bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time-dependent dual effect of NLRP3 inflammasome in brain ischemia
Authors: Palomino-Antolin Alejandra , Narros-Fernández Paloma , Farré-Alins Víctor , Sevilla-Montero Javier , Decouty-Pérez Celine , Lopez-Rodriguez Ana Belen , Fernández Nuria , Monge Luis , Casas Ana I. , Calzada María José , Egea Javier 
Published: October 2020

AbstractBackground and purposePost-ischemic inflammation contributes to worsening of ischemic brain injury and in this process, the inflammasomes play a key role. Inflammasomes are cytosolic multiprotein complexes which upon assembly activate the maturation and secretion of the inflammatory cytokines IL-1β and IL-18. However, participation of the NLRP3 inflammasome in ischemic stroke remains controversial. Our aims were to determine the role of NLRP3 in ischemia and to explore the mechanism involved in the potential protective effect of the neurovascular unit.MethodsWT and NLRP3 knock-out mice were subjected to ischemia by middle cerebral artery occlusion (60 minutes) with or without treatment with MCC950 at different time points post-stroke. Brain injury was measured histologically with 2,3,5-triphenyltetrazolium chloride (TTC) staining.ResultsWe identified a time-dependent dual effect of NLRP3. While neither the pre-treatment with MCC950 nor the genetic approach (NLRP3 KO) proved to be neuroprotective, post-reperfusion treatment with MCC950 significantly reduced the infarct volume in a dose-dependent manner. Importantly, MCC950 improved the neuro-motor function and reduced the expression of different pro-inflammatory cytokines (IL-1β, TNF-α), NLRP3 inflammasome components (NLRP3, pro-caspase-1), protease expression (MMP9) and endothelial adhesion molecules (ICAM, VCAM). We observed a marked protection of the blood-brain barrier (BBB), which was also reflected in the recovery of the tight junctions proteins (ZO-1, Claudin-5). Additionally, MCC950 produced a reduction of the CCL2 chemokine in blood serum and in brain tissue, which lead to a reduction in the immune cell infiltration.ConclusionsThese findings suggest that post-reperfusion NLRP3 inhibition may be an effective acute therapy for protecting the blood-brain barrier in cerebral ischemia with potential clinical translation.
Single-cell transcriptomes of developing and adult olfactory receptor neurons inDrosophila
Authors: McLaughlin Colleen N. , Brbić Maria , Xie Qijing , Li Tongchao , Horns Felix , Kolluru Sai Saroja , Kebschull Justus M. , Vacek David , Xie Anthony , Li Jiefu , Jones Robert C. , Leskovec Jure , Quake Steven R. , Luo Liqun , Li Hongjie 
Published: October 2020

AbstractRecognition of environmental cues is essential for the survival of all organisms. Precise transcriptional changes occur to enable the generation and function of the neural circuits underlying sensory perception. To gain insight into these changes, we generated single-cell transcriptomes ofDrosophilaolfactory receptor neurons (ORNs), thermosensory and hygrosensory neurons from the third antennal segment at an early developmental and adult stage. We discovered that ORNs maintain expression of the same olfactory receptors across development. Using these receptors and computational approaches, we matched transcriptomic clusters corresponding to anatomically and physiologically defined neuronal types across multiple developmental stages. Cell-type-specific transcriptomes, in part, reflected axon trajectory choices in early development and sensory modality in adults. Our analysis also uncovered type-specific and broadly expressed genes that could modulate adult sensory responses. Collectively, our data reveal important transcriptomic features of sensory neuron biology and provides a resource for future studies of their development and physiology.
Rainbow smelt population responses to species invasions and change in environmental condition
Authors: Bruel Rosalie , Marsden J. Ellen , Pientka Bernie , Staats Nick , Mihuc Timothy , Stockwell Jason D. 
Published: October 2020

AbstractInvasive species can have major disruptions on native food webs, yet the impact of species introductions and whether they will become invasive appears to be context-dependent. Rainbow smelt and alewife co-exist as invasive species in the Laurentian Great Lakes and as native species on the Atlantic coast of North America, but in Lake Champlain rainbow smelt is the dominant native forage fish and alewife are invasive. Alewife became abundant by 2007, providing an opportunity to explore the dynamics of these two species in a system where only one is invasive. We used data from a 31-year forage fish survey to compare demographics of rainbow smelt populations in three basins of Lake Champlain with different pelagic volumes, nutrient levels, and predator abundances. Rainbow smelt catch-per-unit-effort (CPUE) remained constant in the large, deep Main Lake before and after alewife invaded, but decreased in the two smaller basins. Declines were primarily a result of increased age-0 and age-1 mortality. Predation by top piscivores, system productivity, and resource competition alone could not explain the patterns in CPUE across the basins. The mechanisms that allow alewife and rainbow smelt to co-exist could be related to system volume and oxythermal habitat availability, and may explain why the two species do not negatively affect each other in other systems. Summer hypoxia in the smaller basins could force individuals into smaller habitat volumes with higher densities of competitors and cannibalistic adult smelt. Our findings suggest that habitat size mediates the impact of invasive alewife on native rainbow smelt.
Exactp-values for global network alignments via combinatorial analysis of shared GO terms
Authors: Hayes Wayne B. 
Published: October 2020

AbstractNetwork alignment aims to uncover topologically similar regions in the protein-protein interaction (PPI) networks of two or more species under the assumption that topologically similar regions perform similar functions. Although there exist a plethora of both network alignment algorithms and measures of topological similarity, currently no “gold standard” exists for evaluating how well either is able to uncover functionally similar regions. Here we propose a formal, mathematically and statistically rigorous method for evaluating the statistical significance of shared GO terms in a global, 1-to-1 alignment between two PPI networks. We use combinatorics to precisely count the number of possible network alignments in whichkproteins share a particular GO term. When divided by the number of all possible network alignments, this provides an explicit, exactp-value for a network alignment with respect to a particular GO term.
Genome engineering ofNannochloropsiswith large deletions for constructing microalgal minigenomes
Authors: Wang Qintao , Gong Yanhai , He Yuehui , Xin Yi , Lv Nana , Du Xuefeng , Li Yun , Jeong Byeong-ryool , Xu Jian 
Published: October 2020

ABSTRACTIndustrial microalgae are promising photosynthetic cell factories, yet tools for targeted genome engineering are limited. Here for the model industrial oleaginous microalgaNannochloropsis oceanicawe established a method to precisely and serially delete large genome fragments of ~100 kb from its 30.01-Mb nuclear genome. We started by identifying the “non-essential” chromosomal regions (i.e., low-expression region or LER) based on minimal gene expression under N-replete and N-depleted conditions. The largest such LER (LER1) is ~98 kb in size, located near the telomere of the 502.09 kb-long Chromosome 30 (Chr 30). We deleted 81 kb and further distal and proximal deletions of up to 110 kb (21.9% of Chr 30) in LER1 by dual targeting the boundaries with the episome-based CRISPR/Cas9 system. The telomere-deletion mutants showed normal telomeres consisting of CCCTAA repeats, revealing telomere regeneration capability after losing distal part of Chr 30. Interestingly, the deletions caused no significant alteration in growth, lipid production or photosynthesis (transcript-abundance change for < 3% genes under N depletion). We also performed double-deletion of both LER1 and LER2 (from Chr 9) that totals ~214 kb, and phenotypes are essentially normal. Therefore, loss of the large yet “non-essential” regions does not necessarily sacrifice important traits. Such serial targeted deletions of large genomic regions have not been reported in plants or microalgae, and will accelerate crafting minimal genomes as chassis for photosynthetic production.
Unbiased identification of nanoparticle cell uptake mechanism via a genome-wide CRISPR/Cas9 knockout screen
Authors: Nostrand Eric L. Van , Barnhill Sarah A. , Shishkin Alexander A. , Nelles David A. , Byeon Eric , Nguyen Thai , Wong Yiu Chueng Eric , Gianneschi Nathan C. , Yeo Gene W. 
Published: October 2020

AbstractA major bottleneck in nanocarrier and macromolecule development for therapeutic delivery is our limited understanding of the processes involved in their uptake into target cells. This includes their active interactions with membrane transporters that co-ordinate cellular uptake and processing. Current strategies to elucidate the mechanism of uptake, such as painstaking manipulation of individual effectors with pharmacological inhibitors or specific genetic knockdowns, are limited in scope and biased towards previously studied pathways or the intuition of the investigators. Furthermore, each of these approaches present significant off-target effects, clouding the outcomes. We set out to develop and examine an unbiased whole-genome screening approach using pooled CRISPR/Cas9 libraries for its ability to provide a robust and rapid approach to identify novel effectors of material uptake. Enabling this, we developed a methodology termed fast-library of inserts (FLI)-seq for library preparation and quantitative readout of pooled screens that shows improved technical reproducibility and is easier to perform than existing methods. In this proof-of-concept study we use FLI-seq to identify a solute carrier protein family member, SLC18B1, as a transporter for polymeric micellar nanoparticles, confirming the viability for this approach to yield novel insights into uptake mechanisms.
Adsorption mechanism of bacteria onto a Na-montmorillonite surface with organic and inorganic calcium
Authors: Tang Guowang , Jia Cangqin , Wang Guihe , Yu Peizhi , Jiang Xihao 
Published: October 2020

AbstractThe adsorption of bacteria onto the Na-montmorillonite (Na-MMT) was studied as a function of time, bacterial concentration, temperature and pH with the introduction of the organic and inorganic calcium sources. The results indicated that albeit revealing the same adsorption mechanism, the organic calcium (i.e., Ca(CH3COO)2) proposed in this study is more beneficial and environmentally friendly than the inorganic calcium (i.e., CaCl2) in terms of the adsorption of bacteria onto the Na-MMT surface, which can be ascribed to the formation of the denser aggregates in the Na-MMT with Ca(CH3COO)2. Meanwhile, the adsorption kinetics and isotherms followed the pseudo-second-order kinetic model and Langmuir Equation for both two calcium sources. Meanwhile, the adsorption bands of the water molecules on the minerals were observed to shift significantly after the bacterial adsorption, showing that the hydrogen bonding on the Na-MMT surface played an important role during this process. A value of ΔH0> 0 indicated that the bacterial adsorption was affected by van der Waals force and hydrophobic interaction. Finally, the negative zeta potentials of the Na-MMT increased with the addition of Ca2+ions, and the experimental data also showed that the adsorption of bacteria onto the Na-MMT was mainly determined by the electrostatic and non-electrostatic forces.
The baculovirus promoter OpIE2 sequence has inhibitory effect on the activity of the Cytomegalovirus (CMV) promoter in HeLa and HEK-293T cells
Authors: Aladdin A , Sahly N , Faty R , Youssef MM , Salem TZ 
Published: October 2020

ABSTRACTUnderstanding how promoters work in non-host cells is complex. Nonetheless, understanding this process is crucial while performing gene expression modulation studies. In this study, inhibitory regions in the 5’ end of the OpIE2 insect viral promoter were found to be blocking the activity of the CMV promoter in mammalian cells. This finding was reached in the process of constructing a shuttle vector with CMV and OpIE2 promoters in a tandem arrangement to achieve gene expression in both mammalian and insect cells, respectively. OpIE2 promoter was cloned downstream of the CMV promoter and upstream of the EGFP reporter gene. After introducing the constructed shuttle vector to insect and mammalian cells, a significant drop in the CMV promoter activity in mammalian cells was observed. To enhance the CMV promoter activity, several modification were made to the shuttle vector including site-directed mutagenesis to remove all ATG codons from the downstream promoter (OpIE2), separating the two promoters to eliminate the effect of transcription interference between them, and finally, identifying some inhibitory regions in the OpIE2 promoter sequence. When these inhibitory regions were removed, high expression levels in insect and mammalian cells were restored. In conclusion, a shuttle vector was constructed that works efficiently in both mammalian and insect cell lines. This study showed that inserting 261 to 313 bp from the 3’ end of the OpIE2 promoter downstream of the CMV promoter maintains efficient gene expression in both Sf9 and mammalian cells.
TheDrosophilahistone demethylase KDM5 is required during early neurodevelopment for proper mushroom body formation and cognitive function
Authors: Hatch Hayden A. M. , Belalcazar Helen M. , Marshall Owen J. , Secombe Julie 
Published: October 2020

ABSTRACTMutations in the lysine demethylase 5 (KDM5) family of transcriptional regulators are associated with intellectual disability, yet little is known regarding the spatiotemporal requirements or neurodevelopmental contributions of KDM5 proteins. Utilizing the mushroom body (MB), a major learning and memory center within theDrosophilabrain, we demonstrate that KDM5 is specifically required within ganglion mother cells and immature neurons for proper neurodevelopment and cognitive function. Within this cellular subpopulation, we identify a core network of KDM5-regulated genes that are critical modulators of neurodevelopment. Significantly, we find that a majority of these genes are direct targets of Prospero (Pros), a transcription factor with well-established roles in neurodevelopment in other neuronal contexts. We demonstrate that Pros is essential for MB development and functions downstream of KDM5 to regulate MB morphology. We therefore provide evidence for a KDM5-Pros axis that orchestrates a transcriptional program critical for proper axonal development and cognitive function.
Stable Protein Sialylation in Physcomitrella
Authors: Bohlender Lennard L. , Parsons Juliana , Hoernstein Sebastian N. W. , Rempfer Christine , Ruiz-Molina Natalia , Lorenz Timo , Rodriguez-Jahnke Fernando , Figl Rudolf , Fode Benjamin , Altmann Friedrich , Reski Ralf , Decker Eva L. 
Published: October 2020

AbstractRecombinantly produced proteins are indispensable tools for medical applications. Since the majority of them are glycoproteins, theirN-glycosylation profiles are major determinants for their activity, structural properties and safety. For therapeutical applications, a glycosylation pattern adapted to product and treatment requirements is advantageous. Physcomitrella (Physcomitrium patens, moss) is able to perform highly homogeneous complex-typeN-glycosylation. Additionally, it has been glyco-engineered to eliminate plant-specific sugar residues by knock-out of the β1,2-xylosyltransferase and α1,3-fucosyltransferase genes (Δxt/ft). Furthermore,P. patensmeets wide-ranging biopharmaceutical requirements such as GMP compliance, product safety, scalability and outstanding possibilities for precise genome engineering. However, all plants, in contrast to mammals, lack the capability to performN-glycan sialylation. Since sialic acids are a common terminal modification on humanN-glycans, the property to performN-glycan sialylation is highly desired within the plant-based biopharmaceutical sector. In this study, we present the successful achievement of proteinN-glycan sialylation in stably transformedP. patens. The sialylation ability was achieved in a Δxt/ft moss line by stable expression of six mammalian coding sequences combined with targeted organelle-specific localization of the encoded enzymes responsible for synthesis, activation, transport and transfer of sialic acid. Production of free and (CMP)-activated sialic acid was proven. The glycosidic anchor for the attachment of terminal sialic acid was generated by the introduction of a chimeric human β1,4-galactosyltransferase gene under the simultaneous knock-out of the gene encoding the endogenous β1,3-galactosyltransferase. Functional complex-typeN-glycan sialylation was confirmed via mass spectrometric analysis of a stably co-expressed recombinant human protein.
Targeting host glycolysis as a strategy for antimalarial development
Authors: Jezewski Andrew J. , Lin Yu-Hsi , Reisz Julie A. , Culp-Hill Rachel , Barekatain Yasaman , Yan Victoria C. , D’Alessandro Angelo , Muller Florian L. , Odom John Audrey R. 
Published: October 2020

ABSTRACTGlycolysis controls cellular energy, redox balance, and biosynthesis. Antiglycolytic therapies are under investigation for treatment of obesity, cancer, aging, autoimmunity, and microbial diseases. Interrupting glycolysis is highly valued as a therapeutic strategy, because glycolytic disruption is generally tolerated in mammals. Unfortunately, anemia is a known dose-limiting side effect of these inhibitors and presents a major caveat to development of antiglycolytic therapies. We developed specific inhibitors of enolase – a critical enzyme in glycolysis – and validated their metabolic and cellular effects on human erythrocytes. Enolase inhibition increases erythrocyte susceptibility to oxidative damage and induces rapid and premature erythrocyte senescence, rather than direct hemolysis. We apply our model of red cell toxicity to address questions regarding erythrocyte glycolytic disruption in the context ofPlasmodium falciparummalaria pathogenesis. Our study provides a framework for understanding red blood cell homeostasis under normal and disease states and clarifies the importance of erythrocyte reductive capacity in malaria parasite growth.
HP1α is a chromatin crosslinker that controls nuclear and mitotic chromosome mechanics
Authors: Strom Amy R. , Biggs Ronald J. , Banigan Edward J. , Wang Xiaotao , Chiu Katherine , Herman Cameron , Collado Jimena , Yue Feng , Politz Joan C. Ritland , Tait Leah J. , Scalzo David , Telling Agnes , Groudine Mark , Brangwynne Clifford P. , Marko John F. , Stephens Andrew D. 
Published: October 2020

AbstractChromatin, which consists of DNA and associated proteins, contains genetic information and is a mechanical component of the nucleus. Heterochromatic histone methylation controls nucleus and chromosome stiffness, but the contribution of heterochromatin protein HP1α (CBX5) is unknown. We used a novel HP1α auxin-inducible degron human cell line to rapidly degrade HP1α. Degradation did not alter transcription, local chromatin compaction, or histone methylation, but did decrease chromatin stiffness. Single-nucleus micromanipulation reveals that HP1α is essential to chromatin-based mechanics and maintains nuclear morphology, separate from histone methylation. Further experiments with dimerization-deficient HP1αI165Eindicate that chromatin crosslinking via HP1α dimerization is critical, while polymer simulations demonstrate the importance of chromatin-chromatin crosslinkers in mechanics. In mitotic chromosomes, HP1α similarly bolsters stiffness while aiding in mitotic alignment and faithful segregation. HP1α is therefore a critical chromatin-crosslinking protein that provides mechanical strength to chromosomes and the nucleus throughout the cell cycle and supports cellular functions.
Pax7 pioneer factor action requires both paired and homeo DNA binding domains
Authors: Pelletier Audrey , Mayran Alexandre , Gouhier Arthur , Omichinski James G , Balsalobre Aurelio , Drouin Jacques 
Published: October 2020

AbstractThe pioneer transcription factor Pax7 contains two DNA binding domains (DBD), a paired and a homeo domain. Previous work on Pax7 and the related Pax3 had shown that each DBD can bind a cognate DNA sequence, thus defining two targets of binding and possibly modalities of action. Genomic targets of Pax7 pioneer action leading to chromatin opening are enriched for composite DNA target sites containing juxtaposed binding sites for both paired and homeo domains. The present work investigated the implication of both DBDs in pioneer action. We now show that the composite sequence is a higher affinity Pax7 binding site compared to either paired or homeo binding sites and that efficient binding to this site involves both DBDs. We also show that a Pax7 monomer binds composite sites and that methylation of cytosines within the binding site does not affect binding, which is consistent with pioneer action exerted at methylated DNA sites within nucleosomal heterochromatin. Finally, introduction of single amino acid mutations in either the paired or homeo domain that impair binding to cognate DNA sequences showed that both DBDs must be intact for pioneer action. In contrast, only the paired domain is required for low affinity binding of heterochromatin sites. Thus, Pax7 pioneer action on heterochromatin requires unique protein:DNA interactions that are more complex compared to its simpler DNA binding modalities at accessible enhancer target sites.Significance StatementPioneer transcription factors have the unique ability to recognize DNA target sites within closed heterochromatin and to trigger chromatin opening. Only a fraction of the heterochromatin recruitment sites of pioneers are subject to chromatin opening. The molecular basis for this selectivity is unknown and the present work addressed the importance of DNA sequence affinity for selection of sites to open. The pioneering ability of the pioneer factor Pax7 is not strictly determined by affinity or DNA sequence of binding sites, nor by number or methylation status of DNA sites. Mutation analyses showed that recruitment to heterochromatin is primarily dependent on the Pax7 paired domain whereas the ability to open chromatin requires both paired and homeo DNA binding domains.