bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three PilZ domain proteins, PlpA, PixA and PixB, have distinct functions in regulation of motility and development inMyxococcus xanthus
Authors: Kuzmich Sofya , Skotnicka Dorota , Szadkowski Dobromir , Klos Philipp , Pérez-Burgos María , Schander Eugenia , Schumacher Dominik , Søgaard-Andersen Lotte 
Published: March 2021

AbstractIn bacteria, the nucleotide-based second messenger bis-(3’-5’)-cyclic dimeric GMP (c-di-GMP) binds to effectors to generate outputs in response to changes in the environment. InMyxococcus xanthus, c-di-GMP regulates type IV pili-dependent motility and the starvation-induced developmental program that results in the formation of spore-filled fruiting bodies; however, little is known about the effectors that bind c-di-GMP. Here, we systematically inactivated all 24 genes encoding PilZ domain-containing proteins, which are among the most common c-di-GMP receptors. We confirm that PlpA, a stand-alone PilZ-domain protein, is specifically important for motility and that Pkn1, which is composed of a Ser/Thr domain and a PilZ domain, is specifically important for development. Moreover, we identify two PilZ-domain proteins that have distinct functions in regulating motility and development. PixB, which is composed of two PilZ domains and an acetyltransferase domain, binds c-di-GMPin vitroand regulates type IV pili-dependent and gliding motility upstream of the Frz chemosensory system as well as development. The acetyltransferase domain is required and sufficient for function during growth while all three domains and c-di-GMP binding are essential for PixB function during development. PixA is a response regulator composed of a PilZ domain and a receiver domain, binds c-di-GMPin vitro, and regulates motility downstream of the Frz chemosensory system by setting up the polarity of the two motility systems. Our results support a model whereby the three proteins PlpA, PixA and PixB act in parallel pathways and have distinct functions to regulation of motility.Importancec-di-GMP signaling controls bacterial motility in many bacterial species by binding to downstream effector proteins. Here, we identify two PilZ domain-containing proteins inMyxococcus xanthusthat bind c-di-GMP. We show that PixB, which contains two PilZ domains and an acetyltransferase domain, acts upstream of the Frz chemosensory system to regulate motility via the acetyltransferase domain while the intact protein and c-di-GMP binding are essential for PixB to support development. By contrast, PixA acts downstream of the Frz system to regulate motility. Together with previous observations, we conclude that PilZ-domain proteins and c-di-GMP act in multiple parallel pathways to regulate motility and development inM. xanthus.
TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data
Authors: Reina Francesco , Wigg John M. A. , Dmitrieva Mariia , Lefebvre Joёl , Rittscher Jens , Eggeling Christian 
Published: March 2021

SummarySingle Particle Tracking (SPT) is one of the most widespread techniques to evaluate particle mobility in a variety of situations, such as in cellular and model membrane dynamics. The proposed TRAIT2D Python library is developed to provide object tracking, trajectory analysis and produce simulated datasets with graphical user interface. The tool allows advanced users to customise the analysis to their requirements.Availability and implementation: the software has been coded in Python, and can be accessed from:https://github.com/Eggeling-Lab-Microscope-Software/TRAIT2D, or the pypi and condaforge repositories.A comprehensive user guide is provided athttps://eggeling-lab-microscope-software.github.io/TRAIT2D/.
Ex vivomass cytometry analysis reveals a profound myeloid proinflammatory signature in psoriatic arthritis synovial fluid
Authors: Yager Nicole , Cole Suzanne , Lara Alicia Lledo , Maroof Ash , Penkava Frank , Knight Julian , Bowness Paul , Al-Mossawi Hussein 
Published: March 2021

AbstractObjectivesA number of immune populations have been implicated in psoriatic arthritis (PsA) pathogenesis. This study used mass cytometry (CyTOF) combined with transcriptomic analysis to generate a high-dimensional dataset of matched PsA synovial fluid (SF) and blood leucocytes, with the aim of identifying cytokine productionex vivoin unstimulated lymphoid and myeloid cells.MethodsFresh SF and paired blood were either fixed or incubated with protein transport inhibitors for 6 h. Samples were stained with two CyTOF panels: a phenotyping panel and an intracellular panel, including antibodies to both T cell and myeloid cell secreted proteins. Transcriptomic analysis by gene array of key expanded cell populations and single-cell RNA-seq, and ELISA and LEGENDplex analysis of PsA SF were also performed.ResultsWe observed marked changes in the myeloid compartment of PsA SF relative to blood, with expansion of intermediate monocytes, macrophages and dendritic cell populations. Classical monocytes, intermediate monocytes and macrophages spontaneously produced significant levels of the proinflammatory mediators osteopontin and CCL2 in the absence of anyin vitrostimulation. By contrast minimal spontaneous cytokine production by T cells was detected. Gene expression analysis showed the genes for osteopontin and CCL2 to be amongst those most highly upregulated by PsA monocytes/macrophages; and both proteins were elevated in PsA SF.ConclusionsUsing multiomic analyses we have generated a comprehensive cellular map of PsA SF and blood to reveal key expanded myeloid proinflammatory modules in PsA of potential pathogenic and therapeutic importance.
Long runs of homozygosity are correlated with marriage preferences across global population samples
Authors: Sahoo Samali Anova , Zaidi Arslan A. , Anagol Santosh , Mathieson Iain 
Published: March 2021

AbstractChildren of consanguineous unions carry long runs of homozygosity (ROH) in their genomes, due to their parents’ recent shared ancestry. This increases the burden of recessive disease in populations with high levels of consanguinity and has been heavily studied in some groups. However, there has been little investigation of the broader effect of consanguinity on patterns of genetic variation on a global scale. Here, we collect published genetic data and information about marriage practices from 396 worldwide populations and show that preference for cousin marriage has a detectable effect on the distribution of long ROH in these samples, increasing the expected number of ROH longer than 10Mb by a factor of 1.5 (P=2.3 × 10−4). Variation in marriage practice and consequent rates of consanguinity is therefore an important aspect of demographic history for the purposes of modeling human genetic variation. However, marriage practices explain a relatively small proportion of the variation in ROH distribution and consequently the ability to predict marriage practices from population genetic samples (for example of ancient populations) is limited.
Projecting climate-driven shifts in demersal fish habitat in Iceland’s waters
Authors: Mason Julia G. , Woods Pamela J. , Thorlacius Magnús , Guðnason Kristinn , Saba Vincent S. , Sullivan Patrick J. , Kleisner Kristin M. 
Published: March 2021

AbstractAs climate change shifts marine species distribution and abundance worldwide, projecting local changes over decadal scales may be a valuable adaptive strategy for managers and industry. In Iceland, one of the top fish-producing nations in the world, long-term monitoring enables model simulations of groundfish species habitat distribution. We used generalized additive models to characterize suitable thermal habitat for 47 fish species in Iceland’s waters. We then projected changes in thermal habitat by midcentury with an ensemble of five general circulation models from the Coupled Model Intercomparison Program 6 (CMIP6) and NOAA (CM2.6) and two scenarios (SSP 5-8.5 and SSP 2-4.5). We find a general northward shift in centroids of habitat distribution, with variable regional dynamics among species. Species thermal affinity was the most significant predictor of future habitat change, with warmer-water species more likely to see projected increases in suitable habitat. We present spatially explicit habitat change projections for commercially and culturally important species. These projections might serve as guideposts to inform long-term management decisions about regional and species-specific suitability for Iceland’s fisheries, infrastructure investment, and risk evaluation under climate change.
Diffusion barriers and adaptive carbon uptake strategies enhance the modeled performance of the algal CO2-concentrating mechanism
Authors: Fei Chenyi , Wilson Alexandra T. , Mangan Niall M. , Wingreen Ned S. , Jonikas Martin C. 
Published: March 2021

AbstractMany photosynthetic organisms enhance the performance of their CO2-fixing enzyme Rubisco by operating a CO2-concentrating mechanism (CCM). Most CCMs in eukaryotic algae supply concentrated CO2to Rubisco in an organelle called the pyrenoid. Ongoing efforts seek to engineer an algal CCM into crops that lack a CCM to increase yields. To advance our basic understanding of the algal CCM, we develop a chloroplast-scale reaction-diffusion model to analyze the efficacy and the energy efficiency of the CCM in the green algaChlamydomonas reinhardtii. We show that achieving an effective and energetically efficient CCM requires a physical barrier such as thylakoid stacks or a starch sheath to reduce CO2leakage out of the pyrenoid matrix. Our model provides insights into the relative performance of two distinct inorganic carbon uptake strategies: at air-level CO2, a CCM can operate effectively by taking up passively diffusing external CO2and catalyzing its conversion to HCO3−, which is then trapped in the chloroplast; however, at lower external CO2levels, effective CO2concentration requires active import of HCO3−. We also find that proper localization of carbonic anhydrases can reduce futile carbon cycling between CO2and HCO3−, thus enhancing CCM performance. We propose a four-step engineering path that increases predicted CO2saturation of Rubisco up to seven-fold at a theoretical cost of only 1.5 ATP per CO2fixed. Our system-level analysis establishes biophysical principles underlying the CCM that are broadly applicable to other algae and provides a framework to guide efforts to engineer an algal CCM into land plants.Significance StatementEukaryotic algae mediate approximately one-third of CO2fixation in the global carbon cycle. Many algae enhance their CO2-fixing ability by operating a CO2-concentrating mechanism (CCM). Our model of the algal CCM lays a solid biophysical groundwork for understanding its operation. The model’s consistency with experimental observations supports existing hypotheses about the operating principles of the algal CCM and the functions of its component proteins. We provide a quantitative estimate of the CCM’s energy efficiency and compare the performance of two distinct CO2assimilation strategies under varied conditions. The model offers a quantitative framework to guide the engineering of an algal CCM into land plants and supports the feasibility of this endeavor.
An in-frame deletion mutation in the degron tail of auxin co-receptorIAA2confers resistance to the herbicide 2,4-D inSisymbrium orientale
Authors: de Figueiredo Marcelo R. A. , Küpper Anita , Malone Jenna M. , Petrovic Tijana , de Figueiredo Ana Beatriz T. B. , Campagnola Grace , Peersen Olve B. , Prasad Kasavajhala V.S.K. , Patterson Eric L. , Reddy Anireddy S.N. , Kubeš Martin F. , Napier Richard , Preston Christopher , Gaines Todd A. 
Published: March 2021

ABSTRACTThe natural auxin indole-3-acetic acid (IAA) is a key regulator of many aspects of plant growth and development. Synthetic auxin herbicides mimic the effects of IAA by inducing strong auxinic signaling responses in plants. Synthetic auxins are crucial herbicides in agriculture, made more important by the recent introduction of transgenic synthetic auxin resistant soybean and cotton. Currently, 41 weed species have evolved resistance to synthetic auxin herbicides and, in all but one case, the molecular basis of these resistance mechanisms is unknown. To determine the mechanism of 2,4-D resistance in aSisymbrium orientale(Indian hedge mustard) weed population, we performed a transcriptome analysis of 2,4-D-resistant (R) and-susceptible (S) genotypes that revealed an in-frame 27-nucleotide deletion removing 9 amino acids in the degron tail (DT) of the auxin co-receptor Aux/IAA2(SoIAA2).The deletion allele co-segregated with 2,4-D resistance in recombinant inbred lines. Further, this deletion was also detected in several 2,4-D resistant field populations of this species. Arabidopsis transgenic lines expressing theSoIAA2mutant allele were resistant to 2,4-D and dicamba. The IAA2-DT deletion reduced binding to TIR1in vitrowith both natural and synthetic auxins, causing reduced association and increased dissociation rates. This novel mechanism of synthetic auxin herbicide resistance assigns a newin plantafunction to the DT region of this Aux/IAA co-receptor for its role in synthetic auxin binding kinetics and reveals a potential biotechnological approach to produce synthetic auxin resistant crops using gene editing.
Characterization of theChlamydomonas reinhardtiiphycosphere reveals conserved features of the plant microbiota
Authors: Durán Paloma , Flores-Uribe José , Wippel Kathrin , Zhang Pengfan , Guan Rui , Garrido-Oter Ruben 
Published: March 2021

AbstractMicroscopic algae release organic compounds to the region immediately surrounding their cells, known as the phycosphere, constituting a niche for colonization by heterotrophic bacteria. These bacteria take up algal photoassimilates and provide beneficial functions to their host, in a process that resembles the establishment of microbial communities associated with the roots and rhizospheres of land plants. Here, we characterize the microbiota of the model algaChlamydomonas reinhardtiiand reveal extensive taxonomic and functional overlap with the root microbiota of land plants. Reconstitution experiments using synthetic communities derived fromC. reinhardtiiandArabidopsis thalianashow that phycosphere and root bacteria assemble into taxonomically equivalent communities on either host. We show that provision of diffusible metabolites is not sufficient for phycosphere community establishment, which additionally requires physical proximity to the host. Our data suggests that the microbiota of photosynthetic organisms, including green algae and flowering plants, assembles according to core ecological principles.
Elevation of TRPV1 expression on T cells during experimental immunosuppression
Authors: Kumar P Sanjai , Mukherjee Tathagata , Khamaru Somlata , Radhakrishnan Anukrishna , Kishore Dalai Jupiter Nanda , Chawla Saurabh , Sahoo Subhransu Sekhar , Chattopadhyay Subhasis 
Published: March 2021

AbstractAn intracellular rise in calcium (Ca2+) is an essential requisite underlying T cell activation and its associated pro-inflammatory cytokine production. Transient receptor potential vanilloid channel (TRPV1) is a thermo-sensitive, polymodal gated and permeable to cations such as Ca2+. It has been reported that TRPV1 expression increases during T cell activation. However, the possible involvement of TRPV1 during immunosuppression of T cells has not been studied yet. Here, we investigated the possible role of TRPV1 in FK506 or B16F10-culture supernatant (B16F10-CS) driven experimental immunosuppression in T cells. Intriguingly, it was found that TRPV1 expression is further elevated during immunosuppression compared to ConA or TCR activated T cells. Similarly, in B16F10 tumor-bearing mice, the TRPV1 expression was upregulated in T cells as compared to control mice,in vivo. Moreover, we observed an immediate rise in intracellular Ca2+levels in FK506 and B16F10-CS treated T cells as compared to ConA or TCR treated T cells. Likewise, in B16F10 tumor-bearing mice, the basal intracellular calcium level was upregulated in T cells as compared to control mice,in vivo. To further investigate the possible mechanism of such rise in intracellular Ca2+levels, TRPV1 specific functional inhibitor, 5 -iodoresiniferatoxin (5 -IRTX) was used in calcium influx studies. It was observed that the total intracellular Ca2+levels decreased significantly in presence of 5 -IRTX for either the FK506 or B16F10-CS as well as with ConA or TCR stimulated T cells, indicating the functional role of TRPV1 channels in FK506 or B16F10-CS mediated increase in intracellular Ca2+levels. The current findings highlight an essential role of the TRPV1 channel in upregulating intracellular calcium levels during both immune-activation and immunosuppression. This study might also have broad implications in the context of other immune-suppressive diseases as well.
Reconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0
Authors: Domenzain Iván , Sánchez Benjamín , Anton Mihail , Kerkhoven Eduard J. , Millán-Oropeza Aarón , Henry Céline , Siewers Verena , Morrissey John P. , Sonnenschein Nikolaus , Nielsen Jens 
Published: March 2021

AbstractGenome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into GEMs was first enabled by the GECKO method, allowing the study of phenotypes constrained by protein limitations. Here, we upgraded the GECKO toolbox in order to enhance models with enzyme and proteomics constraints for any organism with an available GEM reconstruction. With this, enzyme-constrained models (ecModels) for the budding yeastsSaccharomyces cerevisiae, Yarrowia lipolyticaandKluyveromyces marxianuswere generated, aiming to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions revealed that upregulation and high saturation of enzymes in amino acid metabolism were found to be common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO was further developed by the implementation of an automated framework for continuous and version-controlled update of ecModels, which was validated by producing additional high-quality ecModels forEscherichia coliandHomo sapiens.These efforts aim to facilitate the utilization of ecModels in basic science, metabolic engineering and synthetic biology purposes.
Structural basis for the coiled-coil architecture of human CtIP
Authors: Morton C. R. , Rzechorzek N. J. , Maman J. D. , Kuramochi M. , Sekiguchi H. , Rambo R. , Sasaki Y. C. , Davies O. R. , Pellegrini L. 
Published: March 2021

AbstractThe DNA repair factor CtIP has a critical function in Double-Strand Break (DSB) repair by Homologous Recombination, promoting the assembly of the repair apparatus at DNA ends and participating in DNA-end resection. However, the molecular mechanisms of CtIP function in DSB repair remain unclear. Here we present an atomic model for the three-dimensional architecture of human CtIP, derived from a multi-disciplinary approach that includes X-ray crystallography, Small-angle X-ray Scattering (SAXS) and Diffracted X-ray Tracking (DXT). Our data show that CtIP adopts an extended dimer-of-dimers structure, in agreement with a role in bridging distant sites on chromosomal DNA during recombinational repair. The zinc-binding motif in CtIP’s N-terminus alters dynamically the coiled coil structure, with functional implications for the long-range interactions of CtIP with DNA. Our results provide a structural basis for the three-dimensional arrangement of chains in the CtIP tetramer, a key aspect of CtIP function in DNA DSB repair.
Multi-Species Phenotypic Screening across Disease Models of Mucolipidosis Type IV
Authors: Hadjikyriacou Andrea , Iyer Sangeetha , Mast Joshua D. , DiPrimio Nina , Concannon John , Ketterman Joshua , Sigoillot Frederic , Rodriguez Tamy P. , Sam Feba S. , Tsang Hillary , Prangley Madeleine , Bilen Julide , Murthy Kausalya , Hartl Tom A. , Antczak Christophe , Jenkins Jeremy L , Ross Nathan T. , Nyfeler Beat , Jain Rishi K. , Tallarico John A. , Perlstein Ethan O. , Canham Stephen M. 
Published: March 2021

AbstractInvertebrate model organisms (the nematodeCaenorhabditis elegansand the fruit flyDrosophila melanogaster) are valuable tools to bridge the gap between traditional in vitro discovery and preclinical animal models. Invertebrate model organisms are poised to serve as better disease models than 2D cellular monocultures for drug discovery, as well as easier and more cost-effective to scale up than 3D organoids/assembloids or co-cultures. A strength of model organisms is the opportunity to probe conserved biology such as lysosomal function and autophagy in a physiological setting. However, invertebrate models are not without pharmacokinetic and pharmacodynamic challenges, such as poor tissue penetration and confidence in a compound’s mechanism of action. To confront those challenges, we took advantage of the Novartis mechanism-of-action box (MoA Box), a compound library of well-annotated and drug-like chemical probes. Curious as to how the MoA Box, comprised of chemical probes optimized for mammalian targets, would fare in an invertebrate setting we screened the MoA Box across three different models of the lysosomal storage disease mucolipidosis Type IV (MLIV). MLIV is caused by mutations in the lysosomal transient receptor potential ion channel mucolipin-1 (TRPML1) resulting in hyper-acidic lysosomes and dysregulated autophagy. The overlap of screening hits from worm, fly, and patient fibroblast screens identified cyclin-dependent kinase (CDK) inhibition as an evolutionarily conserved disease modifier and potential drug repurposing strategy.Summary statementA trio of phenotypic screens acrossDrosophila,C. elegans,andH. sapiensmodels of mucolipidosis IV was performed and identified overlapping hits including cyclin-dependent kinase inhibitors.
A cell wall invertase controls nectar volume and sugar composition
Authors: Minami Anzu , Kang Xiaojun , Carter Clay J. 
Published: March 2021

ABSTRACTFlowering plants produce nectar to attract pollinators. The main nectar sugars are sucrose, glucose, and fructose, which can vary widely in ratio and concentration across species.Brassicaspp. produce a hexose-dominant nectar (high in the monosaccharides glucose and fructose) with very low levels of the disaccharide sucrose. Cell wall invertases (CWINVs) catalyze the irreversible hydrolysis of sucrose into glucose and fructose in the apoplast. We found thatBrCWINV4Ais highly expressed in the nectaries ofBrassica rapa. Moreover, abrcwinv4anull mutant has (1) greatly reduced cell wall invertase activity in the nectaries, and (2) produces a sucrose-rich nectar with little hexose content, but (3) with significantly less volume. These results were recapitulated via exogenous application of an invertase inhibitor to wild-type flowers. Honeybees prefer nectars with some sucrose, but wild-typeB. rapaflowers were much more heavily visited than those ofbrcwinv4a, suggesting that the potentially attractive sucrose-rich nectar ofbrcwinv4acould not compensate for its low volume. These results cumulatively indicate that BrCWINV4A is not only essential for producing a hexose-rich nectar, but also support a model of nectar secretion in which its hydrolase activity is required for maintaining a high intracellular-to-extracellular sucrose ratio that facilitates the continuous export of sucrose into the apoplast via SWEET9. Extracellular hydrolysis of each sucrose into two hexoses byBrCWINV4Aalso likely creates the osmotic potential required for nectar droplet formation. In summary, modulation of CWINV activity can at least partially account for naturally occurring differences in nectar volume and sugar composition.