bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coordinated Chemokine Expression Defines Macrophage Subsets Across Tissues
Authors: Li Xin , Mara Arlind B. , Musial Shawn , Rawat Kavita , King William T. , Kolling Fred W. , Gerebtsov Nikita , Jakubzick Claudia V. 
Published: May 2023

AbstractTissue-resident macrophages in the lung comprising alveolar and interstitial macrophages (IMs) display a high degree of heterogeneity. In general, macrophage heterogeneity is thought to arise from various forms of activation that are heavily confounded by the recruitment of monocytes to the tissue-resident macrophage pool. To better understand the functional heterogeneity of IMs in the lung, we profiled the transcription of resident CD206hiand CD206loIMs under steady-state and inflammatory conditions, excluding recruited macrophages. Rather than observing conventionalin vitroM1 and M2 activation states, we identified seven chemokine-expressing IM subsets: IMck1 (Ccl2, Ccl7, Ccl12,and someCxcl14), IMck2-4 (Ccl3, Ccl4, Ccl5, Cxcl1, Cxcl2,andCxcl3), IMck5 (Ccl8), IMck6 (Ccl6andCcl9), IMck7 (Cxcl9andCxcl10), IMck8 (Cxcl13), and IMck9 (Ccl24), which were found in steady-state or induced by acute inflammation. Beyond the mouse lung, similar coordinated chemokine signatures were observed in macrophages and monocytes from other tissues and across species. Although all IMs expressedPf4(CXCL4), mainly CD206hiIMs were selectively depleted inPf4CreR26EYFP-DTRmice. Loss of CD206hiIMs resulted in significantly reduced inflammatory cell influx in allergen- and infection-driven models, as well as significantly diminished tertiary lymphoid formation and subsequent accumulation of GL7+germinal center B cells. Overall, our study highlights a division of labor among interstitial macrophages, reflected by the coordinated production of chemokines to control inflammatory cell influx and organize tertiary lymphoid tissue architecture.One Sentence SummaryThe study highlights a division of labor among interstitial macrophages, reflected by the coordinated production of chemokines to control inflammatory cell influx and organize tertiary lymphoid tissue architecture.
Whole Transcriptome and Functional Analyses Identify Novel Genes Involved in Meiosis and Fertility inDrosophila melanogaster
Authors: Sun Siqi , Defosse Tyler , Boyd Ayla , Sop Joel , Verderose Faith , Surray Diya , Aziz Mark , Howland Margaret , Wu Siwen , Changela Neha , Jang Janet , Schindler Karen , Xing Jinchuan , McKim Kim S. 
Published: May 2023

AbstractReproductive success requires the development of viable oocytes and the accurate segregation of chromosomes during meiosis. Failure to segregate chromosomes properly can lead to infertility, miscarriages, or developmental disorders. A variety of factors contribute to accurate chromosome segregation and oocyte development, such as spindle assembly and sister chromatid cohesion. However, many proteins required for meiosis remain unknown. In this study, we aimed to identify and characterize novel meiotic and fertility genes using the genome ofDrosophila melanogaster. To accomplish this goal, genes upregulated within meiotically active tissues were identified. About 200 genes with no known function were silenced using RNA interference (RNAi), and the effects on meiosis and fertility were assessed. We identified 65 genes that when silenced caused infertility and/or high levels of chromosomal nondisjunction. The vast majority of these genes have human and mouse homologs that are also poorly studied. Through this screening process, we identified novel genes that are crucial for meiosis and oocyte development but have not been extensively studied in human or model organisms. Understanding the function of these genes will be an important step towards the understanding of their biological significance during reproduction.Author SummaryIn this study, we aimed to identify and characterize novel meiotic and fertility genes within the genome ofDrosophila melanogaster. We identified 65 genes that when silenced caused infertility and/or high levels of chromosomal nondisjunction. The vast majority of these genes have human and mouse homologs that are also poorly studied. Through this screening process, we identified novel genes that are crucial for meiosis and oocyte development, making them strong candidates for future studies to characterize their functions.
LRP10 as a novel α-synuclein regulator in Lewy body diseases
Authors: Mascaro Ana Carreras , Grochowska Martyna M. , Boumeester Valerie , Dits Natasja F. J. , Bilgiҫ Ece Naz , Breedveld Guido J. , Vergouw Leonie , de Jong Frank Jan , van Royen Martin E. , Bonifati Vincenzo , Mandemakers Wim 
Published: May 2023

AbstractAutosomal dominant variants inLRP10have been identified in patients with Lewy body diseases (LBDs), including Parkinson’s disease (PD), Parkinson’s disease-dementia (PDD), and dementia with Lewy bodies (DLB). Nevertheless, there is little mechanistic insight into the role of LRP10 in disease pathogenesis. In the brains of non-demented individuals, LRP10 is typically expressed in non-neuronal cells like astrocytes and neurovasculature, but in idiopathic and genetic cases of PD, PDD, and DLB it is also present in α-synuclein-positive neuronal Lewy bodies. These observations raise the questions of what leads to the accumulation of LRP10 in Lewy bodies and whether a possible interaction between LRP10 and α-synuclein plays a role in disease pathogenesis. Here, we demonstrate that wild-type LRP10 is secreted via extracellular vesicles (EVs) and can be internalised via clathrin-dependent endocytosis. Additionally, we show that LRP10 secretion is highly sensitive to autophagy inhibition, which induces the formation of atypical LRP10 vesicular structures in neurons in human induced pluripotent stem cells (iPSC)-derived midbrain-like organoids (hMLOs). Furthermore, we show that LRP10 overexpression leads to a strong induction of monomeric α-synuclein secretion, together with time-dependent, stress-sensitive changes in intracellular α-synuclein levels. Interestingly, patient-derived astrocytes carrying thec.1424+5G>A LRP10variant secrete aberrant high-molecular-weight species of LRP10 in EV-free media fractions. Finally, we show that the truncated LRP10spliceprotein binds to wild-type LRP10, reduces LRP10 wild-type levels, and antagonises the regulatory effect of LRP10 on α-synuclein levels and distribution. Together, this work provides initial evidence for a functional role of LRP10 in LBDs by regulating intra- and extracellular α-synuclein levels, and pathogenic mechanisms linked to the disease-associatedc.1424+5G>A LRP10variant, pointing towards potentially important disease mechanisms in LBDs.
Anti-nuclear antibody (ANA) detection in culture supernatant of cloned B cells
Authors: Haque Shabirul , Watanabe Manami , Atisha-Fregoso Yemil , Diamond Betty 
Published: May 2023

AbstractAnti-nuclear antibodies (ANA) of individuals with SLE contribute to disease pathogenesis and tissue injury. Systematic analysis of the fine specificity of ANA produced by individual B cells has been limited, in part, to the low concentration of immunoglobulin in single B cell cultures. We modified single B cell culture methods and developed an ANA ELISA to detect ANA at very low levels (15.0 ng/ml) of IgM in the supernatant of clonally expanded B cell cultures. This approach allows for the analysis of ANA reactivity of the IgM produced by approximately 60% of the single sorted naive B cells expanded in culture and permits a relatively high throughput evaluation at the single cell level of the ANA reactivity of naïve B cells of healthy individuals and patients with autoimmune diseases.
Functional Characterization of Calmodulin-like Proteins, CML13 and CML14, as Novel Light Chains of Arabidopsis Class VIII Myosins
Authors: Symonds Kyle , Teresinski Howard J. , Hau Bryan , Sadot Einat , Dwivedi Vikas , Belausov Eduard , Bar-Sinai Sefi , Tominaga Motoki , Haraguchi Takeshi , Ito Kohji , Snedden Wayne A. 
Published: May 2023

AbstractMyosins are important motor proteins that associate with the actin cytoskeleton. Structurally, myosins function as heteromeric complexes where smaller light chains, such as calmodulin (CaM), bind to isoleucine-glutamine (IQ) domains in the neck regions to facilitate mechano-enzymatic activity. We recently identified Arabidopsis CaM-like (CML) proteins, CML13 and CML14 as interactors of proteins containing multiple IQ domains, including a member of the myosin VIII class. Here, usingin vivoandin vitroassays we demonstrate that CaM, CML13, and CML14 bind the neck region of all four Arabidopsis myosin VIII isoforms. Among ten CML isoforms tested forin plantabinding to myosins VIIIs, CaM, CML13, and CML14 gave the strongest signals usingin plantasplit-luciferase protein-interaction assays.In vitro,recombinant CaM, CML13, and CML14 showed specific, high-affinity, calcium-independent binding to the IQ domains of myosin VIIIs. Subcellular localization analysis indicated that CaM, CML13, and CML14 co-localized to plasma membrane-bound puncta when co-expressed with RFP-myosin fusion proteins containing IQ- and tail-domains of myosin VIIIs. In addition,in vitroactin-motility assays using recombinant myosin holoenzymes demonstrated that CaM, CML13, and CML14 function as light chains for myosin VIIIs. Collectively, our data indicate that Arabidopsis CML13 and CML14 are novel myosin VIII light chains.HighlightMyosins are key proteins in the plant cytoskeleton, but the identity of their light chain components is unknown. Here, we show that calmodulin-like proteins function as novel myosin light chains.
Non-micellar ganglioside GM1 induces an instantaneous conformational change in Aβ42leading to the modulation of the peptide amyloid-fibril pathway
Authors: Kumar Manjeet , Ivanova Magdalena I , Ramamoorthy Ayyalusamy 
Published: May 2023

AbstractAlzheimer’s disease is a progressive degenerative condition that mainly affects cognition and memory. Recently, distinct clinical and neuropathological phenotypes have been identified in AD. Studies revealed that structural variation in Aβ fibrillar aggregates correlates with distinct disease phenotypes. Moreover, environmental surroundings, including other biomolecules such as proteins and lipids, have been shown to interact and modulate Aβ aggregation. Model membranes containing ganglioside (GM1) clusters are specifically known to promote Aβ fibrillogenesis. This study unravels the modulatory effect of non-micellar GM1, a glycosphingolipid frequently released from the damaged neuronal membranes, on Aβ42amyloid fibril formation. Using far-UV circular dichroism experiments, we observed a spontaneous change in the peptide secondary structure from random-coil to β-turn with subsequent generation of predominantly β-sheet-rich species upon interaction with GM1. Thioflavin-T (ThT) fluorescence assays further indicated that GM1 interacts with the amyloidogenic Aβ42primary nucleus leading to a possible formation of GM1-modified Aβ42fibril. Statistically, no significant difference in toxicity to RA-differentiated SH-SY5Y cells was observed between Aβ42fibrils and GM1-tweaked Aβ42aggregates. Moreover, GM1-modified Aβ42aggregates exhibited prion-like properties in catalyzing the amyloid fibril formation of both major isomers of Aβ, Aβ40, and Aβ42.
Serotonin modulates infraslow oscillation in the dentate gyrus during Non-REM sleep
Authors: Turi Gergely F. , Teng Sasa , Chen Xinyue , Lim Emily CY , Dias Carla , Hu Ruining , Wang Ruizhi , Zhen Fenghua , Peng Yueqing 
Published: May 2023

ABSTRACTSynchronous neuronal activity is organized into neuronal oscillations with various frequency and time domains across different brain areas and brain states. For example, hippocampal theta, gamma and sharp wave oscillations are critical for memory formation and communication between hippocampal subareas and the cortex. In this study, we investigated the neuronal activity of the dentate gyrus (DG) with optical imaging tools during sleep-wake cycles. We found that the activity of major glutamatergic cell populations in the DG is organized into infraslow oscillations (0.01 – 0.03 Hz) during NREM sleep. Although the DG is considered a sparsely active network during wakefulness, we found that 50% of granule cells and about 25% of mossy cells exhibit increased activity during NREM sleep, compared to that during wakefulness. Further experiments revealed that the infraslow oscillation in the DG was correlated with rhythmic serotonin release during sleep, which oscillates at the same frequency but in an opposite phase. Genetic manipulation of 5-HT receptors revealed that this neuromodulatory regulation is mediated by 5-HT1a receptors and the knockdown of these receptors leads to memory impairment. Together, our results provide novel mechanistic insights into how the 5-HT system can influence hippocampal activity patterns during sleep.
Decreasing the flexibility of the TELSAM-target protein linker and omitting the cleavable fusion tag improves crystal order and diffraction limits
Authors: Gajjar Parag L. , Romo Maria J. Pedroza , Litchfield Celeste M. , Callahan Miles , Redd Nathan , Nawarathnage Supeshala , Soleimani Sara , Averett Jacob , Wilson Elijah , Lewis Andrew , Stewart Cameron , Tseng Yi-Jie J. , Doukov Tzanko , Lebedev Andrey , Moody James D. 
Published: May 2023

AbstractTELSAM crystallization promises to become a revolutionary tool for the facile crystallization of proteins. TELSAM can increase the rate of crystallization and form crystals at low protein concentrations without direct contact between TELSAM polymers and, in some cases, with very minimal crystal contacts overall (Nawarathnageet al., 2022). To further understand and characterize TELSAM-mediated crystallization, we sought to understand the requirements for the composition of the linker between TELSAM and the fused target protein. We evaluated four different linkers Ala-Ala, Ala-Val, Thr-Val, and Thr-Thr, between 1TEL and the human CMG2 vWa domain. We compared the number of successful crystallization conditions, the number of crystals, the average and best diffraction resolution, and the refinement parameters for the above constructs. We also tested the effect of the fusion protein SUMO on crystallization. We discovered that rigidification of the linker improved diffraction resolution, likely by decreasing the number of possible orientations of the vWa domains in the crystal, and that omitting the SUMO domain from the construct also improved the diffraction resolution.SynopsisWe demonstrate that the TELSAM protein crystallization chaperone can enable facile protein crystallization and high-resolution structure determination. We provide evidence to support the use of short but flexible linkers between TELSAM and the protein of interest and to support the avoidance of cleavable purification tags in TELSAM-fusion constructs.
Drug Repurposing using consilience of Knowledge Graph Completion methods
Authors: Tu Roger , Sinha Meghamala , González Carolina , Hu Eric , Dhuliawala Shehzaad , McCallum Andrew , Su Andrew I. 
Published: May 2023

AbstractWhile link prediction methods in knowledge graphs have been increasingly utilized to locate potential associations between compounds and diseases, they suffer from lack of sufficient evidence to explain why a drug and a disease may be indicated. This is especially true for knowledge graph embedding (KGE) based methods where a drug-disease indication is linked only by information gleaned from a vector representation. Complementary pathwalking algorithms can increase the confidence of drug repurposing candidates by traversing a knowledge graph. However, these methods heavily weigh the relatedness of drugs, through their targets, pharmacology or shared diseases. Furthermore, these methods can rely on arbitrarily extracted paths as evidence of a compound to disease indication and lack the ability to make predictions on rare diseases. In this paper, we evaluate seven link prediction methods on a vast biomedical knowledge graph for drug repurposing. We follow the principle of consilience, and combine the reasoning paths and predictions provided by path-based reasoning approaches with those of KGE methods to identify putative drug repurposing indications. Finally, we highlight the utility of our approach through a potential repurposing indication.
Genomic epidemiology ofTreponema pallidumand circulation of strains with diminishedtprKantigen variation capability in Seattle, 2021-2022
Authors: Lieberman Nicole A.P. , Avendaño Carlos , Mohamed Bakhash Shah A. K. , Nunley Ethan , Xie Hong , Giacani Lorenzo , Berzkalns Anna , Soge Olusegun O. , Reid Tara B. , Golden Matthew R. , Greninger Alexander L. 
Published: May 2023

AbstractBackgroundSyphilis incidence continues to increase dramatically in the United States and yet little is known aboutTreponema pallidum(TP) genomic epidemiology within American metropolitan areas.MethodsWe performed whole genome sequencing andtprKdeep sequencing of 28 TP-containing specimens collected mostly from remnant Aptima swabs from 24 individuals from Seattle Sexual Health Clinic during 2021-2022.ResultsAll 12 individuals infected with Nichols lineage strains were MSM, while a specific SS14 cluster (average 0.33 SNPs) included 1 MSW and five women. All TP strains sequenced were azithromycin resistant via 23S rRNA A2058G mutation. Identical TP genomic sequences were found in pharyngeal and rectal swab specimens taken from the same individuals concurrently.tprKsequences were less variable between patient-matched specimens and between epidemiologically-linked clusters. We detected a 528 bp deletion in thetprKdonor site locus, eliminating ninetprKdonor sites, in TP genomes of three individuals with secondary syphilis, associated with diminution of overalltprKsequence diversity.ConclusionsWe developed an end-to-end workflow for public health genomic surveillance of TP from remnant Aptima swab specimens. With its high rate of gene conversion,tprKsequencing may assist in linking cases beyond routine TP genome sequencing. TP strains with deletions intprKdonor sites currently circulate and are associated with diminished antigenic diversity of the TprK putative outer membrane protein.
A programmable and site-specific anchoring system for biophysical analysis of DNA:protein interactions on large topologically closed DNA molecules
Authors: Gilhooly Neville S. , Kowalczykowski Stephen C. 
Published: May 2023

ABSTRACTSingle-molecule and bulk biophysical approaches to study protein-DNA interactions on surface-immobilised nucleic acid templates typically rely on modifying the ends of linear DNA molecules to enable surface-DNA attachments. Unless both strands are constrained, this results in topologically-free DNA molecules and the inability to observe supercoiling-dependent biological processes, or requires additional means to micro-manipulate the free DNA end to impose rotational constraints or induce supercoiling. We developed a method using RecA protein to induce the formation of a circularised compliment-stabilised D-loop. The resulting joint molecule is topologically closed, surface anchorable and stable under microfluidic flow. Importantly, the method obviates the need for subsequent manipulation of surface tethered DNA; tethered molecules remain supercoiled and retain accessibility to DNA binding proteins. This approach adds to the toolkit for those studying processes on DNA that require supercoiled DNA templates or topologically constrained systems.WHY IT MATTERSSupercoiling plays an important role in regulating genetic processes such as DNA replication and transcription. We have developed a facile method to immobilise large (supra diffraction-limited) supercoiled DNA substrates without the need for complex trapping modalities to allow biophysical interrogation of the surface-tethered DNA molecules. This will expand the toolkit for experimentalists interested in studying protein-DNA interactions at the single-molecule or ensemble level requiring the use of topologically closed or supercoiling-dependent systems such as origin-dependent bacterial DNA replication.
Dysregulated TDP-43 proteostasis perturbs excitability of spinal motor neurons during brainstem-mediated fictive locomotion in zebrafish
Authors: Asakawa Kazuhide , Handa Hiroshi , Kawakami Koichi 
Published: May 2023

ABSTRACTSpinal motor neurons (SMNs) are the primary target of degeneration in amyotrophic lateral sclerosis (ALS). Degenerating motor neurons accumulate cytoplasmic TAR DNA-binding protein 43 (TDP-43) aggregates in most ALS cases. This SMN pathology can occur without mutation in the coding sequence of the TDP-43-encoding gene, TARDBP. Whether and how wild-type TDP-43 drives pathological changes in SMNs in vivo remain largely unexplored. In this study, we develop a two-photon calcium imaging setup in which tactile-evoked neural responses of motor neurons in the brainstem and spinal cord can be monitored using the calcium indicator GCaMP. We devise a piezo-assisted tactile stimulator that reproducibly evokes a brainstem descending neuron upon tactile stimulation of the head. A direct comparison between caudal primary motor neurons (CaPs) with or without TDP-43 overexpression in contiguous spinal segments demonstrates that CaPs overexpressing TDP-43 display attenuated Ca2+transients during fictive escape locomotion evoked by the tactile stimulation. These results show that excessive amounts of TDP-43 protein reduce the neuronal excitability of SMNs and potentially contribute to asymptomatic pathological lesions of SMNs and movement disorders in patients with ALS.
Diabetes and Incidence of Breast Cancer and its Molecular Subtypes: A Systematic Review and Meta-Analysis
Authors: Xiong Fanxiu , Dai Qichen , Zhang Sihan , Bent Stephen , Tahir Peggy , Van Blarigan Erin L. , Kenfield Stacey A. , Chan June M. , Schmajuk Gabriela , Graff Rebecca E. 
Published: May 2023

AbstractDiabetes mellitus (DM) has been proposed to be positively associated with breast cancer (BCa) risk due to shared risk factors, metabolic dysfunction, and use of antidiabetic medications. We conducted a systematic review and meta-analysis to evaluate the association between DM and BCa risk. We searched PubMed, Embase, and Web of Science for cohort and case-control studies assessing the association between DM and BCa published before December 10, 2021. Two reviewers independently screened the studies for inclusion, abstracted article data, and rated study quality. Random effects models were used to estimate summary risk ratios (RRs) and 95% confidence intervals (CIs). From 8396 articles identified in the initial search, 70 independent studies were included in the meta-analysis. DM was associated with an overall increased risk of BCa (RR=1.20, 95% CI: 1.11-1.29). The 24 case-control studies demonstrated a stronger association (RR=1.26, 95% CI: 1.13-1.40) than the 46 cohort studies (RR=1.15, 95% CI: 1.05-1.27). Studies reporting risk by menopausal status found that postmenopausal women had an elevated risk of developing BCa (RR=1.12, 95% CI: 1.07-1.17). No association between DM and BCa risk was observed among premenopausal women (RR=0.95, 95% CI: 0.85-1.05). In addition, DM was associated with significantly increased risks of estrogen receptor (ER)+ (RR=1.09, 95% CI: 1.00-1.20), ER- (RR=1.16, 95% CI: 1.04-1.30), and triple negative BCa (RR=1.41, 95% CI: 1.01-1.96). The association estimate for human epidermal growth factor 2- positive BCa was also positive (RR=1.21, 95% CI: 0.52-2.82), but the confidence interval was wide and crossed the null. Our meta-analysis confirms a modest positive association between DM and BCa risk. In addition, our results suggest that the DM and BCa association may be modified by menopausal status, and DM may be differentially associated with BCa subtypes defined by receptor status. Additional studies are warranted to investigate the mechanisms underlying these associations and any influence of DM on BCa receptor expression.