bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving the diagnosis of severe malaria in African children using platelet counts and plasma Pf HRP2 concentrations
Authors: Watson James A , Uyoga Sophie , Wanjiku Perpetual , Makale Johnstone , Nyutu Gideon M , Mturi Neema , George Elizabeth C , Woodrow Charles J , Day Nicholas PJ , Bejon Philip , Opoka Robert O. , Dondorp Arjen M , John Chandy C , Maitland Kathryn , Williams Thomas N , White Nicholas J 
Published: October 2021

AbstractBackgroundSevere falciparum malaria is difficult to diagnose accurately in children in high transmission settings. Platelet counts and plasma concentrations of P. falciparum histidinerich protein-2 (Pf HRP2) are potential biomarkers to increase diagnostic accuracy.MethodsWe fitted Bayesian latent class models to platelet counts and Pf HRP2 concentrations in 2,649 patients enrolled in four studies of severe illness in three countries (Bangladesh, Kenya, and Uganda). We estimated receiver operating characteristic curves and compared parasite densities, haematocrits, total white blood cell counts, blood culture positivity rates, and haemoglobin S genotypes (HbAS and HbSS) across the subgroups defined by the probabilistic models.FindingsThe platelet count and the plasma Pf HRP2 concentration have substantial diagnostic value in severe malaria. In severely ill patients with clinical features consistent with severe malaria, a combined platelet count ≤ 150,000 per µL and a plasma Pf HRP2 concentration ≥ 1,000 ng/mL had an estimated sensitivity of 74% and specificity of 93% in identifying ‘true’ severe falciparum malaria. We estimate one third of African children enrolled in the two clinical studies of severe malaria had another cause of severe illness. Under the model, patients with severe malaria had higher parasite densities, lower haematocrits, lower rates of invasive bacterial disease, and a lower prevalence of both HbAS and HbSS than children misdiagnosed. Mortality in ‘true’ severe malaria was consistent across the African sites at ∼ 10%.InterpretationStudies of severe falciparum malaria in African children would be improved by including only patients with platelet counts ≤ 150,000 per µL and plasma Pf HRP2 concentrations ≥ 1,000 ng/mL.FundingWellcome
Endogenous retroviruses mediate transcriptional rewiring in response to oncogenic signaling in colorectal cancer
Authors: Ivancevic Atma , Simpson David M. , Joyner Olivia M. , Bagby Stacey M. , Nguyen Lily L. , Bitler Ben G. , Pitts Todd M. , Chuong Edward B. 
Published: October 2021

AbstractCancer cells exhibit rewired transcriptional regulatory networks that promote tumor growth and survival. However, the mechanisms underlying the formation of these pathological networks remain poorly understood. Through a pan-cancer epigenomic analysis, we found that primate-specific endogenous retroviruses (ERVs) are a rich source of enhancers displaying cancer-specific activity. In colorectal cancer and other epithelial tumors, oncogenic AP1/MAPK signaling drives the activation of enhancers derived from the primate-specific ERV family LTR10. Functional studies in colorectal cancer cells revealed that LTR10 elements regulate tumor-specific expression of multiple genes associated with tumorigenesis, such asATG12andXRCC4. Within the human population, individual LTR10 elements exhibit germline and somatic structural variation resulting from a highly mutable internal tandem repeat region, which affects AP1 binding activity. Our findings reveal that ERV-derived enhancers contribute to transcriptional dysregulation in response to oncogenic signaling and shape the evolution of cancer-specific regulatory networks.
Modulatory potentials of zerumbone isolated from ginger (Zingiber zerumbet) on eicosanoids: evidence from LPS induced peripheral blood leukocytes
Authors: Uppin Vinayak , Kamala Hamsavi Gopal , Kempaiah Bettadaiah Bheemanakere , Talahalli Ramaprasad Ravichandra 
Published: October 2021

AbstractSeveral bioactive molecules from plant origin have been studied for their anti-inflammatory properties. In this study, we deciphered the anti-eicosanoid properties of zerumbone (sesquiterpene) isolated from ginger (Zingiber zerumbet) in LPS induced peripheral blood leukocytes from rats. Molecular interaction between zerumbone (Z) and eicosanoid metabolizing enzymes (COX-2, 5-LOX, FLAP, and LTA4-hydrolase) and receptors (EP-4, BLT-1, and ICAM-1) along with NOS-2 were assessed using Auto-Dock 4.2 docking software. Further, the rat peripheral blood leukocytes were isolated and treated with zerumbone (5μM) and activated using bacterial lipopolysaccharide (10nM). Oxidative stress (OS) markers, reactive oxygen species, antioxidant enzymes, COX-2, 5-LOX, BLT-1, EP-4 were assessed along with the activity of COX-2. Zerumbone showed a higher binding affinity with mPGES-1, NOS-2, FLAP, COX-2, LTA-4-hydrolase, and BLT-1 mediators of the eicosanoid pathway. Further, zerumbone significantly (p<0.05) inhibited COX-2, 5-LOX, NOS-2, EP-4, BLT-1, and ICAM-1 expression in LPS induced peripheral blood leukocytes from rats. Zerumbone positively modulates critical enzymes and receptors of eicosanoids in leukocytes activated with lipopolysaccharides. Thus, zerumbone offers a promising therapeutic strategy in the management of inflammation.
Near-infrared carbon nanotube tracking reveals the nanoscale extracellular space around synapses
Authors: Paviolo Chiara , Ferreira Joana S. , Lee Antony , Hunter Daniel , Groc Laurent , Cognet Laurent 
Published: October 2021

ABSTRACTWe provide evidence of a local synaptic nano-environment in the brain extracellular space (ECS) lying within 500 nm of postsynaptic densities. To reveal this brain compartment, we developed a correlative imaging approach dedicated to thick brain tissue based on single-particle tracking of individual fluorescent single wall carbon nanotubes (SWCNTs) in living samples and on speckle-based HiLo microscopy of synaptic labels. We show that the extracellular space around synapses bears specific properties in terms of morphology at the nanoscale and inner diffusivity. We finally show that the ECS juxta-synaptic region changes its diffusion parameters in response to neuronal activity, indicating that this nano-environment might play a role in the regulation of brain activity.
Double-edged role of resource competition in gene expression noise and control
Authors: Goetz Hanah , Stone Austin , Zhang Rong , Lai Ying-Cheng , Tian Xiao-Jun 
Published: October 2021

AbstractDespite extensive investigation demonstrating that resource competition can significantly alter the circuits’ deterministic behaviors, a fundamental issue is how resource competition contributes to the gene expression noise and how the noise can be controlled. Utilizing a two-gene circuit as a prototypical system, we uncover a surprising double-edged role of resource competition in gene expression noise: the competition decreases noise through a resource constraint but generates its own type of noise which we name as “resource competitive noise.” Utilization of orthogonal resources enables retaining the noise reduction conferred by resource constraint while removing the added resource competitive noise. The noise reduction effects are studied using three negative feedback controller types: negatively competitive regulation (NCR), local, and global controllers, each having four placement architectures in the protein biosynthesis pathway (mRNA or protein inhibition on transcription or translation). Our results show that both local and NCR controllers with mRNA-mediated inhibition are efficacious at reducing noise, with NCR controllers demonstrating a superior noise-reduction capability. We also find that combining negative feedback controllers with orthogonal resources can improve the local controllers. This work provides deep insights into the origin of stochasticity in gene circuits with resource competition and guidance for developing effective noise control strategies.
Effect of G4C2 Repeat Expansions on the Motion of Lysosomes Inside Neurites
Authors: Mytiliniou Maria , Wondergem Joeri A. J. , Feliksik Marleen , Schmidt Thomas , Heinrich Doris 
Published: October 2021

AbstractThe G4C2 hexanucleotide repeat expansion in the c9orf72 locus is one among a plethora of mutations associated with amyotrophic lateral sclerosis. It accounts for the majority of disease cases. The exact processes underlying the pathology of this mutation remain elusive, yet recent evidence suggests a mechanism that disrupts axonal trafficking. Here, we used a neuronal cell line with and without the G4C2 repeats, and implemented time-resolved local mean squared displacement analysis to characterize the motion of lysosomes inside neurites. Neurites were either aligned along chemically patterned lines, or oriented randomly on the substrate. We confirmed that in the presence of the G4C2 repeats, lysosome motion was affected. Lysosomes had a smaller reach exhibited lower velocity, especially inside aligned neurites. At the same time they became more active with increasing length of the G4C2 repeats when the neurites were randomly oriented. The duration of diffusive and super-diffusive lysosome transport remained unaffected for both neurite geometries and for all lengths of the repeats, but the displacement and velocity was decreased on varying the repeat number and neurite geometry. Lastly, the ratio of anterograde/retrograde/neutral trajectories was affected disparately for the two neurite geometries. Our observations support the hypothesis that impaired axonal trafficking emerges in the presence of the G4C2 hexanucleotide repeat expansion.
Maintenance of copy number variation at the human salivary agglutinin gene (DMBT1) by balancing selection driven by host-microbe interactions
Authors: Alharbi Adel F. , Sheng Nongfei , Nicol Katie , Strömberg Nicklas , Hollox Edward J. 
Published: October 2021

AbstractMost genetic variation in humans occurs in a pattern consistent with neutral evolution, but a small subset is maintained by balancing selection. Identifying loci under balancing selection is important not only for understanding the processes explaining variation in the genome, but also to identify loci with alleles that affect response to the environment and disease. Several genome scans using genetic variation data have identified the 5’ end of theDMBT1gene as a region undergoing balancing selection.DMBT1encodes the pattern-recognition glycoprotein DMBT1, also known as SALSA, gp340 or salivary agglutinin. It binds to a wide variety of pathogens through a tandemly-arranged scavenger receptor cysteine-rich (SRCR) domain, with the number of SRCR domains varying in humans. Here we use expression analysis, linkage in pedigrees, and long range single transcript sequencing, to show that the signal of balancing selection is driven by one haplotype usually carrying shorter SRCR repeats, and another usually carrying a longer SRCR repeat, within the coding region ofDMBT1. The DMBT1 protein size isoform encoded by a shorter SRCR domain repeat allele showed complete loss of binding of a cariogenic and invasiveStreptococcus mutansstrain in contrast to the long SRCR allele. Taken together, our results suggest that balancing selection atDMBT1is due to host-microbe interactions of encoded SRCR tandem repeat alleles.
Liberibacter solanacearum interacts with host psyllid vitellogenin with its membrane proteins
Authors: Sarkar Poulami , Ghanim Murad 
Published: October 2021

ABSTRACTCandidatus Liberibacter solanacearum (CLso) haplotype D, transmitted by the carrot psyllid Bactericera trigonica is a major constraint in carrot production in Israel. Understanding the molecular interactions between the psyllid vector and CLso can facilitate non-chemical approaches for controlling CLso caused-diseases. In this study, we used CLso outer membrane protein (OmpA) and flagellin as baits to screen for psyllid interacting proteins in a yeast-two hybrid assay. We identified psyllid vitellogenin (Vg) protein to interact with both OmpA and flagellin of CLso. As Vg is often involved in innate immunity with its expression tightly linked to autophagy, a major component of the immune response in the cell, we also analyzed the expression of autophagy-related genes to further elucidate this interaction. We used the juvenile hormone (JH-III) to induce the expression of Vg, thapsigargin for suppressing autophagy, and rapamycin for inducing autophagy. The results revealed that Vg negatively regulates autophagy and vice versa. JH-III induced Vg expression significantly suppressed autophagy and, the levels of CLso significantly increased resulting in a significant mortality of the insect. Although the specific role of Vg remains obscure, the findings presented here identify Vg as an important component in the insect immune responses against CLso and may help in understanding the initial molecular response in the vector against Liberibacter.
Sulfotyrosine, an interaction specificity determinant for extracellular protein-protein interactions
Authors: Stewart Valley , Ronald Pamela C. 
Published: October 2021

AbstractTyrosine sulfation, a post-translational modification, can enhance and often determine protein-protein interaction specificity. Sulfotyrosyl residues (sTyr) are formed by tyrosyl-protein sulfotransferase during maturation in the golgi apparatus, and most often occur singly or as a cluster of two or three sTyr within a six-residue span. With both negative charge and aromatic character, sTyr enables numerous atomic contacts as visualized in binding interface structural models, and so there is no discernible binding site consensus. Found exclusively in secreted proteins, sTyr residues occur in four broad sequence contexts. First, a single sTyr residue is critical for diverse high-affinity interactions between peptide hormones and their receptor in both plants and animals. Second, sTyr clusters within structurally flexible anionic segments are essential for a variety of processes including coreceptor binding to the HIV-1 envelope spike protein during virus entry, chemokine interactions with many chemokine receptors, and leukocyte rolling cell adhesion. Third, a subcategory of sTyr clusters occurs in the context of conserved acidic sequences termed hirudin-like motifs that enable several proteins to interact with thrombin, central to normal blood-clotting. Consequently, many proven and potential therapeutic proteins derived from blood-consuming invertebrates depend on sTyr residues for their activity. Fourth, a few proteins that interact with collagen or other proteins contain one or more sTyr residues within an acidic residue array. Refined methods to direct sTyr incorporation in peptides synthesized both in vitro and in vivo, together with continued advances in MS and affinity detection, promise to accelerate discoveries of sTyr occurrence and function.
A comprehensive evaluation of CRISPR lineage recorders using TraceQC
Authors: Hu Jingyuan , Jeong Hyun-Hwan , Al-Ouran Rami , Bado Igor , Zhang Weijie , Zhang Xiang , Liu Zhandong 
Published: October 2021

AbstractThe CRISPR-Cas9 genome editing-based lineage tracing system is emerging as a powerful tool to track cell lineages at unprecedented scale and resolution. However, the complexity of CRISPR-Cas9 induced mutations has raised challenges in lineage reconstruction, which requires a unique computational analysis framework. Meanwhile, multiple distinctive CRISPR-based high-throughput lineage recorders have been developed over the years in which the data analysis is incompatible across platforms. To address these challenges, first, we present the TraceQC, a cross-platform open-source package for data processing and quality evaluation of CRISPR lineage tracing data. Second, by using the TraceQC package, we performed a comprehensive analysis across multiple CRISPR lineage recorders to uncover the speed and distribution of CRISPR-induced mutations. Together, this work provides a computational framework for the CRISPR lineage tracing system that should broadly benefit the design and application of this promising technology.
Intracellular pH links energy metabolism to lymphocyte death and proliferation
Authors: Zeng Wei-ping , Yang Shuangshuang , Zhou Baohua 
Published: October 2021

SUMMARYThe role of intracellular pH (pHi) of lymphocytes in the control of the magnitude of immune response is unknown. We found that low pHi induces apoptosis of proliferating lymphocytes, whereas high pHi promotes their survival. In the ovalbumin sensitization and challenge model, energy metabolism is a major mechanism for regulating pHi. TCA cycle using carbohydrates lowers whereas glutaminolysis or aerobic glycolysis increases pHi. Proliferation powered by high mitochondrial membrane potentials (MMPs) in lymphocytes of low but not high pHi causes apoptosis. After antigenic challenge, lymphocytes of high pHi gradually increase and assume a positive relation between pHi and MMPs while lymphocytes of low pHi and an inverse relation between pHi and MMPs diminish. This change is at least partly dependent on glutaminolysis and aerobic glycolysis.One Sentence SummaryTCA cycle fueled with carbohydrates but not glutaminolysis or aerobic glycolysis lowers intracellular pH to induce apoptosis.
Natural transformation protein ComFA exhibits single-stranded DNA translocase activity
Authors: Foster Hannah R. , Lin Xiaoxuan , Srikant Sriram , Cueny Rachel R. , Falbel Tanya G. , Keck James L. , Gaudet Rachelle , Burton Briana M. 
Published: October 2021

SummaryNatural transformation is one of the major mechanisms of horizontal gene transfer in bacterial populations and has been demonstrated in numerous species of bacteria. Despite the prevalence of natural transformation, much of the molecular mechanism remains unexplored. One major outstanding question is how the cell powers DNA import, which is rapid and highly processive. ComFA is one of a handful of proteins required for natural transformation in gram-positive bacteria. Its structural resemblance to the DEADbox helicase family has led to a long-held hypothesis that ComFA acts as a motor to help drive DNA import into the cytosol. Here, we explored the helicase and translocase activity of ComFA to address this hypothesis. We followed the DNA-dependent ATPase activity of ComFA and, combined with mathematical modeling, demonstrated that ComFA likely translocates on single-stranded DNA from 5’ to 3’. However, this translocase activity does not lead to DNA unwinding in the conditions we tested. Further, we analyzed the ATPase cycle of ComFA and found that ATP hydrolysis stimulates the release of DNA, providing a potential mechanism for translocation. These findings help define the molecular contribution of ComFA to natural transformation and support the conclusion that ComFA plays a key role in powering DNA uptake.ImportanceCompetence, or the ability of bacteria to take up and incorporate foreign DNA in a process called natural transformation is common in the bacterial kingdom, but understanding of the mechanism is still limited. Increasing evidence in several bacteria confirms that long, contiguous stretches of DNA are imported into cells, and yet how bacteria power processive transformation remains unclear. Our finding that ComFA, a DExD-box helicase required for competence in gram-positive bacteria, translocates on single-stranded DNA from 5’ to 3’, supports the long held hypothesis that ComFA may be the motor powering DNA transport during natural transformation. Moreover, ComFA may be a previously unidentified type of DExD-box helicase—one with the capability of extended translocation on single-stranded DNA.
Illumina But With Nanopore: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
Authors: Zee Alexander , Deng Dori Z. Q. , Adams Matthew , Schimke Kayla D. , Corbett-Detig Russell , Russell Shelbi L. , Zhang Xuan , Schmitz Robert J. , Vollmers Christopher 
Published: October 2021

AbstractHigh-throughput short-read sequencing has taken on a central role in research and diagnostics. Hundreds of different assays exist today to take advantage of Illumina short-read sequencers, the predominant short-read sequencing technology available today. Although other short read sequencing technologies exist, the ubiquity of Illumina sequencers in sequencing core facilities, and the high capital costs of these technologies have limited their adoption. Among a new generation of sequencing technologies, Oxford Nanopore Technologies (ONT) holds a unique position because the ONT MinION, an error-prone long-read sequencer, is associated with little to no capital cost. Here we show that we can make short-read Illumina libraries compatible with the ONT MinION by using the R2C2 method to circularize and amplify the short library molecules. This results in longer DNA molecules containing tandem repeats of the original short library molecules. This longer DNA is ideally suited for the ONT MinION, and after sequencing, the tandem repeats in the resulting raw reads can be converted into high-accuracy consensus reads with similar error rates to that of the Illumina MiSeq. We highlight this capability by producing and benchmarking RNA-seq, ChIP-seq, as well as regular and target-enriched Tn5 libraries. We also explore the use of this approach for rapid evaluation of sequencing library metrics by implementing a real-time analysis workflow.
Characterization of heterologously expressed fibril filaments, a shape and motility determining cytoskeletal protein of the helical bacteriumSpiroplasma
Authors: Harne Shrikant , Gayathri Pananghat 
Published: October 2021

AbstractFibril is a constitutive filament forming cytoskeletal protein of unidentified fold, exclusive to members of genusSpiroplasma. It is hypothesized to undergo conformational changes necessary to bring aboutSpiroplasmamotility through changes in body helicity. However, in the absence of a cofactor such as nucleotide that binds to the protein and drives polymerization, the mechanism driving conformational changes in fibril remains unknown. Sodium dodecyl sulphate (SDS) solubilized the fibril filaments and facilitated fibril purification by affinity chromatography. An alternate protocol for obtaining enriched insoluble fibril filaments has been standardized using density gradient centrifugation method. Visualization of purified protein using electron microscopy demonstrated that it forms filament bundles. Probable domain boundaries of fibril protein were identified based on mass spectrometric analysis of proteolytic fragments. Presence of both α-helical and β-sheet signatures in FT-IR measurements suggests that fibril filaments consist of assembly of folded globular domains, and not a β-strand based aggregation similar to amyloid fibrils.