bluuebunny/crossref_metadata_2025_split huggingface dataset:
Determining clinically relevant features in cytometry data using persistent homology
Authors: Mukherjee Soham , Wethington Darren , Dey Tamal K. , Das Jayajit 
Published: April 2021

AbstractCytometry experiments yield high-dimensional point cloud data that is difficult to interpret manually. Boolean gating techniques coupled with comparisons of relative abundances of cellular subsets is the current standard for cytometry data analysis. However, this approach is unable to capture more subtle topological features hidden in data, especially if those features are further masked by data transforms or significant batch effects or donor-to-donor variations in clinical data. We present that persistent homology, a mathematical structure that summarizes the topological features, can distinguish different sources of data, such as from groups of healthy donors or patients, effectively. Analysis of publicly available cytometry data describing non-naïve CD8+ T cells in COVID-19 patients and healthy controls shows that systematic structural differences exist between single cell protein expressions in COVID-19 patients and healthy controls.Our method identifies proteins of interest by a decision-tree based classifier and passes them to a kernel-density estimator (KDE) for sampling points from the density distribution. We then compute persistence diagrams from these sampled points. The resulting persistence diagrams identify regions in cytometry datasets of varying density and identify protruded structures such as ‘elbows’. We compute Wasserstein distances between these persistence diagrams for random pairs of healthy controls and COVID-19 patients and find that systematic structural differences exist between COVID-19 patients and healthy controls in the expression data for T-bet, Eomes, and Ki-67. Further analysis shows that expression of T-bet and Eomes are significantly downregulated in COVID-19 patient non-naïve CD8+ T cells compared to healthy controls. This counter-intuitive finding may indicate that canonical effector CD8+ T cells are less prevalent in COVID-19 patients than healthy controls. This method is applicable to any cytometry dataset for discovering novel insights throughtopological data analysiswhich may be difficult to ascertain otherwise with a standard gating strategy or in the presence of large batch effects.Author summaryIdentifying differences between cytometry data seen as a point cloud can be complicated by random variations in data collection and data sources. We applypersistent homologyused intopological data analysisto describe the shape and structure of the data representing immune cells in healthy donors and COVID-19 patients. By looking at how the shape and structure differ between healthy donors and COVID-19 patients, we are able to definitively conclude how these groups differ despite random variations in the data. Furthermore, these results are novel in their ability to capture shape and structure of cytometry data, something not described by other analyses.
Single-virus content mixing assay reveals cholesterol-enhanced influenza membrane fusion efficiency
Authors: Liu Katherine N. , Boxer Steven G. 
Published: April 2021

AbstractIn order to infect a cell, enveloped viruses must first undergo membrane fusion, which proceeds through a hemifusion intermediate, followed by the formation of a fusion pore through which the viral genome is transferred to a target cell. Single-virus fusion studies to elucidate the dynamics of content mixing typically require extensive fluorescent labeling of viral contents. The labeling process must be optimized depending on the virus identity and strain and can potentially be perturbative to viral fusion behavior. Here, we introduce a single-virus assay where content-labeled vesicles are bound to unlabeled influenza A virus (IAV) to eliminate the problematic step of content-labeling virions. We use fluorescence microscopy to observe individual, pH-triggered content mixing and content loss events between IAV and target vesicles of varying cholesterol compositions. We show that target membrane cholesterol increases the efficiency of IAV content mixing and decreases the fraction of content mixing events that result in content loss. These results are consistent with previous findings that cholesterol stabilizes pore formation in IAV entry and limits leakage following pore formation. We also show that content loss due to hemagglutinin fusion peptide engagement with the target membrane is independent of composition. This approach is a promising strategy for studying the single-virus content mixing kinetics of other enveloped viruses.Statement of SignificanceTo replicate, enveloped viruses, like influenza A virus, must successfully deliver their contents to a host cell through viral membrane fusion. Most single-virus fusion assays require extensive fluorescent labeling of virions which can be perturbative to fusion kinetics. Here, we utilize content-labeled vesicles in a single-virus content mixing assay, which eliminates the need to fluorescently label virus contents. We use this assay to show that target membrane cholesterol increases the fraction of stable influenza virus content mixing events. This assay also enables the study of target membrane destabilization due to viral fusion peptide engagement.
Nucleocapsid vaccine elicits spike-independent SARS-CoV-2 protective immunity
Authors: Matchett William E. , Joag Vineet , Stolley J. Michael , Shepherd Frances K. , Quarnstrom Clare F. , Mickelson Clayton K. , Wijeyesinghe Sathi , Soerens Andrew G. , Becker Samuel , Thiede Joshua M. , Weyu Eyob , O’Flanagan Stephen , Walter Jennifer A. , Vu Michelle N. , Menachery Vineet D. , Bold Tyler D. , Vezys Vaiva , Jenkins Marc K. , Langlois Ryan A. , Masopust David 
Published: April 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the COVID-19 pandemic. Neutralizing antibodies target the receptor binding domain of the spike (S) protein, a focus of successful vaccine efforts. Concerns have arisen that S-specific vaccine immunity may fail to neutralize emerging variants. We show that vaccination with HAd5 expressing the nucleocapsid (N) protein can establish protective immunity, defined by reduced weight loss and viral load, in both Syrian hamsters and k18-hACE2 mice. Challenge of vaccinated mice was associated with rapid N-specific T cell recall responses in the respiratory mucosa. This study supports the rationale for including additional viral antigens, even if they are not a target of neutralizing antibodies, to broaden epitope coverage and immune effector mechanisms.
Inositol lipid synthesis is widespread in host-associated Bacteroidetes
Authors: Heaver S. L. , Le H. H. , Tang P. , Baslé A. , Marles-Wright J. , Johnson E. L. , Campopiano D. J. , Ley R. E. 
Published: April 2021

AbstractUbiquitous in eukaryotes, inositol lipids have finely tuned roles in cellular signaling and membrane homeostasis. In Bacteria, however, inositol lipid production is rare. Recently, the prominent human gut bacteriumBacteroides thetaiotaomicron(BT) was reported to produce inositol lipids, including inositol sphingolipids, but the pathways remain ambiguous and their prevalence unclear. Here, we investigated the gene cluster responsible for inositol lipid synthesis in BT using a novel strain with inducible control of sphingolipid synthesis. We characterized the biosynthetic pathway frommyo-inositol-phosphate (MIP) synthesis to phosphoinositol-dihydroceramide, including structural and kinetic studies of the enzyme MIP synthase (MIPS). We determined the crystal structure of recombinant BT MIPS with bound NAD cofactor at 2.0 Å resolution, and identified the first reported phosphatase for the conversion of bacterially-derived phosphatidylinositol phosphate (PIP) to phosphatidylinositol (PI). Transcriptomic analysis indicated inositol production is nonessential but its loss alters BT capsule expression. Bioinformatic and lipidomic comparisons of Bacteroidetes species revealed a novel second putative pathway for bacterial PI synthesis without a PIP intermediate. Our results indicate that inositol sphingolipid production, via one of the two pathways, is widespread in host-associated Bacteroidetes, and may be implicated in host interactions both indirectly via the capsule and directly through inositol lipid provisioning.
Genomically mined acoustic reporter genes enable real-timein vivomonitoring of tumors and tumor-homing probiotics
Authors: Hurt Robert C. , Buss Marjorie T. , Duan Mengtong , Wong Katie , You Mei Yi , Sawyer Daniel P. , Swift Margaret B. , Dutka Przemysław , Barturen-Larrea Pierina , Mittelstein David R. , Jin Zhiyang , Abedi Mohamad H. , Farhadi Arash , Deshpande Ramya , Shapiro Mikhail G. 
Published: April 2021

ABSTRACTA major outstanding challenge in the fields of biological research, synthetic biology and cell-based medicine is visualizing the function of natural and engineered cells noninvasively inside opaque organisms. Ultrasound imaging has the potential to address this challenge as a widely available technique with a tissue penetration of several centimeters and spatial resolution below 100 μm. Recently, the first genetically encoded acoustic reporters were developed based on bacterial gas vesicles to link ultrasound signals to molecular and cellular function. However, the properties of these first-generation acoustic reporter genes (ARGs) resulted in limited sensitivity and specificity for imaging gene expressionin vivo.Here, we describe second-generation ARGs with greatly improved acoustic properties and expression characteristics, identified through a phylogenetic screen of candidate gene clusters from diverse bacteria and archaea. The resulting constructs offer major qualitative and quantitative improvements, including much stronger ultrasound contrast, the ability to produce nonlinear signals distinguishable from background tissue, and stable long-term expression. We demonstrate the capabilities of these next-generation ARGs by imagingin situgene expression in mouse models of breast cancer and tumor-homing therapeutic bacteria, noninvasively revealing the unique spatial distributions of tumor growth and colonization by therapeutic cells in living subjects and providing real-time guidance for interventions such as needle biopsies.
Differentiation of speech-induced artifacts from physiological high gamma activity in intracranial recordings
Authors: Bush Alan , Chrabaszcz Anna , Peterson Victoria , Saravanan Varun , Dastolfo-Hromack Christina , Lipski Witold J. , Richardson R. Mark 
Published: April 2021

AbstractThere is great interest in identifying the neurophysiological underpinnings of speech production. Deep brain stimulation (DBS) surgery is unique in that it allows intracranial recordings from both cortical and subcortical regions in patients who are awake and speaking. The quality of these recordings, however, may be affected to various degrees by mechanical forces resulting from speech itself. Here we describe the presence of speech-induced artifacts in local-field potential (LFP) recordings obtained from mapping electrodes, DBS leads, and cortical electrodes. In addition to expected physiological increases in high gamma (60-200 Hz) activity during speech production, time-frequency analysis in many channels revealed a narrowband gamma component that exhibited a pattern similar to that observed in the speech audio spectrogram. This component was present to different degrees in multiple types of neural recordings. We show that this component tracks the fundamental frequency of the participant’s voice, correlates with the power spectrum of speech and has coherence with the produced speech audio. A vibration sensor attached to the stereotactic frame recorded speech-induced vibrations with the same pattern observed in the LFPs. No corresponding component was identified in any neural channel during the listening epoch of a syllable repetition task. These observations demonstrate how speech-induced vibrations can create artifacts in the primary frequency band of interest. Identifying and accounting for these artifacts is crucial for establishing the validity and reproducibility of speech-related data obtained from intracranial recordings during DBS surgery.
Effect of Disease Causing Missense Mutations on Intrinsically Disordered Regions in Proteins
Authors: Seera Suryanarayana , Nagarajaram H.A. 
Published: April 2021

AbstractIt is well known that disease-causing missense mutations (DCMMs) reduce the structural stability/integrity of the proteins with well-defined 3D structures thereby impacting their molecular functions. However, it is not known in what way DCMMs affect the intrinsically disordered proteins (IDPs) that do not adopt well defined stable 3D structures. In order to investigate how DCMMs may impact intrinsically disordered regions (IDRs) in proteins we undertook Molecular Dynamics (MD) based studies on three different examples of functionally important IDRs with known DCMMs. Our studies revealed that the functional impact of DCMMs is in reducing the conformational heterogeneity of IDRs which is intrinsic and quintessential for their multi-faceted cellular roles. These results are reinforced by energy landscapes of the wildtype and mutant IDRs where the former is characterized by many local minima separated by low barriers whereas the latter are characterized by one global minimum and several local minima separated by high energy barriers. Our MD based studies also indicate that DCMMs stabilize a very few structural possibilities of IDRs either by the newly formed interactions induced by the substituted side chains or by means of restricted or increased flexibilities of the backbone conformations at the mutation sites. Furthermore, the structural possibilities stabilized by DCMMs do not support the native functional roles of the IDRs thereby leading to disease conditions.
Maternal Western-Style Diet Impairs Bone Marrow Development and Drives a Hyperinflammatory Phenotype in Hematopoietic Stem and Progenitor Cells in Fetal Rhesus Macaques
Authors: Sureshchandra Suhas , Chan Chi N. , Robino Jacob J. , Parmelee Lindsay K. , Nash Michael J. , Wesolowski Stephanie R. , Pietras Eric M. , Friedman Jacob E. , Takahashi Diana , Shen Weining , Hennebold Jon D. , Goldman Devorah , Packwood William , Lindner Jonathan R , Roberts Charles T. , Burwitz Benjamin J. , Messaoudi Ilhem , Varlamov Oleg 
Published: April 2021

ABSTRACTBackgroundMaternal obesity adversely impacts the in utero metabolic environment and offspring’s health, but its effect on fetal hematopoiesis and immune cell development remains incompletely understood, particularly in models that resemble human development.MethodsWe studied gestational day 130-135 fetuses derived from rhesus macaque dams chronically exposed to a high-fat Western-style diet (WSD) or a low-fat control diet. Fetal immune cell phenotypes and fetal bone marrow architecture and hematopoietic stem and progenitor cell (FBM HSPC) function were examined using bone computed tomography, histology, flow cytometry, single-cell RNA-sequencing, and HSPC transplantation assays.FindingsMaternal WSD induced premature FBM cavity opening and a codominant increase in the number of FBM adipocytes. Furthermore, a maternal WSD induced a proinflammatory transcriptional response in FBM HSPCs. FBM macrophages from the WSD group exhibited heightened proinflammatory responses to toll-like receptor agonist stimulation. Maternal WSD exposure suppressed the expression of genes required for B-cell development and decreased the frequencies of FBM B-cells. Finally, maternal WSD led to poor engraftment of FBM HSPCs in nonlethally irradiated immunodeficient NOD/SCID/IL2rγ-/-mice.InterpretationsMaternal WSD impairs FBM development, drives a hyperinflammatory phenotype, and induces functional and differentiation impairment in FBM HSPCs in a translationally relevant nonhuman primate model.FundingNational Institute of HealthRESEARCH IN CONTEXTEvidence before this studyMaternal obesity is associated with increased risk of infections and proinflammatory disease in offspring. The translationally-relevant rhesus macaque model was utilized to address the effects of maternal obesogenic diet on fetal hematopoietic and immune cell development.Added value of this studyWe assessed changes in fetal immune cell phenotypes and fetal hematopoietic stem and progenitor cell function using immunohistochemistry, flow cytometry, single-cell RNA sequencing, and transplantation assays. We determined that chronic consumption of a maternal obesogenic diet induced the development of adipogenic and proinflammatory environments in the fetal bone marrow. Additionally, we detected the impairment in B-cell differentiation program in fetal hematopoietic stem and progenitor cells.Implications of all the available evidenceThese data demonstrate that maternal obesogenic diet modulates fetal hematopoietic development and could impact the offspring’s immune system, including proinflammatory phenotype and a decline in B-cell function.
Engagement of the contralateral limb can enhance the facilitation of motor output by loud acoustic stimuli
Authors: McInnes Aaron N. , Nguyen An T. , Carroll Timothy J. , Lipp Ottmar V. , Marinovic Welber 
Published: April 2021

AbstractWhen intense sound is presented during light muscle contraction, inhibition of the corticospinal tract is observed. During action preparation, this effect is reversed, with sound resulting in excitation of the corticospinal tract. We investigated how the combined maintenance of a muscle contraction during preparation for a ballistic action impacts the magnitude of the facilitation of motor output by a loud acoustic stimulus (LAS) – a phenomenon known as the StartReact effect. Participants executed ballistic wrist flexion movements and a LAS was presented simultaneously with the imperative signal in a subset of trials. We examined whether the force level or muscle used to maintain a contraction during preparation for the ballistic response impacted reaction time and/or the force of movements triggered by the LAS. These contractions were sustained either ipsilaterally or contralaterally to the ballistic response. The magnitude of facilitation by the LAS was greatest when low force flexion contractions were maintained in the limb contralateral to the ballistic response during preparation. There was little change in facilitation when contractions recruited the contralateral extensor muscle, or when they were sustained in the same limb that executed the ballistic response. We conclude that a larger network of neurons which may be engaged by a contralateral sustained contraction prior to initiation may be recruited by the LAS, further contributing to the motor output of the response. These findings may be particularly applicable in stroke rehabilitation where engagement of the contralesional side may increase the benefits of a LAS to the functional recovery of movement.
Efficiency of neutral honey as a tissue fixative in histopathology
Authors: Alwahaibi Nasar , Al Dhahli Buthaina , Al Issaei Halima , Al Wahaibi Loai , Al Sinawi Shadia 
Published: April 2021

AbstractIn the routine laboratory, 10% neutral buffered formalin (NBF) is the fixative of choice. However, formalin is a human carcinogen. To the best of our knowledge, neutral honey, not natural or artificial honey, has not been tested to fix histological tissues. This study aimed to examine the efficiency of neutral buffered honey and other types of honey fixatives to fix histological tissues. The most two natural common Omani honey were used as fixatives, namely Sumar and date. We tested samples of rat liver, kidney, and stomach. Nine types of fixatives were used. All tissues were treated equally. The evaluation was performed blindly by three senior biomedical scientists who work in a histopathology laboratory. Hematoxylin and eosin showed adequate staining in all groups when compared to 10% NBF. The intensity and specificity of Jones Methenamine silver stain in 10% Sumer and Date honey and 10% alcoholic Sumer honey showed similar findings of 10% NBF. The specificity and intensity of all groups for Periodic acid–Schiff were comparable with 10% neutral buffered formalin accepts for 10% Sumer honey and 10% Alcoholic Date honey. However, all honey groups showed weak staining for the reticulin fibers using Gordon and Sweets method. Vimentin showed comparable findings with 10% NBF as there were no significant differences. The findings of this study are promising. Further in depth research on honey as a possible safe substitute fixative for formalin should be conducted.
Adjuvant and immunomodulatory potential ofin vivoNatural Killer T (NKT) activation by NKTT320
Authors: Bond Nell G. , Fahlberg Marissa , Yu Shan , Rout Namita , Tran Dollnovan , Fitzpatrick-Schmidt Taylor , Sprehe Lesli , Scheef Elizabeth , Mudd Joseph C. , Schaub Robert , Kaur Amitinder 
Published: April 2021

AbstractInvariant natural killer T-lymphocytes (iNKT) are unique immunomodulatory innate T-cells with an invariant TCRα recognizing glycolipids presented on MHC class-I-like CD1d molecules. Activated iNKT rapidly secrete pro-and anti-inflammatory cytokines, potentiate innate and adaptive immunity, and modulate inflammation. Here, we report the effects ofin vivoiNKT activation by a novel humanized monoclonal antibody, NKTT320, that binds to the invariant region of the iNKT TCR. NKTT320 led to rapid iNKT activation, increased polyfunctionality, and elevation of multiple plasma analytes within 24 hours of administration. Flow cytometry and RNA-Seq confirmed downstream activation of multiple immune subsets, enrichment of JAK/STAT and PI3K/AKT pathway genes, and upregulation of inflammation-modulating genes CMKLR1, ARG2 and NLRP12. NKTT320 also induced iNKT trafficking to adipose tissue and did not cause iNKT anergy. Our data indicate that NKTT320 has a sustained effect onin vivoiNKT activation, potentiation of innate and adaptive immunity, and resolution of inflammation, which supports its future use as an immunotherapeutic and vaccine adjuvant.SummaryiNKTs are known immunomodulatory cells whose activation is a potential target for immunotherapies and use as an adjuvant. Here we report the potential utility ofin vivoiNKT activation using the novel humanized monoclonal antibody NKTT320 for this purpose.
The genomic basis of domestic colonisation and dispersal in Chagas disease vectors
Authors: Hernandez-Castro Luis E , Villacís Anita G , Jacobs Arne , Cheaib Bachar , Day Casey C , Ocaña-Mayorga Sofía , Yumiseva Cesar A , Bacigalupo Antonella , Andersson Björn , Matthews Louise , Landguth Erin L , Costales Jaime A , Llewellyn Martin S , Grijalva Mario J 
Published: April 2021

AbstractThe biology of vector adaptation to the human habitat remains poorly understood for many arthropod-borne diseases but underpins effective and sustainable disease control. We adopted a landscape genomics approach to investigate gene flow, signatures of local adaptation, and drivers of population structure among multiple linked wild and domestic population pairs in Rhodnius ecuadoriensis, an important vector of Chagas Disease. Evidence of high triatomine gene flow (FST) between wild and domestic ecotopes at sites throughout the study area indicate insecticide-based control will be hindered by constant re-infestation of houses. Genome scans revealed genetic loci with strong signal of local adaptation to the domestic setting, which we mapped to annotated regions in the Rhodnius prolixus genome. Our landscape genomic mixed effects models showed Rhodnius ecuadoriensis population structure and connectivity is driven by landscape elevation at a regional scale. Our ecologically- and spatially-explicit vector dispersal model enables targeted vector control and recommends spatially discrete, periodic interventions to local authorities as more efficacious than current, haphazard approaches. In tandem, evidence for parallel genomic adaptation to colonisation of the domestic environment at multiple sites sheds new light on the evolutionary basis of adaptation to the human host in arthropod vectors.