bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nuclear dengue virus NS5 antagonizes expression of PAF1-dependent immune response genes
Authors: Petit Marine J. , Kenaston Matthew W. , Nagainis Ariana A. , Shah Priya S. 
Published: April 2021

AbstractDengue virus (DENV) disruption of the innate immune response is critical to establish infection. DENV non-structural protein 5 (NS5) plays a central role in this disruption, such as antagonism of STAT2. We recently found that DENV serotype 2 (DENV2) NS5 interacts with Polymerase associated factor 1 complex (PAF1C). The primary members of PAF1C are PAF1, LEO1, CTR9 and CDC73. This nuclear complex is an emerging player in the immune response. It promotes the expression of many genes, including genes related to the antiviral, antimicrobial and inflammatory responses, through close association with the chromatin of these genes. Our previous work demonstrated that NS5 antagonizes PAF1C recruitment to immune response genes. However, it remains unknown if NS5 antagonism of PAF1C is complementary to its antagonism of STAT2. Here, we show that knockout of PAF1 enhances DENV2 infectious virion production. By comparing gene expression profiles in PAF1 and STAT2 knockout cells, we find that PAF1 is necessary to express immune response genes that are STAT2-independent. Finally, we mapped the viral determinants for the NS5-PAF1C protein interaction. We found that NS5 nuclear localization and the C-terminal region of the methyltransferase domain are required for its interaction with PAF1C. Mutation of these regions rescued the expression of PAF1-dependent immune response genes that are antagonized by NS5. In sum, our results support a role for PAF1C in restricting DENV2 replication that NS5 antagonizes through its protein interaction with PAF1C.Author summaryDengue virus (DENV) is a pathogen that infects nearly 400 million people a year and thus represents a major challenge for public health. Productive infection by DENV relies on the effective evasion of intrinsic antiviral defenses and is often accomplished through virus-host protein interactions. Here, we investigate the recently discovered interaction between DENV non-structural protein 5 (NS5) and the transcriptional regulator Polymerase associated factor 1 complex (PAF1C). Our work demonstrates PAF1C member PAF1 acts as an antiviral factor and inhibits DENV replication. In parallel, we identified immune response genes involved in intrinsic antiviral defense that depend on PAF1 for expression. We further identified the regions of NS5 required for the protein interaction with PAF1C. Breaking the NS5-PAF1C protein interaction restores the expression of PAF1-dependent immune response genes. Together, our work establishes the antiviral role of PAF1C in DENV infection and NS5 antagonism of PAF1-dependent gene expression through a virus-host protein interaction.
The barley mutantmultiflorus2.breveals quantitative genetic variation for new spikelet architecture
Authors: Koppolu Ravi , Jiang Guojing , Milner Sara G , Muqaddasi Quddoos H , Rutten Twan , Himmelbach Axel , Stein Nils , Mascher Martin , Schnurbusch Thorsten 
Published: April 2021

AbstractUnderstanding the genetic basis of yield forming factors in small grain cereals is of extreme importance, especially in the wake of stagnation of further yield gains in these crops. One such yield forming factor in these cereals is the number of grain-bearing florets produced per spikelet. Wildtype barley (Hordeum vulgareL.) spikelets are determinate structures, the spikelet axis (rachilla) degenerates after producing single floret. In contrast, the rachilla of wheat (Triticum ssp.) spikelets, which are indeterminate, elongates to produce up to 12 florets. In our study, we characterized the barley spikelet determinacy mutantmultiflorus2.b(mul2.b) that produced up to three fertile florets on elongated rachillae of lateral spikelets. Apart from the lateral spikelet indeterminacy (LS-IN), we also characterized the supernumerary spikelet phenotype in the central spikelets (CS-SS) ofmul2.b. Through our phenotypic and genetic analyses, we identified two major QTLs on chromosomes 2H and 6H, and two minor QTLs on 3H for the LS-IN phenotype. For, the CS-SS phenotype we identified one major QTL on 6H, and a minor QTL on 5H chromosomes. Notably, the 6H QTLs for CS-SS and LS-IN phenotypes co-located with each other, potentially indicating that a single genetic factor might regulate both phenotypes. Thus, our in-depth phenotyping combined with genetic analyses revealed the quantitative nature of the LS-IN and CS-SS phenotypes inmul2.b, paving the way for cloning the genes underlying these QTLs in the future.Key messageSpikelet indeterminacy and supernumerary spikelet phenotypes in barleymultiflorus2.bmutant show polygenic inheritance. Genetic analysis ofmultiflorus2.brevealed major QTLs for spikelet determinacy and supernumerary spikelet phenotypes on 2H and 6H chromosomes.
Target identification of drug candidates with machine-learning algorithms: how choosing negative examples for training
Authors: Najm Matthieu , Azencott Chloé-Agathe , Playe Benoit , Stoven Véronique 
Published: April 2021

Abstract(1) Background:Identification of hit molecules protein targets is essential in the drug discovery process. Target prediction with machine-learning algorithms can help accelerate this search, limiting the number of required experiments. However, Drug-Target Interactions databases used for training present high statistical bias, leading to a high number of false positive predicted targets, thus increasing time and cost of experimental validation campaigns. (2) Methods: To minimize the number of false positive predicted proteins, we propose a new scheme for choosing negative examples, so that each protein and each drug appears an equal number of times in positive and negative examples. We artificially reproduce the process of target identification for 3 particular drugs, and more globally for 200 approved drugs. (3) Results: For the detailed 3 drugs examples, and for the larger set of 200 drugs, training with the proposed scheme for the choice of negative examples improved target prediction results: the average number of false positive among the top ranked predicted targets decreased and overall the rank of the true targets was improved. (4) Conclusion: Our method enables to correct databases statistical bias and reduces the number of false positive predictions, and therefore the number of useless experiments potentially undertaken.
Comprehensive Proteomic Quantification of Bladder Stone Progression in a Cystinuric Mouse Model Using Data-Independent Acquisitions
Authors: Rose Jacob , Basisty Nathan , Zee Tiffany , Wehrfritz Cameron , Bose Neelanjan , Desprez Pierre-Yves , Kapahi Pankaj , Stoller Marshall , Schilling Birgit 
Published: April 2021

AbstractCystinuria is one of various disorders that cause biomineralization in the urinary system, including bladder stone formation in humans. It is most prevalent in children and adolescents and more aggressive in males. There is no cure, and only limited disease management techniques help to solubilize the stones. Recurrence, even after treatment, occurs frequently. Other than a buildup of cystine, little is known about factors involved in the formation, expansion, and recurrence of these stones. This study sought to define the growth of bladder stones, guided by micro-computed tomography imaging, and to profile dynamic stone proteome changes in a cystinuria mouse model. After bladder stones developed in vivo, they were harvested and separated into four developmental stages (sand, small, medium and large stone), based on their size. Data-dependent and data-independent acquisitions allowed deep profiling of stone proteomics. The proteomic signatures and pathways illustrated major changes as the stones grew. Stones initiate from a small nidus, grow outward, and show major enrichment in ribosomal proteins and factors related to coagulation and platelet degranulation, suggesting a major dysregulation in specific pathways that can be targeted for new therapeutic options.
Effects of imidacloprid and thiamethoxam at LC30and LC50on the life table of soybean aphidAphis glycines(Hemiptera: Aphididae)
Authors: Zhang Aonan , Zhu Lin , Shi Zhenghao , Zhao Kuijun , Liu Tianying , Han Lanlan 
Published: April 2021

AbstractThe soybean aphid,Aphis glycinesMatsumura (Hemiptera: Aphididae), is a main pests of soybean that poses a serious threat to its production. Studies were conducted to understand effects of the different concentrations of the insecticides (imidacloprid and thiamethoxam) on the life table ofA. glycinesto provide vital information for its effective management. We found that the mean generation time, adult and total pre-oviposition periods inA. glycinesspecimens exposed to LC50imidacloprid and thiamethoxam were significantly longer than those in the control group. However, when exposed to LC30imidacloprid and thiamethoxam, the adult pre-ovipositional period was significantly shorter than that in the control group. The mean fecundity per female adult, net reproductive rate, intrinsic rate of increase, and finite rate of increase were significantly decreased in individuals exposed to LC30and LC50concentrations of imidacloprid and thiamethoxam, respectively (P< 0.05). Both insecticides produce stress effects onA. glycines, and specimens treated with LC50concentrations of the two insecticides exhibited a significant decrease in their growth rates than those treated with LC30concentrations. This study provides data that can be used as a reference to predict the effect of imidacloprid and thiamethoxam on the population dynamics in the field, and agricultural producers could attach importance to prevent stimulation the reproduction made by low-lethal concentrations during actually applying pesticides.
Promoter-sequence determinants and structural basis of primer-dependent transcription initiation inEscherichia coli
Authors: Skalenko Kyle S. , Li Lingting , Zhang Yuanchao , Vvedenskaya Irina O. , Winkelman Jared T. , Cope Alexander , Taylor Deanne M. , Shah Premal , Ebright Richard H. , Kinney Justin B. , Zhang Yu , Nickels Bryce E. 
Published: April 2021

AbstractChemical modifications of RNA 5′ ends enable “epitranscriptomic” regulation, influencing multiple aspects of RNA fate. In transcription initiation, a large inventory of substrates compete with nucleoside triphosphates (NTPs) for use as initiating entities, providing anab initiomechanism for altering the RNA 5′ end. InEscherichia colicells, RNAs with a 5′-end hydroxyl are generated by use of dinucleotide RNAs as primers for transcription initiation, “primer-dependent initiation.” Here we use massively systematic transcript end readout (“MASTER”) to detect and quantify RNA 5′ ends generated by primer-dependent initiation for ~410(~1,000,000) promoter sequences inE. coli. The results show primer-dependent initiation inE. coliinvolves any of the 16 possible dinucleotide primers and depends on promoter sequences in, upstream, and downstream of the primer binding site. The results yield a consensus sequence for primer-dependent initiation, YTSS-2NTSS-1NTSSWTSS+1, where TSS is the transcription start site, NTSS-1NTSSis the primer binding site, Y is pyrimidine, and W is A or T. Biochemical and structure-determination studies show that the base pair (nontemplate-strand base:template-strand base) immediately upstream of the primer binding site (Y:RTSS-2, where R is purine) exerts its effect through the base on the DNA template strand (RTSS-2) through inter-chain base stacking with the RNA primer. Results from analysis of a large set of natural, chromosomally-encodedE.colipromoters support the conclusions from MASTER. Our findings provide a mechanistic and structural description of how TSS-region sequence hard-codes not only the TSS position, but also the potential for epitranscriptomic regulation through primer-dependent transcription initiation.
Millisecond Mix-and-Quench Crystallography (MMQX) Enables Time-Resolved Studies of PEPCK With Remote Data Collection
Authors: Clinger Jonathan A. , Moreau David W. , McLeod Matthew J. , Holyoak Todd , Thorne Robert E. 
Published: April 2021

AbstractTime-resolved crystallography of biomolecules in action has advanced rapidly as methods for serial crystallography have improved, but the large number of crystals and complex experimental infrastructure required remain serious obstacles to widespread application. We have developed Millisecond Mix-and-Quench crystallography (MMQX), which yields millisecond time-resolved data using far fewer crystals and routine remote synchrotron data collection. To demonstrate the capabilities of MMQX, the conversion of oxaloacetic acid to phosphoenolpyruvate by phosphoenolpyruvate carboxykinase is observed with a time resolution of 40 ms. MMQX, by lowering the entry barrier to time-resolved crystallography, should enable broad expansion in structural studies of protein dynamics.
Anuran Heart Metamorphosis: Anatomical Support for Pulmonary Blood Separation in the Early Aquatic Phase
Authors: Kraus Nina , Metscher Brian 
Published: April 2021

1.AbstractBackgroundIn both larval and adult anurans, blood separation and respiratory physiology have remained an enigma. While various blood separation mechanisms have been proposed, the same structure is seen as playing a key role: the conus arteriosus. However, previous findings on its internal structure are contradictory, depending on the specifics of the 2D imaging methods used by different authors. To resolve this problem, we used high-resolution X-ray microtomography of wholeBufo bufospecimens to acquire the first detailed 3D descriptions of this complex structure through metamorphosis.ResultsIn early tadpoles two small valvular openings develop at the ventricular-conal junction, providing two paths separated by the septum coni and continuing into the aortic arches. Thus, structures to support segregated pulmonary circulation are fully developed well before the lungs appear. The external gills undergo partial resorption and retreat asymmetrically into a gill chamber formed by a hyoidal cover, leaving only a single opening on the left side, the opercular spout.ConclusionsThe timing of events inBufocirculatory development does not track the changing modes of respiration used by the developing tadpole. In particular, a system capable of double circulation carries only oxygen-depleted blood for a significant portion of the tadpole stage.
“Multi-Agent” Screening Improves the Efficiency of Directed Enzyme Evolution
Authors: Yang Tian , Ye Zhixia , Lynch Michael D. 
Published: April 2021

AbstractEnzyme evolution has enabled numerous advances in biotechnology. However, directed evolution programs can still require many iterative rounds of screening to identify optimal mutant sequences. This is due to the sparsity of the fitness landscape, which in turn, is due to “hidden” mutations that only offer improvements synergistically in combination with other mutations. These “hidden” mutations are only identified by evaluating mutant combinations, necessitating large combinatorial libraries or iterative rounds of screening. Here, we report a multi-agent directed evolution approach that incorporates diverse substrate analogues in the screening process. With multiple substrates acting like multiple agents navigating the fitness landscape, we are able to identify “hidden” mutant residues that impact substrate specificity without a need for testing numerous combinations. We initially validate this approach in engineering a malonyl-CoA synthetase for improved activity with a wide variety of non-natural substrates. We found that “hidden” mutations are often distant from the active site, making them hard to predict using popular structure-based methods. Interestingly, many of the “hidden” mutations identified in this case are expected to destabilize interactions between elements of tertiary structure, potentially affecting protein flexibility. This approach may be widely applicable to accelerate enzyme engineering. Lastly, multi-agent system inspired approaches may be more broadly useful in tackling other complex combinatorial search problems in biology.Highlights- “Multi-agent” screening improves directed evolution.- The incorporation of multiple substrates leads to the identification of “hidden” mutations, which can be hard to identify through one substrate.- “Hidden” mutations are often remote from the active site and are expected to interrupt stabilizing side-chain interactions, thus increasing enzyme flexibility.
Fast slow folding of an Outer Membrane Porin
Authors: Weatherill Eve E. , Fahie Monifa A. , Marshall David P. , Andvig Rachel A. , Cheetham Matthew R. , Chen Min , Wallace Mark I. 
Published: April 2021

AbstractIn comparison to globular proteins, the spontaneous folding and insertion ofβ-barrel membrane proteins is surprisingly slow, typically occurring on the order of minutes. Using single-molecule Förster Resonance Energy Transfer to report on the folding of fluorescently-labelled Outer Membrane Protein G we measured the real-time insertion of aβ-barrel membrane protein from an unfolded state. Folding events were rare, and fast (<20 ms); occurring immediately upon arrival at the membrane. This combination of infrequent, but rare, folding resolves this apparent dichotomy between slow ensemble kinetics, and the typical timescales of biomolecular folding.
Nuclear RNA-acetylation can be erased by the deacetylase SIRT7
Authors: Kudrin Pavel , Meierhofer David , Vågbø Cathrine Broberg , Ørom Ulf Andersson Vang 
Published: April 2021

AbstractA large number of RNA modifications are known to affect processing and function of rRNA, tRNA and mRNA1. The N4-acetylcytidine (ac4C) is the only known RNA acetylation event and is known to occur on rRNA, tRNA and mRNA2,3. RNA modification by acetylation affects a number of biological processes, including translation and RNA stability2. For a few RNA methyl modifications, a reversible nature has been demonstrated where specific writer proteins deposit the modification and eraser proteins can remove them by oxidative demethylation4–6. The functionality of RNA modifications is often mediated by interaction with reader proteins that bind dependent on the presence of specific modifications1. The NAT10 acetyltransferase has been firmly identified as the main writer of acetylation of cytidine ribonucleotides, but so far neither readers nor erasers of ac4C have been identified2,3. Here we show, that ac4C is bound by the nucleolar protein NOP58 and deacetylated by SIRT7, for the first time demonstrating reversal by another mechanism than oxidative demethylation. NOP58 and SIRT7 are involved in snoRNA function and pre-ribosomal RNA processing7–10, and using a NAT10 deficient cell line we can show that the reduction in ac4C levels affects both snoRNA sub-nuclear localization and pre-rRNA processing. SIRT7 can deacetylate RNAin vitroand endogenous levels of ac4C on snoRNA increase in a SIRT7 deficient cell line, supporting its endogenous function as an RNA deacetylase. In summary, we identify the first eraser and reader proteins of the RNA modification ac4C, respectively, and suggest an involvement of RNA acetylation in snoRNA function and pre-rRNA processing.
Morphology of migration: Associations between wing, and bill morphology and migration in kingbirds (Tyrannus)
Authors: MacPherson Maggie P. , Jahn Alex E. , Mason Nicholas A. 
Published: April 2021

AbstractMorphology is closely linked to locomotion and diet in animals. In animals that undertake long-distance migrations, limb-morphology is under selection to maximize mobility and minimize energy expenditure. Migratory behaviors also interact with diet, such that migratory animals tend to be dietary generalists, while sedentary taxa tend to be dietary specialists. Despite a hypothesized link between migration status and morphology, phylogenetic comparative studies have yielded conflicting findings. We tested for evolutionary associations between migratory status and limb and bill morphology across kingbirds, a pan-American genus of birds with migratory, partially migratory, and sedentary taxa. Migratory kingbirds had longer wings, in agreement with expectations if selection favors improved aerodynamics for long-distance migration. We also found an association between migratory status and bill shape, such that more migratory taxa had wider, deeper, and shorter bills compared to sedentary taxa. However, there was no difference in intraspecific morphological variation among migrants, partial migrants, and residents, suggesting that dietary specialization has evolved independently of migration strategy. The evolutionary links between migration, diet, and morphology in kingbirds uncovered here further strengthen ecomorphological associations that underlie long-distance seasonal movements in animals.
Potassium channel-driven bioelectric signaling regulates metastasis in triple-negative breast cancer
Authors: Payne Samantha L , Ram Priyanka , Srinivasan Deepti H. , Le Thanh T. , Levin Michael , Oudin Madeleine J 
Published: April 2021

AbstractThere is a critical need to better understand the mechanisms that drive local cell invasion and metastasis to develop new therapeutics targeting metastatic disease. Bioelectricity is an important mediator of cellular processes and changes in the resting membrane potential (RMP) are associated with increased cancer cell invasion. However, the mechanism is not well understood. Our data demonstrate that altering the RMP of triple-negative breast cancer (TNBC) cells by manipulating potassium channel expression increasesin vitroinvasion,in vivotumor growth, and metastasis, and is accompanied by changes in gene expression associated with cell adhesion. We describe a novel mechanism for RMP-mediated cell migration involving cadherin-11 and the MAPK pathway. Importantly, we identify a new strategy to target metastatic TNBCin vivoby repurposing FDA-approved potassium channel blockers. Our results provide an understanding of the mechanisms by which bioelectricity regulates cancer cell invasion and metastasis that could lead to a new class of therapeutics for patients with metastatic disease.
Intron Losses and Gains in Nematodes: Not Eccentric at All
Authors: Ma Ming-Yue , Xia Ji , Shu Kunxian , Niu Deng-Ke 
Published: April 2021

AbstractThe evolution of spliceosomal introns has been widely studied among various eukaryotic groups. Researchers nearly reached the consensuses on the pattern and the mechanisms of intron losses and gains across eukaryotes. However, according to previous studies that analyzed a few genes or genomes of nematodes, Nematoda seem to be an eccentric group. Taking advantage of the recent accumulation of sequenced genomes, we carried out an extensive analysis on the intron losses and gains using 104 nematodes genomes across all the five Clades of the phylum. Nematodes have a wide range of intron density, from less than one to more than nine per 1kbp coding sequence. The rates of intron losses and gains exhibit significant heterogeneity both across different nematode lineages and across different evolutionary stages of the same lineage. The frequency of intron losses far exceeds that of intron gains. Five pieces of evidence supporting the model of cDNA-mediated intron loss have been observed in tenCaenorhabditisspecies, the dominance of the precise intron losses, frequent loss of adjacent introns, and high-level expression of the intron-lost genes, preferential losses of short introns, and the preferential losses of introns close to 3′-ends of genes. Like studies in most eukaryotic groups, we cannot find the source sequences for the limited number of intron gains detected in theCaenorhabditisgenomes. All the results indicate that nematodes are a typical eukaryotic group rather than an outlier in intron evolution.