bluuebunny/crossref_metadata_2025_split huggingface dataset:
Balance between extracellular matrix production and macrophage survival by aSalmonella-specific SPI-2 encoded transcription factor
Authors: Echarren María Laura , Figueroa Nicolás R. , Vitor-Horen Luisina , Pucciarelli M. Graciela , Portillo Francisco García-del , Soncini Fernando C. 
Published: March 2021

AbstractCellulose is a major component of theSalmonellabiofilm extracellular matrix and it is considered an antivirulence factor because it interferes withSalmonellasurvival inside macrophages and virulence in mice. Its synthesis is stimulated by CsgD, the master regulator of biofilm extracellular matrix formation in enterobacteria, which in turn is under the control of MlrA, a MerR-like transcription factor. In this work we identified a SPI-2 encodedSalmonella-specific transcription factor homolog to MlrA, MlrB, that represses transcription of its downstream gene, STM1389, also known asorf319, and ofcsgDinside host cells. MlrB is induced in laboratory media mimicking intracellular conditions and inside macrophages, and it is required for intramacrophage survival. An increased expression ofcsgDis observed in the absence of MlrB inside host cells. Interestingly, inactivation of the CsgD-controlled cellulose synthase coding-gene,bcsA, restored intramacrophage survival to rates comparable to wild type bacteria in the absence of MlrB. These data indicate that MlrB represses CsgD expression inside host cells and in consequence activation of the cellulose synthase. Our findings provide a novel link between biofilm formation andSalmonellavirulence.
Cost-effective long-read assembly of a hybrid Formica aquilonia × Formica polyctena wood ant genome from a single haploid individual
Authors: Nouhaud Pierre , Beresford Jack , Kulmuni Jonna 
Published: March 2021

ABSTRACTFormica red wood ants are a keystone species of boreal forest ecosystems and an emerging model system in the study of speciation and hybridization. Here we performed a standard DNA extraction from a single, field-collected Formica aquilonia × Formica polyctena haploid male and assembled its genome using ∼60× of PacBio long reads. After polishing and contaminant removal, the final assembly was 272 Mb (4,687 contigs, N50 = 1.16 Mb). Our reference genome contains 98.5% of the core Hymenoptera BUSCOs and was scaffolded using the pseudo-chromosomal assembly of a related species, F. selysi (28 scaffolds, N50 = 8.49 Mb). Around one third of the genome consists of repeats, and 17,426 gene models were annotated using both protein and RNAseq data (97.4% BUSCO completeness). This resource is of comparable quality to the few other single individual insect genomes assembled to date and paves the way to genomic studies of admixture in natural populations and comparative genomic approaches in Formica wood ants.
A linear response theory based method for prediction of large scale protein conformational changes upon ligand binding
Authors: Punia Rajat , Goel Gaurav 
Published: March 2021

ABSTRACTPrediction of ligand-induced protein conformational transitions is a challenging task due to a large and rugged conformational space, and limited knowledge of probable direction(s) of structure change. These transitions can involve a large scale, global (at the level of entire protein molecule) structural change and occur on a timescale of milliseconds to seconds, rendering application of conventional molecular dynamics simulations prohibitive even for small proteins. We have developed a computational protocol to efficiently and accurately predict these ligand-induced structure transitions solely from the knowledge of protein apo structure and ligand binding site. Our method involves a series of small scale conformational change steps, where at each step linear response theory is used to predict the direction of small scale global response to ligand binding in the protein conformational space (dLRT) followed by construction of a linear combination of slow (low frequency) normal modes (calculated for the structure from the previous step) that best overlaps withdLRT. Protein structure is evolved along this direction using molecular dynamics with excited normal modes (MDeNM) wherein excitation energy along each normal mode is determined by excitation temperature, mode frequency, and its overlap withdLRT. We show that excitation temperature (ΔT) is a very important parameter that allows limiting the extent of structural change in any one step and develop a protocol for automated determination of its optimal value at each step. We have tested our protocol for three protein–ligand systems, namely, adenylate Kinase – di(adenosine-5’)pentaphosphate, ribose binding protein –β-D-ribopyranose, and DNAβ-glucosyltransferase – uridine-5’-diphosphate, that incorporate important differences in type and range of structural changes upon ligand binding. We obtain very accurate prediction for not only the structure of final protein–ligand complex (holo-structure) having a large scale conformational change, but also for biologically relevant intermediates between the apo and the holo structures. Moreover, most relevant set of normal modes for conformational change at each step are an output from our method, which can be used as collective variables for determination of free energy barriers and transition timescales along the identified pathway.
Flexible reprogramming ofPristionchus pacificusmotivation for attackingCaenorhabditis elegansin predator-prey competition
Authors: Quach Kathleen T. , Chalasani Sreekanth H. 
Published: March 2021

SummaryAnimals with diverse diets must adapt their food priorities to a wide variety of environmental conditions. This diet optimization problem is especially complex for predators that compete with prey for food. Although predator-prey competition is widespread and ecologically critical, it remains difficult to disentangle predatory and competitive motivations for attacking competing prey. Here, we dissect the foraging decisions of the omnivorous nematodePristionchus pacificusto reveal that its seemingly failed predatory attempts againstCaenorhabditis elegansare actually motivated acts of efficacious territorial aggression. WhileP. pacificuseasily kills and eats larvalC. eleganswith a single bite, adultC. eleganstypically survives and escapes from bites. However, nonfatal biting can provide competitive benefits by reducing access of adultC. elegansand its progeny to bacterial food thatP. pacificusalso eats. We show thatP. pacificusconsiders costs and benefits of both predatory and territorial outcomes to decide which food goal, prey or bacteria, should guide its motivation for biting. These predatory and territorial motivations impose different sets of rules for adjusting willingness to bite in response to changes in bacterial abundance. In addition to biting, predatory and territorial motivations also influence which search tacticP. pacificususes to increase encounters withC. elegans. When treated with an octopamine receptor antagonist,P. pacificusswitches from territorial to predatory motivation for both biting and search. Overall, we demonstrate thatP. pacificusassesses alternate outcomes of attackingC. elegansand flexibly reprograms its foraging strategy to prioritize either prey or bacterial food.
An optogenetic tool to raise intracellular pH in single cells and drive localized membrane dynamics
Authors: Donahue Caitlin E. T. , Siroky Michael D. , White Katharine A. 
Published: March 2021

AbstractIntracellular pH (pHi) dynamics are critical for regulating normal cell physiology. For example, transient increases in pHi (7.2-7.6) regulate cell behaviors like cell polarization, actin cytoskeleton remodeling, and cell migration. Most studies on pH-dependent cell behaviors have been performed at the population level and use non-specific methods to manipulate pHi. The lack of tools to specifically manipulate pHi at the single-cell level has hindered investigation of the role of pHi dynamics in driving single cell behaviors. In this work, we show that Archaerhodopsin (ArchT), a light-driven outward proton pump, can be used to elicit robust and physiological pHi increases over the minutes timescale. We show that activation of ArchT is repeatable, enabling the maintenance of high pHi in single cells for approximately 45 minutes. We apply this spatiotemporal pHi manipulation tool to determine whether increased pHi is a sufficient driver of membrane ruffling in single cells. Using the ArchT tool, we show that increased pHi in single cells can drive localized membrane ruffling responses within seconds and increased membrane dynamics (both protrusion and retraction events) compared to unstimulated ArchT cells as well as control cells. Overall, this tool allows us to directly investigate the relationship between increased pHi and cell behaviors such as membrane ruffling. This tool will be transformative in facilitating experiments required to determine if increased pHi drives these cell behaviors at the single-cell level.
WNK1 Enhances Migration and Invasion in Breast Cancer Models
Authors: Jaykumar Ankita B. , Jung Jiung , Parida Pravat , Dang Tuyen T. , Grzemska Magdalena , Earnest Svetlana , Wichaidit Chonlarat , Goldsmith Elizabeth J. , Pearson Gray W. , Malladi Srinivas , Cobb Melanie H. 
Published: March 2021

AbstractMetastasis is the major cause of mortality in breast cancer patients. Many signaling pathways have been linked to cancer invasiveness, but blockade of few protein components has succeeded in reducing metastasis. Thus, identification of proteins contributing to invasion that are manipulable by small molecules may be valuable in inhibiting spread of the disease. The protein kinase WNK1 (with no lysine (K) 1) has been suggested to induce migration of cells representing a range of cancer types. Analyses of mouse models and patient data have implicated WNK1 as one of a handful of genes uniquely linked to invasive breast cancer. Here we present evidence that inhibition of WNK1 slows breast cancer metastasis. We show that depletion or inhibition of WNK1 reduces migration of several breast cancer cell lines in wound healing assays and decreases invasion in collagen matrices. Furthermore, WNK1 depletion suppresses expression of AXL, a tyrosine kinase implicated in metastasis. Finally, we demonstrate that WNK inhibition in mice attenuates tumor progression and metastatic burden. These data showing reduced migration, invasion, and metastasis upon WNK1 depletion in multiple breast cancer models suggest that WNK1 contributes to the metastatic phenotype and that WNK1 inhibition may offer a therapeutic avenue for attenuating progression of invasive breast cancers.
Prioritization of regulatory variants with tissue-specific function in the non-coding regions of human genome
Authors: Dong Shengcheng , Boyle Alan P. 
Published: March 2021

AbstractUnderstanding the functional consequences of genetic variation in the non-coding regions of the human genome remains a challenge. We introduce here a computational tool, TURF, to prioritize regulatory variants with tissue-specific function by leveraging evidence from functional genomics experiments, including over three thousand functional genomics datasets from the ENCODE project provided in the RegulomeDB database. TURF is able to generate prediction scores at both organism and tissue/organ-specific levels for any non-coding variant on the genome. We present that TURF has an overall top performance in prediction by using validated variants from MPRA experiments. We also demonstrate how TURF can pick out the regulatory variants with tissue-specific function over a candidate list from associate studies. Furthermore, we found that various GWAS traits showed the enrichment of regulatory variants predicted by TURF scores in the trait-relevant organs, which indicates that these variants can be a valuable source for future studies.
Hippocampal replay reflects specific past experiences rather than a plan for subsequent choice
Authors: Gillespie Anna K. , Astudillo Maya Daniela A. , Denovellis Eric L. , Liu Daniel F. , Kastner David B. , Coulter Michael E. , Roumis Demetris K. , Eden Uri T. , Frank Loren M. 
Published: March 2021

ABSTRACTExecuting memory-guided behavior requires both the storage of information about experience and the later recall of that information to inform choices. Awake hippocampal replay, when hippocampal neural ensembles briefly reactivate a representation related to prior experience, has been proposed to critically contribute to these memory-related processes. However, it remains unclear whether awake replay contributes to memory function by promoting the storage of past experiences, by facilitating planning based on an evaluation of those experiences, or both. We designed a dynamic spatial task which promotes replay before a memory-based choice and assessed how the content of replay related to past and future behavior. We found that replay content was decoupled from subsequent choice and instead was enriched for representations of previously rewarded locations and places that had not been recently visited, indicating a role in memory storage rather than in directly guiding subsequent behavior.
SSR1 is a vital regulator in plant mitochondrial iron-sulfur biosynthesis
Authors: Feng Xuanjun , Han Huiling , Bonea Diana , Liu Jie , Ying Wenhan , Cai Yuanyuan , Zhang Min , Lu Yanli , Zhao Rongmin , Hua Xuejun 
Published: March 2021

AbstractThe ArabidopsisSHORT AND SWOLLEN ROOT1(SSR1) gene encodes a mitochondrial TPR domain-containing protein and was previously reported to function in maintaining mitochondria function. In a screen for suppressors of the short-root phenotype of the loss-of-function mutantssr1-2, two mutations,sus1andsus2(suppressor ofssr1-2), were isolated.sus1andsus2result from G87D and T55M single amino acid substitution in HSCA2 (At5g09590) and ISU1 (At4g22220), both of which are core components in iron-sulfur cluster biosynthesis pathway in mitochondria (ISC). We here demonstrated that SSR1 displayed a strong chaperone-like activity and was able to enhance the binding of HSCA2 to ISU1, an essential step for the normal operation of ISC machinery. Accordingly, the enzymatic activities of several iron-sulfur proteins, the mitochondrial membrane potential and ATP content are reduced inssr1-2. Interestingly,SSR1appears to exist only in plant lineages, possibly conferring adaptive advantages on plant ISC machinery to environment.
High resolution structure of the membrane embedded skeletal muscle ryanodine receptor
Authors: Melville Zephan , Kim Kookjoo , Clarke Oliver B. , Marks Andrew R. 
Published: March 2021

AbstractThe type 1 ryanodine receptor (RyR1)/calcium release channel on the sarcoplasmic reticulum (SR) is required for skeletal muscle excitation-contraction coupling and is the largest known ion channel, comprised of four 565 kDa protomers. Cryogenic electron microscopy (cryoEM) studies of the RyR have primarily used detergent to solubilize the channel, though a recent study resolved the structure with limited resolution in nanodiscs1. In the present study we have used cryoEM to solve high-resolution structures of the channel in liposomes using a gel-filtration approach with on-column detergent removal to form liposomes and incorporate the channel simultaneously, a method that improved the incorporation rate by more than 20-fold compared to a dialysis-based approach. In conjunction with new direct-detection cameras, this allowed us to resolve the structure of the channel in the closed and open states at 3.36 and 3.98 Å, respectively. This method offers validation for detergent-based structures of the RyR and lays the groundwork for studies utilizing an electrochemical gradient mimicking the native environment, such as that of the SR, where Ca2+concentrations are millimolar in the lumen and nanomolar in the cytosol of the cell at rest.
KDM6A knockout in human iPSCs alters the genome-wide histone methylation profile at active and poised enhancers, activating expression of ectoderm gene expression pathways
Authors: Maurya Shailendra S. , Yang Wei , Zhang Qiang , Erdmann-Gilmore Petra , Bystry Amelia , Townsend Reid , Druley Todd E. 
Published: March 2021

AbstractKDM6A is a histone demethylase, known to remove methyl moieties at the lysine residues of histone 3-labeled (H3K27me3) poised enhancers and bivalent promoters, which regulates gene expression during the differentiation of embryonic stem cells and tissue-specific development. However, while tissue- and disease-specific analyses have been performed, little is known about the location and consequences on gene expression of these regulatory regions in human pluripotent cells. Poised enhancers and bivalent promoters function in a coordinated fashion during development, which requires timely and efficient histone modifications. Identification of KDM6A-specific gene-regulatory domains is important for understanding the developmental mechanisms controlled by these histone modifications in pluripotency. In this study, we compared genome-wide histone modification and gene expression differences in isogenic wild type and cas9-mediatedKDM6Aknockout human induced pluripotent stem cells (hiPSC) lines. Here, we report that the absence of KDM6A does not alter the pluripotent phenotype but does substantially alter the histone modification profile at poised and active enhancers, resulting in decreased expression of associated COMPASS complex genes KMT2C and KMT2D and subsequently increasing the expression of gene pathways involved in ectoderm differentiation.
Movement patterns and activity levels are shaped by the neonatal environment in Antarctic fur seal pups
Authors: Nagel Rebecca , Mews Sina , Adam Timo , Stainfield Claire , Fox-Clarke Cameron , Toscani Camille , Langrock Roland , Forcada Jaume , Hoffman Joseph I. 
Published: March 2021

AbstractTracking studies of juveniles are rare compared to those of adults, and consequently little is known about the influence of intrinsic and extrinsic factors on activity during this critical life stage. We used hourly GPS data, collected from 66 Antarctic fur seal pups from birth until moulting, to investigate the explanatory power of multiple individual-based and environmental variables on activity levels. Pups were sampled from two nearby breeding colonies of contrasting density during two subsequent years, and a two-state hidden Markov model was used to identify modalities in their movement behaviour, specifically ‘active’ and ‘inactive’ states. We found that movement was typified by central place exploration, with active movement away from and subsequent return to a location of inactivity. The probability of such directed exploration was unaffected by several factors known to influence marine mammal movement including sex, body condition, and temperature. Compared to pups born at the high-density colony, pups at low-density were more active, increased their activity with age, and transitioned earlier into the tussock grass, which offers protection from predators and extreme weather. Our study illustrates the importance of extrinsic factors, such as colony of birth, to early-life activity patterns and highlights the adaptive potential of movement.
A recombinant ‘ACE2 Triple Decoy’ that traps and neutralizes SARS-CoV-2 shows enhanced affinity for highly transmissible SARS-CoV-2 variants
Authors: Tanaka Shiho , Nelson Gard , Olson Anders , Buzko Oleksandr , Higashide Wendy , Shin Annie , Gonzales Marcos , Taft Justin , Patel Roosheel , Buta Sofija , Martin-Fernandez Marta , Bogunovic Dusan , Spilman Patricia , Niazi Kayvan , Rabizadeh Shahrooz , Soon-Shiong Patrick 
Published: March 2021

ABSTRACTThe highly-transmissible SARS-CoV-2 variants now replacing the first wave strain pose an increased threat to human health by their ability, in some instances, to escape existing humoral protection conferred by previous infection, neutralizing antibodies, and possibly vaccination. Thus, other therapeutic options are necessary. One such therapeutic option that leverages SARS-CoV-2 initiation of infection by binding of its spike receptor binding domain (S RBD) to surface-expressed host cell angiotensin-converting enzyme 2 (ACE2) is an ACE2 ‘decoy’ that would trap the virus by competitive binding and thus inhibit propagation of infection. Here, we used Molecular Dynamic (MD) simulations to predict ACE2 mutations that might increase its affinity for S RBD and screened these candidates for binding affinityin vitro. A double mutant ACE2(T27Y/H34A)-IgG1FCfusion protein was found to have very high affinity for S RBD and to show greater neutralization of SARS-CoV-2 in a live virus assay as compared to wild type ACE2. We further modified the double mutant ACE2 decoy by addition of an H374N mutation to inhibit ACE2 enzymatic activity while maintaining high S RBD affinity. We then confirmed the potential efficacy of our ACE2(T27Y/H34A/H374N)-IgG1FCTriple Decoy against S RBD expressing variant-associated E484K, K417N, N501Y, and L452R mutations and found that our ACE2 Triple Decoy not only maintains its high affinity for S RBD expressing these mutations, but shows enhanced affinity for S RBD expressing the N501Y or L452R mutations and the highest affinity for S RBD expressing both the E484K and N501Y mutations. The ACE2 Triple Decoy also demonstrates the ability to compete with wild type ACE2 in the cPass™ surrogate virus neutralization in the presence of S RBD with these mutations. Additional MD simulation of ACE2 WT and decoy interactions with S RBD WT or B.1.351 variant sequence S RBD provides insight into the enhanced affinity of the ACE2 decoy for S RBD and reveals its potential as a tool to predict affinity and inform therapeutic design. The ACE2 Triple Decoy is now undergoing continued assessment, including expression by a human adenovirus serotype 5 (hAd5) construct to facilitate deliveryin vivo.Summary sentenceAn ACE2(N27Y/H34A/H374N)-IgG1FCfusion protein decoy sustains high affinity to all SARS-CoV-2 spike receptor binding domain (RBD) protein variants tested, shows enhanced affinity for the N501Y and L452R variants, and the highest affinity for combined N501Y and E484K variants.