bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quantification of astrocytic synaptic pruning in hippocampus in response to in vitro Aβ oligomer incubation via colocalization analysis with C1q
Authors: Pradhan Arpit Kumar , Shi Qinfang , Tartler Katharina Johanna , Rammes Gerhard 
Published: May 2022

SummaryQuantification of synaptic engulfment is an indirect measurement of synaptic pruning. Here, we provide a detailed protocol for the volumetric rendering of individual high-resolution astrocytes in the CA1 region of hippocampus in an in vitro slice model of Amyloid-beta (Aβ) treatment. This includes free floating slice preparation, treatment with Aβ oligomers, immunofluorescence, confocal imaging and analysis of individual astrocytes. We also provide a comprehensive analysis for 3D rendering of astrocytes and assessment of synaptic engulfment via “eat-me tag” C1q protein and synaptic marker PSD95.HighlightsMeasurement of synaptic engulfment in response to treatment with Aβ peptideVolumetric reconstruction of high resolution individual astrocyteColocalization analysis of astrocyte and complementary “eat-me” protein C1qGraphical abstract
The Role of Conjunctive Representations in Prioritizing and Selecting Planned Actions
Authors: Kikumoto Atsushi , Mayr Ulrich , Badre David 
Published: May 2022

AbstractFor flexible goal-directed behavior, prioritizing and selecting a specific action among multiple candidates is often important. Working memory has long been assumed to play a role in prioritization and planning, while bridging cross-temporal contingencies during action selection. However, studies of working memory have mostly focused on memory for single components of an action plan, such as a rule or a stimulus, rather than management of all of these elements during planning. Therefore, it is not known how post-encoding prioritization and selection operate on the entire profile of representations for prospective actions. Here, we assessed how such control processes unfold over action representations, highlighting the role of conjunctive representations that nonlinearly integrate task-relevant features during maintenance and prioritization of action plans. For each trial, participants prepared two independent rule-based actions simultaneously, then they were retro-cued to select one as their response. Prior to the start of the trial, one rule-based action was randomly assigned to be high priority by cueing that it was more likely to be tested. We found that both full action plans were maintained as conjunctive representations during action preparation, regardless of priority. However, during output selection, the conjunctive representation of the high priority action plan was more enhanced and readily selected as an output. Further, the strength of conjunctive representation was related to behavioral interference when the low priority action was tested. Thus, multiple integrated representations were maintained for upcoming actions and served as the target of post-encoding attentional selection mechanisms to prioritize and select an action from those in working memory.
A general mechanism of air-borne hearing in Recent and early non-tympanate tetrapods
Authors: Christensen-Dalsgaard Jakob , Lauridsen Tanya Bojesen , Capshaw Grace , Carr Catherine E. 
Published: May 2022

AbstractTetrapod tympanic hearing probably emerged in the Triassic with independent origins in each of the major groups, more than 120 Myr after the water-land transition. During this long period, any auditory sensitivity must have been based on non-tympanic, bone conduction mechanisms. However, ‘bone conduction’ is a non-specific term describing several different modes of vibration that can stimulate the inner ear.To understand hearing in a non-tympanic ear, we focus on the simplest model: that sound translates the head, i.e., that the head is pushed and pulled by the sound wave, and that this vibration is transduced by the inner ear. Simple translation is the mode of human low-frequency bone conduction sensitivity and translation by underwater sound is also the mode of auditory stimulation for most fishes. It is therefore a straightforward assumption that this may have been the mechanism of hearing in the early tetrapods. According to acoustic theory, the efficiency of translation of an object by sound is determined by its density and ka, the product of the acoustic wavenumber (k) and the radius (a) of the head. Simple finite-element models of translation by sound show that vibration velocities only depend on ka and density (for objects of the same shape and composition) and are almost constant (between 4 and 5 µm/s/Pa depending on shape) for objects with ka<1. We compare sensitivity to sound and to vibrations of the skull in animals lacking tympanic middle ears (snakes, salamanders, earless frogs, and lungfish) and show that the low-frequency air-borne sound sensitivity in these species is largely consistent with a translation mechanism. How translation of the head or body can stimulate the inner ear is most evident in an inertial system like the otolithic/otoconial ears of fish and early tetrapods, but fluid inertia in the inner ear may also generate hydrodynamic waves that can stimulate hair cells in the tetrapod inner ear, providing a mechanism for this simple mode of sound reception to confer hearing in earless animals.
The Drosophila ZAD zinc finger protein Kipferl guides Rhino to piRNA clusters
Authors: Baumgartner Lisa , Handler Dominik , Platzer Sebastian , Duchek Peter , Brennecke Julius 
Published: May 2022

SUMMARYRNA interference systems depend on the synthesis of small RNA precursors whose sequences define the target spectrum of these silencing pathways. The Drosophila Heterochromatin Protein 1 (HP1) variant Rhino permits transcription of PIWI-interacting RNA (piRNA) precursors within transposon-rich heterochromatic loci in germline cells. Current models propose that Rhino’s specific chromatin occupancy at piRNA source loci is determined by histone marks and maternally inherited piRNAs, but also imply the existence of other, undiscovered specificity cues. Here, we identify a member of the diverse family of zinc finger associated domain (ZAD)-C2H2 proteins, Kipferl, as critical Rhino cofactor in ovaries. By binding to guanosine-rich DNA motifs and interacting with the Rhino chromodomain, Kipferl recruits Rhino to specific loci and stabilizes it on chromatin. In kipferl mutant flies, Rhino is lost from most of its target chromatin loci and instead accumulates on pericentromeric satellite arrays, resulting in decreased levels of transposon targeting piRNAs and impaired fertility. Our findings reveal that DNA sequence, in addition to the H3K9me3 mark, determines the identity of piRNA source loci and provide insight into how Rhino might be caught in the crossfire of genetic conflicts.
Adenovirus-Vectored SARS-CoV-2 Vaccine Expressing S1-N Fusion Protein
Authors: Khan Muhammad S. , Kim Eun , McPherson Alex , Weisel Florian J. , Huang Shaohua , Kenniston Thomas W. , Percivalle Elena , Cassaniti Irene , Baldanti Fausto , Meisel Marlies , Gambotto Andrea 
Published: May 2022

AbstractAdditional COVID-19 vaccines that are safe, easy to manufacture, and immunogenic are needed for global vaccine equity. Here, we developed a recombinant type 5 adenovirus vector encoding for the SARS-CoV-2-S1 subunit antigen and nucleocapsid as a fusion protein (Ad5.SARS-CoV-2-S1N) delivered to BALB/c mice through multiple vaccine administration routes. A single subcutaneous (S.C.) immunization with Ad5.SARS-CoV-2-S1N induced a similar humoral response, along with a significantly higher S1-specific cellular response, as a recombinant type 5 adenovirus vector encoding for S1 alone (Ad5.SARS-CoV-2-S1). Immunogenicity was improved by homologous prime boost strategies, using either S.C. or intranasal (I.N.) delivery of Ad5.SARS-CoV-2-S1N, and further improved through heterologous prime boost, with traditional intramuscular (I.M.) injection, using subunit recombinant S1 protein. Priming with low dose (1×1010 v.p.) of Ad5.SARS-CoV-2-S1N and boosting with either wildtype recombinant rS1 or B.1.351 recombinant rS1 induced a robust neutralizing response, that was sustained against immune evasive Beta and Gamma SARS-CoV-2 variants, along with a long-lived plasma cell response in the bone marrow 29 weeks post vaccination. This novel Ad5-vectored SARS-CoV-2 vaccine candidate showed promising immunogenicity in mice and supports the further development of COVID-19 based vaccines incorporating the nucleoprotein as a target antigen.
Identification of Banana heat responsive long non-coding RNAs and their gene expression analysis
Authors: Murthy Vidya Srinivasa , Murthy Swarupa Venkatesa , Ramesh Pooja , Niranjan Vidya , Kumar Vasanth , Bharthi H Vidya , Bhatt Ravindra M. , Hunashikatti Laxman R. , Ravishankar Kundapura Venkataramana 
Published: May 2022

AbstractIdentification and characterization of long non-coding RNAs (lncRNAs) in the last decade has attained great attention because of their importance in gene regulatory functions in response to various plant stresses. Rising temperature is a potential threat to the agriculture world. Banana being an important economic crop, identification and characterization of genes and RNAs that regulate high temperature stress is imperative. As the prediction of lncRNAs in response to heat stress in banana is largely unknown, the present study was focused to identify the heat stress responsive lncRNA in banana (DH Pahang). Perl script was written to identify the novel transcripts, using the work flow. StringTie and CPC softwares were used and a total of 363 novel HS-lncRNA were identified in banana. Further, lncRNA were classified as 288 lincRNAs, 71 antisense LncRNA, 5 sense lncRNAs. The functional classification was done and transcripts were broadly classified into molecular function, cellular components and biological processes. Differential expression of lncRNA showed the varied patterns at different stages of heat stress. Finally, qPCR results confirmed DGE expression pattern of lncRNAs. Further, the Cytoscape analysis was performed which showed protein coding genes involved in membrane integrity and other signal transduction pathways. Taken together, these findings expand our understanding of lncRNAs as ubiquitous regulators under heat stress conditions in banana.
Structure of maize BZR1-type β-amylase BAM8 provides new insights into its noncatalytic adaptation
Authors: Sun Fuai , Palayam Malathy , Shabek Nitzan 
Published: May 2022

AbstractPlant β-Amylase (BAM) proteins play an essential role in growth, development, stress response, and hormone regulation. Despite their typical (β/α)8 barrel structure as active catalysts in starch breakdown, catalytically inactive BAMs are implicated in diverse yet elusive functions in plants. The noncatalytic BAM7/8 contain N-terminal BZR1 domains and were shown to be involved in the regulation of brassinosteroid signaling and possibly serve as sensors of yet an uncharacterized metabolic signal. While the structures of several catalytically active BAMs have been reported, structural characterization of the catalytically inactive BZR1-type BAMs remain unknown. Here, we determine the crystal structure of Zea mays BZR1-type BAM8 and provide comprehensive insights into its noncatalytic adaptation. Using structural-guided comparison combined with biochemical analysis and molecular dynamics simulations, we revealed conformational changes in multiple distinct highly conserved regions resulting in rearrangement of the binding pocket. Altogether, this study adds a new layer of understanding to starch breakdown mechanism and elucidates the acquired adjustments of noncatalytic BZR1-type BAMs as putative regulatory domains and/or metabolic sensors in plants.
A histone deacetylase network regulates epigenetic reprogramming and viral silencing in HIV infected cells
Authors: Peterson Jackson J , Lewis Catherine A , Burgos Samuel D , Manickam Ashokkumar , Xu Yinyan , Rowley Allison A , Clutton Genevieve , Richardson Brian , Zou Fei , Simon Jeremy M , Margolis David M , Goonetilleke Nilu , Browne Edward P 
Published: May 2022

AbstractApproximately 70% of the HIV-1 latent reservoir originates from infections of CD4 T cells that occur in the months near the time of ART initiation, raising the possibility that interventions during this period might prevent reservoir seeding and reduce reservoir size. We identify class 1 histone deacetylase inhibitors (HDACi) as potent agents of latency prevention. Inhibiting HDACs in productively infected cells caused extended maintenance of HIV expression and this activity was associated with persistently elevated H3K9 acetylation and reduced H3K9 methylation at the viral LTR promoter region. HDAC inhibition in HIV-infected CD4 T cells during effector-to-memory transition led to striking changes in the memory phenotype of infected cells. Proviral silencing is accomplished through distinct activities of HDAC1/2 and HDAC3. Thus HDACs regulate a critical gateway process for HIV latency establishment and are required for the development of CD4 T-cell memory subsets that preferentially harbor long-lived, latent provirus.
COVID-19 mRNA third dose induces a unique hybrid immunity-like antibody response
Authors: Andreano Emanuele , Paciello Ida , Pierleoni Giulio , Piccini Giulia , Abbiento Valentina , Antonelli Giada , Pileri Piero , Manganaro Noemi , Pantano Elisa , Maccari Giuseppe , Marchese Silvia , Donnici Lorena , Benincasa Linda , Giglioli Ginevra , Leonardi Margherita , De Santi Concetta , Fabbiani Massimiliano , Rancan Ilaria , Tumbarello Mario , Montagnani Francesca , Sala Claudia , Medini Duccio , De Francesco Raffaele , Montomoli Emanuele , Rappuoli Rino 
Published: May 2022

ABSTRACTThe continuous evolution of SARS-CoV-2 generated highly mutated variants, like omicron BA.1 and BA.2, able to escape natural and vaccine-induced primary immunity1,2. The administration of a third dose of mRNA vaccines induces a secondary response with increased protection. We investigated, at single-cell level, the longitudinal evolution of the neutralizing antibody response in four donors after three mRNA doses3. A total of 4,100 spike protein specific memory B cells were single cell sorted and 350 neutralizing antibodies were identified. The third dose increased the antibody neutralization potency and breadth against all SARS-CoV-2 variants of concern as previously observed with hybrid immunity3. However, the B cell repertoire that stands behind the response is dramatically different. The increased neutralizing response was largely due to the expansion of B cell germlines poorly represented after two doses, and the reduction of germlines predominant after primary immunization such as IGHV3-53;IGHJ6-1 and IGHV3-66;IGHJ4-1. Divergently to hybrid immunity, cross-protection after a third dose was mainly guided by Class 1/2 antibodies encoded by IGHV1-58;IGHJ3-1 and IGHV1-69;IGHJ4-1 germlines. The IGHV2-5;IGHJ3-1 germline, which induced broadly cross-reactive Class 3 antibodies after infection or viral vector vaccination, was not induced by a third mRNA dose. Our data show that while neutralizing breadth and potency can be improved by different immunization regimens, each of them has a unique molecular signature which should be considered while designing novel vaccines and immunization strategies.
A novel ALDH1A1 inhibitor blocks platinum-induced senescence and stemness in ovarian cancer
Authors: Muralikrishnan Vaishnavi , Fang Fang , Given Tyler C. , Podicheti Ram , Chchterbinine Mikhail , Sriramkumar Shruthi , O’Hagan Heather M. , Hurley Thomas D. , Nephew Kenneth P. 
Published: May 2022

AbstractOvarian cancer is a deadly disease attributed to late-stage detection as well as recurrence and development of chemoresistance. Ovarian cancer stem cells (OCSCs) are hypothesized to be largely responsible for emergence of chemoresistant tumors. Although chemotherapy may initially succeed at decreasing the size and number of tumors, it leaves behind residual malignant OCSCs. In this study, we demonstrate that Aldehyde dehydrogenase 1A1 (ALDH1A1) is essential for the survival of OCSCs. We identified a first in class ALDH1A1 inhibitor, compound 974, and used 974 as a tool to decipher the mechanism of stemness regulation by ALDH1A1. Treatment of OCSCs with 974 significantly inhibited ALDH activity, expression of stemness genes, spheroid, and colony formation. In vivo limiting dilution assay demonstrated that 974 significantly inhibited CSC frequency. Transcriptomic sequencing of cells treated with 974 revealed significant downregulation of genes related to stemness and chemoresistance as well as senescence and senescence associated secretory phenotype (SASP). We confirmed that 974 inhibited senescence and stemness induced by platinum-based chemotherapy in functional assays. Overall, these data establish that ALDH1A1 is essential for OCSCs survival and ALDH1A1 inhibition suppresses chemotherapy induced senescence and stemness. Targeting ALDH1A1 using small molecule inhibitors in combination with chemotherapy therefore presents a promising strategy to prevent ovarian cancer recurrence and has potential for clinical translation.
ORIGINS: a protein network-based approach to quantify cell pluripotency from scRNA-seq data
Authors: Senra Daniela , Guisoni Nara , Diambra Luis 
Published: May 2022

ABSTRACTTrajectory inference is a common application of scRNA-seq data. However, it is often necessary to previously determine the origin of the trajectories, the stem or progenitor cells. In this work, we propose a computational tool to quantify pluripotency from single cell transcriptomics data. This approach uses the protein-protein interaction (PPI) network associated with the differentiation process as a scaffold and the gene expression matrix to calculate a score that we call differentiation activity. This score reflects how active the differentiation network is for each cell. We benchmark the performance of our algorithm with two previously published tools, LandSCENT [1] and CytoTRACE [2], for four data sets: breast, colon, hematopoietic and lung. We show that our algorithm is more efficient than LandSCENT and requires less RAM memory than the other programs. We also illustrate a complete workflow from the count matrix to trajectory inference using the breast data set.Graphical abstract
Retinoic acid signaling in mouse retina endothelial cells is required for early angiogenic growth
Authors: Como Christina N. , Cervantes Cesar , Pawlikowski Brad , Siegenthaler Julie 
Published: May 2022

ABSTRACTThe development of the retinal vasculature is essential to maintain health of the tissue, but the developmental mechanisms are not completely understood. The aim of this study was to investigate the cell-autonomous role of retinoic acid signaling in endothelial cells during retina vascular development. Using a temporal and cell-specific mouse model to disrupt retinoic acid signaling in endothelial cells in the postnatal retina (Pdgfbicre/+ dnRAR403fl/fl mutants), we discovered that angiogenesis in the retina is significantly decreased with a reduction in retina vascularization, endothelial tip cell number and filipodia, and endothelial ‘crowding’ of stalk cells. Interestingly, by P15, the vasculature can overcome the early angiogenic defect and fully vascularized the retina. At P60, the vasculature is intact with no evidence of retina cell death or altered blood retinal barrier integrity. Further, we identified that the angiogenic defect seen in mutants at P6 correlates with decreased Vegfr3 expression in endothelial cells. Collectively, our work identified a previously unappreciated function for endothelial retinoic acid signaling in early retinal angiogenesis.
A role for gene expression and mRNA stability in nutritional compensation of the circadian clock
Authors: Kelliher Christina M. , Stevenson Elizabeth-Lauren , Loros Jennifer J. , Dunlap Jay C. 
Published: May 2022

AbstractCompensation is a defining principle of a true circadian clock, where its approximately 24-hour period length is relatively unchanged across environmental conditions. Known compensation effectors directly regulate core clock factors to buffer the oscillator’s period length from variables in the environment. Temperature Compensation mechanisms have been experimentally addressed across circadian model systems, but much less is known about the related process of Nutritional Compensation, where circadian period length is maintained across physiologically relevant nutrient levels. Using the filamentous fungus Neurospora crassa, we performed a genetic screen under glucose and amino acid starvation conditions to identify new regulators of Nutritional Compensation. Our screen uncovered 16 novel mutants, and together with 4 mutants characterized in prior work, a model emerges where Nutritional Compensation of the fungal clock is achieved at the levels of transcription, chromatin regulation, and mRNA stability. However, eukaryotic circadian Nutritional Compensation is completely unstudied outside of Neurospora. To test for conservation in cultured mammalian cells, we selected the top two hits from our fungal genetic screen, performed siRNA knockdown experiments of the mammalian homologs, and characterized the cell lines with respect to compensation. We find that the wild-type mammalian clock is also compensated across a large range of external glucose concentrations, as observed in Neurospora, and that knocking down CPSF6 or SETD2 in human cells also results in nutrient-dependent period length changes. We conclude that, like Temperature Compensation, Nutritional Compensation is a conserved circadian process in fungal and mammalian clocks and that it may share common molecular determinants.
Functional connectivity dynamics reflect disability and multi-domain clinical impairment in patients with relapsing-remitting multiple sclerosis
Authors: Romanello Amy , Krohn Stephan , Schwanenflug Nina von , Chien Claudia , Bellmann-Strobl Judith , Ruprecht Klemens , Paul Friedemann , Finke Carsten 
Published: May 2022

ABSTRACTBackgroundFunctional neuroimaging studies have revealed complex and heterogeneous patterns of aberrant functional connectivity (FC) in multiple sclerosis (MS), yet it remains unclear how time-resolved FC relates to variance in clinical disease severity.ObjectivesTo characterize brain activity in MS patients with time-resolved FC analysis and explore the relationship between disease severity, multi-domain impairments, and altered network dynamics.MethodsResting-state functional MRI data were acquired from 101 MS patients and 101 age- and sex-matched healthy controls (HC). Dynamic FC analysis identified five connectivity states that were compared between HC and patients with high vs. low disability.ResultsPatients with higher disease severity exhibited a more widespread spatiotemporal pattern of altered FC and spent more time in a high-connectivity, low-occurrence state compared to patients with lower disease severity and HC. Depressive symptom severity was positively related to functional dynamics on global and network scales in patients, while fatigue and motor impairment were inversely related to frontoparietal network connectivity with the basal ganglia.ConclusionsTime-resolved FC analysis uncovered alterations in network dynamics and clinical correlations that remained undetected with a static account of brain activity. Such time-varying approaches are thus crucial for disentangling the relationship between brain dynamics, disease severity, and symptoms in MS.