bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptional activity is shaped by the chromatin landscapes in Arabidopsis
Authors: Jamge Bhagyshree , Lorković Zdravko J. , Axelsson Elin , Yelagandula Ramesh , Akimcheva Svetlana , Berger Frédéric 
Published: June 2022

SummaryHow histone variants and histone modifications shape nucleosome-mediated transcriptional repression, and how transcriptional activity shapes the enrichment of histone modifications and variants remain unclear. To clarify these relationships, we examined chromatin organization in the Arabidopsis thaliana genome, identifying a limited number of chromatin landscapes that distinguish transposon families and distinct groups of genes based on their transcriptional regulation. Unexpectedly, H2A variants are strong determinants of the landscape architecture. Combinations of H2A.W and four histone modifications define six domains that are occupied by specific transposon families and organized concentrically around the centromere. Moreover, H2A.Z defines transcriptional gene repression in specific domains. Expressed genes occupy four chromatin landscapes with specific RNA Polymerase II profiles. Although the composition of each chromatin landscape is invariant, they cover genes with a wide range of expression levels. Therefore, chromatin landscapes control the range of transcriptional activity, but transcriptional activity has little effect on chromatin composition.One Sentence SummaryHistone variants and histone modifications build a limited number of distinct chromatin landscapes that instruct the transcriptional regulation of genes and transposons in Arabidopsis.
Research Productivity and Training Support for Doctoral Students in the Biological and Biomedical Sciences
Authors: Schaller Michael D. 
Published: June 2022

AbstractTraining of doctoral students as part of the next generation of the biomedical workforce is essential for sustaining the scientific enterprise in the US. Training of doctoral students primarily occurs at institutions of higher education and these trainees comprise an important part of the workforce at these institutions. Federal investment in the support of doctoral students in the biological and biomedical sciences is distributed differently than the distribution of students across different types of institutions, e.g. Public vs Private. Institutions in states that historically receive less federal support for research also receive less support for doctoral student training. Analysis of F31 awardees at different types of institution reveal little difference in research productivity and subsequent receipt of additional NIH awards. Analysis of a large cohort of doctoral students at different types of institutions also reveal little difference in research productivity, with the exception of citations. Thus, training outcomes, which are related to the quality of the student and training environment, are similar across different institutions. Factors that correlate with F31 funding include R01 funding levels and program size. The findings suggest strategies for institutions to increase success at securing F31s and modification of policy to promote more equitable distribution of F31s across institutions.
A Genetically Encoded Far-Red Fluorescent Indicator for Imaging Synaptically-Released Zn2+
Authors: Wu Tianchen , Kumar Manoj , Zhao Shengyu , Drobizhev Mikhail , Tian Xiaodong , Tzounopoulos Thanos , Ai Hui-wang 
Published: June 2022

AbstractSynaptic Zn2+ has emerged as a key neuromodulator in the brain. However, the lack of research tools for directly tracking synaptic Zn2+ in the brain in live animals hinders our rigorous understanding of the physiological and pathological roles of synaptic Zn2+. In this study, we developed a genetically encoded far-red fluorescent indicator for monitoring synaptic Zn2+ dynamics in the nervous system. Our engineered far-red fluorescent indicator for synaptic Zn2+ (FRISZ) displayed a substantial Zn2+-specific turn-on response and low micromolar affinity. We genetically anchored FRISZ to the mammalian extracellular membrane via a transmembrane α-helix. We further successfully used membrane-tethered FRISZ (FRISZ-TM) to image synaptic Zn2+ dynamics in response to sound in the primary auditory cortex (A1) in awake mice. This study thus establishes a new technology for studying the roles of synaptic Zn2+ in the nervous system.
“The anti-apoptotic effect ofLonomia obliquahemolymph is associated with the mitochondria pathway”
Authors: Mendonça Ronaldo Z. , Martins Luciana Moreira 
Published: June 2022

AbstractThe apoptosis death is a very important factors in production processes that limited the industrial production of some proteins of economic interest. However, one of the forms to increase the cellular productivity would be inhibit or attenuate the cellular death. Recently we have demonstrated the presence of a potent anti-apoptotic protein inLonomia obliquahemolymph which extends the cell culture viability through apoptosis prevention. By the other side, has been reported that mitochondria have one important action in the apoptosis control process, being that mitochondria membrane permeabilization (MMP) can be an important stage in this process. MMP associated or not with the loss of the electrochemical potential of the mitochondria and alteration of the matrix is responsible for the inter membranes protein release (e.g. cytochrome c, the AIF, etc) of cytosol. The result obtained showed that the addition of a protein fromLonomia obliquahemolymph in the culture lead to a prolongation of the cellular life (3-4 days) and the cells leading a high electrochemical potential of the mitochondria. This protein can has its action in mitochondria membrane, avoiding the loss of the membrane permeability and the Cytochrome-C release. As positive control, apoptosis death in these cultures was induced by 50 μm of t-BHP or 600 μm of H202. The presence of apoptosis was characterized by flow citometry, microscopy electronic and agarose gel electrophoresis. The potential electrochemical of the mitochondria was determined by JC-1, Hoechst 33324 and DIOC6. Cytochrome C was identified in cytosol by an anti-cytochrome antibody.
Chemical screening of food-related chemicals for human fatty liver risk: Combining high content imaging of cellular responses with in vitro to in vivo extrapolation
Authors: Müller Fabrice A. , Stamou Marianna , Englert Felix , Frenzel Ole , Diedrich Sabine , Wambaugh John F. , Sturla Shana J. 
Published: June 2022

1AbstractNonalcoholic fatty liver disease (NAFLD) is an increasingly prevalent human disease with accumulating evidence linking its pathophysiology and co-morbidities to chemical exposures. The complex pathophysiology of NAFLD has limited the elucidation of potential chemical etiologies. In this study we generated a high-content imaging analysis method for the simultaneous quantification of sentinel steatosis cellular markers in chemically exposed human liver cells in vitro combined with a computational model for the extrapolation of human oral equivalent doses (OED). First, the in vitro test method was generated using 14 reference chemicals with known capacities to induce cellular alterations in nuclear morphology, lipid accumulation, mitochondrial membrane potential and oxidative stress. These effects were quantified on a single cell- and population-level, and then, using physiologically based pharmacokinetic modelling and reverse dosimetry, OEDs were extrapolated from these in vitro data. The extrapolated OEDs were confirmed to be within biologically relevant exposure ranges for the reference chemicals. Next, we tested 14 chemicals found in food, selected from thousands of putative chemicals on the basis of structure-based prediction for nuclear receptor activation. Amongst these, orotic acid had an extrapolated OED overlapping with realistic exposure ranges. By the strategy developed in this study, we were able to characterize known NAFLD-inducing chemicals and translate to data scarce food-related chemicals, amongst which we identified orotic acid to induce steatosis. This strategy addresses needs of next generation risk assessment, and can be used as a first chemical prioritization hazard screening step in a tiered approach to identify chemical risk factors for NAFLD.
Calcium-Mediated Modulation of Blood-Brain Barrier Permeability by Laser Stimulation of Endothelial-Targeted Nanoparticles
Authors: Li Xiaoqing , Cai Qi , Wilson Blake A. , Fan Hanwen , Giannotta Monica , Bachoo Robert , Qin Zhenpeng 
Published: June 2022

AbstractThe blood-brain barrier (BBB) maintains an optimal environment for brain homeostasis but excludes most therapeutics from entering the brain. Strategies that can reversibly increase BBB permeability will be essential for treating brain diseases and is the focus of significant preclinical and translational interest. Recently, we reported that picosecond laser excitation of molecular-targeted gold nanoparticles (AuNPs) induced a graded and reversible increase in BBB permeabilityin vivo(OptoBBB). Here we investigate how to increase the targeting efficiency and how picosecond lase stimulation of AuNP leads to an increase in endothelial paracellular permeability. Our results suggest that targeting brain endothelial glycoproteins leads to >20-fold higher targeting efficiency compared with tight junction targeting. We report that OptoBBB is associated with a transient elevation of Ca2+that propagates to adjacent endothelial cells after laser excitation and extends the region of BBB opening. The Ca2+response involves both internal Ca2+depletion and Ca2+influx. Furthermore, we demonstrate that the involvement of actin polymerization and Ca2+-dependent phosphorylation of ERK1/2 lead to cytoskeletal activation, increasing paracellular permeability. Taken together, we provide mechanistic insight into how excitation of endothelial targeted AuNPs leads to an increase in BBB permeability. These insights will be critical for guiding the future developments of this technology for brain disease treatment.
The developmental progression of eight opsin spectral signals recorded from the zebrafish retinal cone layer is altered by the timing and cell type expression of thyroxin receptor β2 (trβ2) gain-of-function transgenes
Authors: Nelson Ralph F. , Balraj Annika , Suresh Tara , Elias Leah J. , Yoshimatsu Takeshi , Patterson Sara S. 
Published: June 2022

AbstractZebrafish retinal cone signals shift in spectral shape through larval, juvenile, and adult development as expression patterns of eight cone-opsin genes change. An algorithm extracting signal amplitudes for the component cone spectral types is developed and tested on two thyroxin receptor β2 (trβ2) gain-of-function lines crx:mYFP-2A-trβ2 and gnat2:mYFP-2A-trβ2, allowing correlation between opsin signaling and opsin immunoreactivity in lines with different developmental timing and cell-type expression of this red-opsin-promoting transgene. Both adult transgenics became complete, or nearly complete, ‘red-cone dichromats’, with disproportionately large LWS1 opsin amplitudes as compared to controls, where LWS1 and LWS2 amplitudes were about equal, and significant signals from SWS1, SWS2, and Rh2 opsins were detected. But in transgenic larvae and juveniles of both lines it was LWS2 amplitudes that increased, with LWS1 cone signals rarely encountered. In gnat2:mYFP-2A-trβ2 embryos at 5 days post fertilization (dpf), red-opsin immunoreactive cone density doubled, but red-opsin amplitudes (LWS2) increased < 10%, and green, blue and UV opsin signals were unchanged, despite co-expressed red opsins, and the finding that an sws1 UV-opsin reporter gene was shut down by the gnat2:mYFP-2A-trβ2 transgene. By contrast both LWS2 red-cone amplitudes and the density of red-cone immunoreactivity more than doubled in 5 dpf crx:mYFP-2A-trß2 embryos, while UV-cone amplitudes were reduced 90%. Embryonic cones with trβ2 gain-of-function transgenes were morphologically distinct from control red, blue or UV cones, with wider inner segments and shorter axons than red cones, suggesting cone spectral specification, opsin immunoreactivity and shape are influenced by the abundance and developmental timing of trβ2 expression.Significance StatementAs different combinations of eight cone-opsin mRNAs are successively expressed during zebrafish development and maturation, the composite cone-ERG spectral signal shifts. Amplitudes of each of the eight resulting cone signals are inferred computationally from the composite signal, both in controls and in two thyroxin-receptor β2 (trβ2) gain-of-function transgenics, crx:mYFP-2A-trβ2 and gnat2:mYFP-2A-trβ2, trβ2 being a transcription factor required for expression of the red-cone opsins LWS1 and LWS2. Adult transgenics become red cone dichromats with excess LWS1 amplitudes, but larvae and juveniles evoke excess LWS2 amplitudes. Controls retain 5 to 6 cone signals of changing composition throughout development. The progression of transgene-induced amplitude alterations is slower in gnat2:mYFP-2A-trβ2, with supernormal red-opsin antigenicity not immediately correlating with red-cone signaling.
Stable and ancient endocytic structures navigate the complex pellicle of apicomplexan parasites
Authors: Koreny Ludek , Mercado-Saavedra Brandon N. , Klinger Christen M. , Barylyuk Konstantin , Butterworth Simon , Hirst Jennifer , Rivera-Cuevas Yolanda , Zaccai Nathan R. , Holzer Victoria J. C. , Klingl Andreas , Dacks Joel B. , Carruthers Vern B. , Robinson Margaret S. , Gras Simon , Waller Ross F. 
Published: June 2022

ABSTRACTApicomplexan parasites have an immense impact on humanity, but their basic cellular processes are often poorly understood. The sites of endocytosis, the conservation of this process with other eukaryotes, and its functions across Apicomplexa are major unanswered questions. Yet endocytosis inPlasmodiumis implicated in antimalarial drug failure. Using the apicomplexan modelToxoplasma, we identified the molecular composition and behavior of unusual, fixed endocytic structures. Here, stable complexes of endocytic proteins differ markedly from the dynamic assembly/disassembly of these machineries in other eukaryotes. Moreover, conserved molecular adaptation of this structure is seen in Apicomplexa, including the kelch-domain protein K13 central to malarial drug-resistance. We determine that an essential function of endocytosis inToxoplasmais plasma membrane homeostasis, rather than parasite nutrition, and that these specialized endocytic structures originated early in infrakingdom Alveolata, likely in response to the complex cell pellicle that defines this medically and ecologically important ancient eukaryotic lineage.
Topical Delivery of Elastic Liposomal Vesicles for Treatment of Middle and Inner Ear Disease
Authors: Sadabad Raana Kashfi , Xia Anping , Benkafadar Nesrine , Faniku Chrysovalantou , Preciado Diego , Yang Stella , Valdez Tulio A. 
Published: June 2022

AbstractWe present a topical drug delivery mechanism through the ear canal to the middle and inner ear using liposomal nanoparticles without disrupting the integrity of the tympanic membrane. The current delivery method provides a non-invasive,and safer alternative to trans-tympanic membrane injections, ear tubes followed by ear drops administration and systemic drug formulations. We investigate the capability of liposomal NPs, particularly transfersomes (TLipo), used as drug delivery vesicles to penetrate the tympanic membrane (TM) and round window membrane (RWM) with high affinity, specificity, and retention time. The TLipo is applied to the ear canal and found to pass through tympanic membrane quickly in 3 hours post drug administration. They are identified in the middle ear cavity 6 hours and in the inner ear 24 hours after drug administration. We performed cytotoxicity in vitro and ototoxicity in vivo studies. Cell viability shows no significant difference between the applied TLipo concentration and control. Furthermore, auditory brainstem response (ABR) reveals no hearing loss in 1 week and 1 month post administration. Immunohistochemistry results demonstrates no evidence of hair cell loss in the cochlea at 1 month following TLipo administration. Together, the data suggested that TLipo can be used as a vehicle for topical drug delivery to the middle ear and inner ear.
Novel insights into the fundamentals of palatal shelf elevation dynamics in normal mouse embryos
Authors: Goering Jeremy P. , Moedritzer Michael , Stetsiv Marta , Isai Dona Greta , Hufft-Martinez Brittany M. , Umar Zaid , Rickabaugh Madison K. , Keselman Paul , Chauhan Munish , Brooks William M. , Fischer Kenneth J. , Czirok Andras , Saadi Irfan 
Published: June 2022

AbstractEmbryonic palate development involves bilateral vertical growth of palatal shelves – extensions from the maxillary processes – next to the tongue until embryonic day (E) 13.5. Following vertical growth, palatal shelves elevate and adhere above the tongue by E14.5. Current models indicate that this process of elevation involves a complex vertical to horizontal reorienting of the palatal shelves. While earlier studies have implied that this is a rapid process, the precise timing has not been resolved. To understand the dynamics of palatal shelf elevation, we employed time-restricted pregnancies with a one-hour resolution and magnetic resonance imaging of intermediate stages. Our data showed that in almost all C57BL/6J embryos, palatal shelves have not yet elevated by E14.0. However, six hours later at E14.25, palatal shelves have completed elevation in 80% of embryos. Interestingly, all E14.25 embryos with unelevated palatal shelves (20%) were female, suggesting a delay in female embryos. In FVB/NJ embryos, the elevation window started earlier (E13.875-E14.25) without any noticeable sex differences. We frequently captured an intermediate stage with unilateral elevation of either right or left palatal shelf. Magnetic resonance imaging of various stages showed that palatal shelf elevation began with the formation of bilateral bulges in the posterior. These bulges progressed laterally and anteriorly over time. During elevation, we observed increased cell proliferation in the lingual region of the palatal shelf. Within the bulge, cell orientation was acutely tilted towards the tongue and actomyosin activity was increased, which together may participate in the projection of the bulge in the horizontal direction. Thus, our data reveal novel insights into the rapid dynamic changes in palatal shelf elevation that lay the foundation for future studies of normal and abnormal palatogenesis.
Transcriptome analysis of human preimplantation embryo reveals expressed waves associated with blastulation failure based on embryonic grade and age
Authors: Yuan Ping , Liu Ying , Zhao Haijing , Ma Guangwei , Zheng Lingyan , Zhang Qingxue , Chen Hui , Wang Wenjun , Guo Yabin 
Published: June 2022

AbstractIn thein vitrofertilization and embryo transfer (IVF-ET) treatments, blastocyst culture is the method of choice for the generation of the embryos. Blastocysts can present different growth, quality, availability, and morphological characteristics that can be used to evaluate them. Although extreme blastocyst formation failures have been associated with the alteration of a single gene, the molecular factors responsible for arrested embryos remain unknown. RNA-sequencing (RNA-seq) is a promising tool for facilitating transcriptomic studies in early human embryos, thus allowing the investigation of gene expression discrepancies associated with different morphological criteria. Herein, we performed transcriptome analyses of the different stages of arrested human embryos. We identified candidate genes and related cell signaling pathways potentially associated with either arrested or developed embryos. Specifically, the three genes (MOV10L1, DDX4, andFKBP6) related to both DNA methylation and piRNA metabolic pathway might be involved in embryo development. Additionally, the transcriptome of arrested early blastocysts was significantly different from developed late blastocysts. Although the gene expression profiles identified were not significantly different between low- and high-quality late blastocysts, a significant difference in the profiles of day 5 and day 6 available late blastocysts was observed, which may be related to the clinical pregnancy rate associated with IVF-ET. Furthermore, we show that some chimeric RNAs may be functional in blastocyst development. Our findings uncovered new molecular markers that can be used for embryonic development detection, which might act as a tool for blastocyst selection for subsequent transfer.
Characterizing the role of Ca2+ fluxes in defining fast and slow components of spontaneous Ca2+ local transients in OPCs using computational modeling
Authors: Desjardins Nicolas , Jiang Xiaoyu , Oprea Laurentiu , Sareen Kushagra , Zheng James Q. , Khadra Anmar 
Published: June 2022

1AbstractSpontaneous Ca2+ local transients (SCaLTs) in isolated oligodendrocyte precursor cells (OPCs) are largely regulated by the following fluxes: store-operated Ca2+ entry (SOCE), Na+/Ca2+ exchange (NCX), Ca2+ pumping through Ca2+-ATPases, and Ca2+-induced Ca2+-release through Ryanodine receptors (RyR) and inositoltriphosphate receptors (IP3R). However, the relative contributions of these fluxes in mediating fast spiking and slow baseline oscillations seen in SCaLTs remain incompletely understood. Here, we developed a stochastic spatiotemporal computational model to simulate SCaLTs in a homogeneous medium with ion flow between the extracellular, cytoplasmic and endoplasmic-reticulum compartments. By simulating the model and plotting both the histograms of SCaLTs obtained experimentally and from the model as well as the standard deviation of interspike intervals (ISI) against ISI averages of multiple model and experimental realizations we revealed that: SCaLTs exhibit very similar characteristics between the two datasets, they are mostly random, they encode information in their frequency, and the slow baseline oscillations could be due to the stochastic slow clustering of IP3R (modeled as an Ornstein-Uhlenbeck noise process). Bifurcation analysis of a deterministic temporal version of the model shows that the contribution of fluxes to SCaLTs depends on the parameter regime and that the combination of excitability, stochasticity, and mixed-mode oscillations are responsible for irregular spiking and doublets in SCaLTs. Additionally, our results demonstrate that blocking each flux reduces SCaLTs frequency and that the reverse (forward) mode of NCX decreases (increases) SCaLTs. Taken together, these results provide a quantitative framework for SCaLT formation in OPCs.