal over echo time indicates that BOLD-like noise is the dominant source of physiological noise. Consequently, the functional contrast to noise ratio is not strongly echo-time or field-strength dependent. The results show that compared to 7T, the gold standard, laminar GE-BOLD fMRI at lower field strengths is feasible at the cost of poorer spatial resolution (larger cortical integration extensions) and lower efficiency.
ESRP1-Mediated Alternative Splicing During Oocyte Development is Required for Mouse Fertility
Authors: Yu Luping , Zhang Huiru , Guan Xuebing , Qin Dongdong , Zhou Jian , Wu Xin 
Published: July 2020

AbstractAlternative splicing (AS) contributes to gene diversification in cells, but the importance of AS during germline development remains largely undefined. Here, we interrupted pre-mRNA splicing events controlled by epithelial splicing regulatory protein 1 (ESRP1) and found that it induced female infertility in mice. Germline-specific knockout ofEsrp1perturbed spindle organization, chromosome alignment, and metaphase-to-anaphase transformation in oocytes. The first polar body extrusion (PBE) was blocked during oocyte meiosis and was found to be due to abnormal activation of spindle assembly checkpoint (SAC) and insufficiency of anaphase-promoting complex/cyclosome (APC/C) inEsrp1-knockout oocytes.Esrp1-knockout in oocytes hampered follicular development and ovulation; eventually, premature ovarian failure (POF) occurred in six-month-oldEsrp1-knockout mouse. Using single-cell RNA sequencing analysis, 528 aberrant AS events of maternal mRNA transcripts were revealed and were preferentially associated with microtubule cytoskeletal organization inEsrp1-knockout oocytes. Notably, we found that loss of ESRP1 disturbed a comprehensive set of gene-splicing sites—including those withinTrb53bp1, Rac1, Bora, Kif2c, Kif23, Ndel1, Kif3a, Cenpa, andLsm14b—that ultimately caused abnormal spindle organization. Taken together, our findings provide the first report elucidating the AS program of maternal mRNA transcripts, mediated by the splicing factor, ESRP1, that is required for oocyte meiosis and female fertility in mice.
The half-life of the bone-derived hormone osteocalcin is regulated throughO-glycosylation in mice, but not in humans
Authors: Rifai Omar Al , Julien Catherine , Faubert Denis , Lira-Navarrete Erandi , Narimatsu Yoshiki , Lacombe Julie , Clausen Henrik , Ferron Mathieu 
Published: July 2020

ABSTRACTOsteocalcin (OCN) is an osteoblast-derived hormone with pleiotropic physiological functions. Like many peptide hormones, OCN is subjected to post-translational modifications (PTMs) which control its activity. Here, we uncoverO-glycosylation as a novel PTM present on mouse OCN and occurring on a single serine (S8) independently of its carboxylation and endoproteolysis, two other PTMs regulating this hormone. We also show thatO-glycosylation increases OCN half-life in plasma ex vivo and in the circulation in vivo. Remarkably, in human OCN (hOCN), the residue corresponding to S8 is a tyrosine (Y12), which is notO-glycosylated. Yet, the Y12S mutation is sufficient toO-glycosylate hOCN and to increase its half-life in plasma compared to wildtype hOCN. These findings reveal an important species difference in OCN regulation, which may explain why serum concentrations of OCN are higher in mouse than in human.The authors have nothing to disclose
Single cell characterization of a synthetic bacterial clock with a hybrid feedback loop containing dCas9-sgRNA
Authors: Henningsen John , Schwarz-Schilling Matthaeus , Leibl Andreas , Guttierez Joaquin A. M. , Sagredo Sandra , Simmel Friedrich C. 
Published: July 2020

AbstractGenetic networks that generate oscillations in gene expression activity are found in a wide range of organisms throughout all kingdoms of life. Oscillatory dynamics facilitates the temporal orchestration of metabolic and growth processes inside cells and organisms, as well as the synchronization of such processes with periodically occurring changes in the environment. Synthetic oscillator gene circuits such as the ‘repressilator’ can perform similar functions in bacteria. Until recently, such circuits were mainly based on a relatively small set of well-characterized transcriptional repressors and activators. A promising, sequence-programmable alternative for gene regulation is given by CRISPR interference (CRISPRi), which enables transcriptional repression of nearly arbitrary gene targets directed by short guide RNA molecules. In order to demonstrate the use of CRISPRi in the context of dynamic gene circuits, we here replaced one of the nodes of a repressilator circuit by the RNA-guided dCas9 protein. Using single cell experiments in microfluidic reactors we show that this system displays robust relaxation oscillations over multiple periods and over the time course of several days. Through statistical analysis of the single cell data, the potential for the circuit to act as a synthetic pacemaker for cellular processes is evaluated. The use of CRISPRi in the context of an oscillator circuit is found to have profound effects on its dynamics. Specifically, irreversible binding of dCas9-sgRNA appears to prolong the period of the oscillator. Further, we demonstrate that the oscillator affects cellular growth, leading to variations in growth rate with the oscillator’s frequency.
Keratin 17 regulates nuclear morphology and chromatin organization
Authors: Jacob Justin T. , Nair Raji R. , Poll Brian G. , Pineda Christopher M. , Hobbs Ryan P. , Matunis Michael J. , Coulombe Pierre A. 
Published: July 2020

AbstractKeratin 17 (KRT17; K17), a non-lamin intermediate filament protein, was recently found to occur in the nucleus. We report here on K17-dependent differences in nuclear morphology, chromatin organization, and cell proliferation. Human tumor keratinocyte cell lines lacking K17 exhibit flatter nuclei relative to normal. Re-expression of wildtype K17, but not a mutant form lacking an intact nuclear localization signal (NLS), rescues nuclear morphology inKRT17null cells. Analyses of primary cultures of skin keratinocytes from a mouse strain expressing K17 with a mutated NLS corroborated these findings. Proteomics screens identified K17-interacting nuclear proteins with known roles in gene expression, chromatin organization, and RNA processing. Key histone modifications and LAP2β localization within the nucleus are altered in the absence of K17, correlating with decreased cell proliferation and suppression of GLI1 target genes. Nuclear K17 thus impacts nuclear morphology with an associated impact on chromatin organization, gene expression, and proliferation in epithelial cells.SummaryKeratin 17 (K17) is one of two non-lamin intermediate filament proteins recently identified to localize to and function in the cell nucleus. K17 is here shown to regulate nuclear morphology, chromatin organization, LAP2 localization, and cell proliferation.
ShcA promotes chondrocyte hypertrophic commitment and osteoarthritis in mice through RunX2 nuclear translocation and YAP1 inactivation
Authors: Abou-Jaoude A. , Courtes M. , Badique L. , Elhaj Mahmoud D. , Abboud C. , Mlih M. , Justiniano H. , Lemle A. , Awan S. , Terrand J. , Niemeier A. , Barbero A. , Houard X. , Boucher P. , Matz RL 
Published: July 2020

AbstractChondrocyte hypertrophic differentiation, a key process in endochondral ossification (EO), is also a feature of osteoarthritis leading to articular cartilage destruction. ShcA (Src homology and Collagen A) is an adaptor protein that binds to the cytoplasmic tail of receptor tyrosine kinases. We found that deletion of ShcA in chondrocytes of mice inhibits hypertrophic differentiation, alters the EO process, and leads to dwarfism. ShcA promotes ERK1/2 activation, nuclear translocation of the master transcription factor for chondrocyte hypertrophy, RunX2, while maintaining the Runx2 inhibitor YAP1 in its cytosolic inactive form. This leads to hypertrophic commitment and expression of markers of hypertrophy, such as Collagen X. In addition, ShcA deletion in chondrocytes protects from age-related osteoarthritis development in mice. Our results reveal that ShcA integrates multiple stimuli which affect the intracellular signaling processes leading to the hypertrophic commitment of chondrocytes and osteoarthritis.
Psychosocial experiences modulate asthma-associated genes through gene-environment interactions
Authors: Resztak Justyna A. , Farrell Allison K. , Mair-Meijers Henriette E. , Alazizi Adnan , Wen Xiaoquan , Wildman Derek E. , Zilioli Samuele , Slatcher Richard B. , Pique-Regi Roger , Luca Francesca 
Published: July 2020

AbstractSocial interactions and the overall psychosocial environment have a demonstrated impact on health, particularly for people living in disadvantaged urban areas. Here we investigated the effect of psychosocial experiences on gene expression in peripheral blood immune cells of children with asthma in Metro Detroit. Using RNA-sequencing and a new machine learning approach, we identified transcriptional signatures of 20 variables including psychosocial factors, blood cell composition and asthma symptoms. Importantly, we found 174 genes associated with asthma that are regulated by psychosocial factors, and 349 significant gene-environment interactions for gene expression levels. These results demonstrate that immune gene expression mediates the link between negative psychosocial experiences and asthma risk.
Drone phenotyping and machine learning enable discovery of loci regulating daily floral opening in lettuce
Authors: Han Rongkui , Wong Andy J.Y. , Tang Zhehan , Truco Maria J. , Lavelle Dean O. , Kozik Alexander , Jin Yufang , Michelmore Richard W. 
Published: July 2020

AbstractFlower opening and closure are traits of reproductive importance in all angiosperms because they determine the success of self- and cross-pollination. The temporal nature of this phenotype rendered it a difficult target for genetic studies. Cultivated and wild lettuce,Lactuca spp., have composite inflorescences comprised of multiple florets that open only once. Different accessions were observed to flower at different times of day. An F6recombinant inbred line population (RIL) had been derived from accessions ofL. serriolaxL. sativathat originated from different environments and differed markedly for daily floral opening time. This population was used to map the genetic determinants of this trait; the floral opening time of 236 RILs was scored over a seven-hour period using time-course image series obtained by drone-based remote phenotyping on two occasions, one week apart. Floral pixels were identified from the images using a support vector machine (SVM) machine learning algorithm with an accuracy above 99%. A Bayesian inference method was developed to extract the peak floral opening time for individual genotypes from the time-stamped image data. Two independent QTLs,qDFO2.1(Daily Floral Opening2.1) andqDFO8.1, were discovered. Together, they explained more than 30% of the phenotypic variation in floral opening time. Candidate genes with non-synonymous polymorphisms in coding sequences were identified within the QTLs. This study demonstrates the power of combining remote imaging, machine learning, Bayesian statistics, and genome-wide marker data for studying the genetics of recalcitrant phenotypes such as floral opening time.One sentence summaryMachine learning and Bayesian analyses of drone-mediated remote phenotyping data revealed two genetic loci regulating differential daily flowering time in lettuce (Lactuca spp.).
An automated, high throughput methodology optimized for quantitative cell-free mitochondrial and nuclear DNA isolation from plasma
Authors: Ware Sarah A. , Desai Nikita , Lopez Mabel , Leach Daniel , Zhang Yingze , Giordano Luca , Nouraie S. Mehdi , Picard Martin , Kaufman Brett A. 
Published: July 2020

AbstractCirculating, cell-free mitochondrial DNA (ccf-mtDNA) and nuclear DNA (ccf-nDNA) are under investigation as biomarkers for various diseases. Optimal ccf-mtDNA isolation parameters, like those outlined for ccf-nDNA, have not been established. Here, we optimized a protocol for both ccf-mtDNA and ccf-nDNA recovery using a magnetic bead-based isolation process on an automated 96-well platform. Using the optimized protocol, our data show 6-fold improved yields of ccf-mtDNA when compared to the starting protocol. Digestion conditions, liquid handling characteristics, and magnetic particle processor programming all contributed to increased recovery and improved reproducibility. To our knowledge, this is the first high-throughput approach optimized for mtDNA and nDNA recovery and serves as an important starting point for clinical studies.Graphical Abstract