bluuebunny/crossref_metadata_2025_split huggingface dataset:
Generating parallel representations of position and identity in the olfactory system
Authors: Taisz István , Donà Erika , Münch Daniel , Bailey Shanice N. , Morris Billy J. , Meechan Kimberly I. , Stevens Katie M. , Varela Irene , Gkantia Marina , Schlegel Philipp , Ribeiro Carlos , Jefferis Gregory S.X.E. , Galili Dana S. 
Published: May 2022

SummarySex pheromones are key social signals in most animals. In Drosophila a dedicated olfactory channel senses a male pheromone, cis-vaccenyl acetate (cVA) that promotes female courtship while repelling males. Here we show that flies use separate cVA processing streams to extract qualitative and positional information. cVA olfactory neurons are sensitive to concentration differences in a 5 mm range around a male. Second-order projection neurons detect inter-antennal differences in cVA concentration, encoding the angular position of a male. We identify a circuit mechanism increasing left-right contrast through an interneuron which provides contralateral inhibition. At the third layer of the circuit we identify neurons with distinct response properties and sensory integration motifs. One population is selectively tuned to an approaching male with speed-dependent responses. A second population responds tonically to a male’s presence and controls female mating decisions. A third population integrates a male taste cue with cVA; only a simultaneous presentation of both signals promotes female mating via this pathway. Thus the olfactory system generates a range of complex percepts in discrete populations of central neurons that allow the expression of appropriate behaviors depending on context. Such separation of olfactory features resembles the mammalian what and where visual streams.HighlightscVA male pheromone has a 5 mm signaling range, activating two parallel central pathwaysPheromone-sensing neurons have spatial receptive fields sharpened by contralateral inhibitionPosition (where) and identity (what) are separated at the 3rd layer of cVA processingIntegrating taste and cVA in sexually dimorphic aSP-g controls female receptivity
Topological analysis of brain dynamics in autism based on graph and persistent homology
Authors: Jafadideh Alireza Talesh , Asl Babak Mohammadzadeh 
Published: May 2022

AbstractAutism spectrum disorder (ASD) is a heterogeneous disorder with a rapidly growing prevalence. In recent years, the dynamic functional connectivity (DFC) technique has been used to reveal the transient connectivity behavior of ASDs’ brains by clustering connectivity matrices in different states. However, the states of DFC have not been yet studied from a topological point of view. In this paper, this study was performed using global metrics of the graph and persistent homology (PH) and resting-state functional magnetic resonance imaging (fMRI) data. The PH has been recently developed in topological data analysis and deals with persistent structures of data. The structural connectivity (SC) and static FC (SFC) were also studied to better show the advantages of DFC analysis. Significant discriminative features between ASDs and typical controls (TC) were only found in states of DFC. Moreover, the best classification performance was offered by persistent homology-based metrics in two out of four states. In these two states, some networks of ASDs compared to TCs were more segregated and isolated (showing the disruption of network integration in ASDs). The results of this study demonstrated that topological analysis of DFC states could offer discriminative features which were not discriminative in SFC and SC. Also, PH metrics compared to graph global metrics can open a brighter avenue for studying ASD and finding candidate biomarkers.HighlightsStates of dynamic functional connectivity (DFC) were more informative than static FC and structural connectivity when comparing ASDs with controls.Global metrics of persistent homology (PH) in comparison to graph ones could better distinguish between ASDs and controls.The PH metrics could offer the best classification performance in dynamic states where the networks of ASDs compared to controls were more segregated and isolated.
Negative emotional behavior during fentanyl abstinence is mediated by adaptations in nucleus accumbens neuron subtypes
Authors: Fox Megan E. , Wulff Andreas B. , Franco Daniela , Choi Eric , Calarco Cali A. , Engeln Michel , Turner Makeda D. , Chandra Ramesh , Rhodes Victoria M. , Thompson Scott M. , Ament Seth A. , Lobo Mary Kay 
Published: May 2022

SummaryOpioid discontinuation generates a withdrawal syndrome marked by a negative emotional state. Increased anxiety and dysphoria during opioid discontinuation are a significant barrier to achieving long-term abstinence in opioid-dependent individuals. Adaptations in brain-reward circuitry are implicated in the opioid abstinence syndrome, but current knowledge is limited to changes following natural and semi-synthetic opioids. Here we report abstinence from the synthetic opioid fentanyl engenders structural, functional, and molecular plasticity in nucleus accumbens neuron subtypes (MSNs) that mediate negative emotional behaviors. We show fentanyl abstinence causes dendritic atrophy and increased excitatory drive exclusive to D1-receptor containing MSNs. Using subtype specific RNAseq and Weighted Gene Co-Expression Network Analysis, we identified molecular signatures of fentanyl abstinence in MSN subtypes. We found a network of co-expressed genes downregulated selectively in D1-MSNs, and transcriptionally co-regulated by E2F1. We show targeting abstinence-induced molecular changes protects D1-MSNs from maladaptive plasticity and alleviates negative emotional behaviors after fentanyl abstinence.
Remote sensing tools for plant invasions assessment in native tropical forests of a volcanic island
Authors: Guillaume Roussel , Olivier Flores 
Published: May 2022

AbstractSurveying and monitoring biological invasions by plants can greatly benefit from the application of remote sensing techniques. In tropical insular enviroments however, multiple challenges makes the task difficult. Invasive species can be diverse and many, so that evaluating an overall invasion level may help to distinguish uninvaded native forests from forests invaded at various levels. Also, accessibility can limit the availability of field-based data documenting the ground truth of plant invasions. Here we present a methodological study with the doublefold objective of first estimating an overall index of invasion and level of native forest canopies and second detect two particular exotic (Cinamomum camphora, Lauraceae and Cryptomeria japonica, Taxodiaceae) planted in monospecific stands. The index of overall invasion level comprises four classes derived elsewhere from field observations and expert knowledge. A thematic map provided polygons representing monospecif plantations. Textural features of sub-regional regions of interest and polygons were derived using Haralick coefficients on co-occurrence matrices, and morphological profiles. Classification algorithms were applied to produce invasion classes (k-means) or detect target species (Support Vector Machine, SVM) based on pixels features.
Late Fetal and Newborn Granulopoiesis but not Active Renin is Increased by Maternal Captopril Treatment During Perinatal Kidney Development
Authors: Buckley C , L’Huillier N , Mullins L , Semprini S , Christian H , Mullins JJ 
Published: May 2022

AbstractRenin expression follows vascular development through the mouse kidney, regressing to glomerular poles by about P10, where renin is stored in dense core granules in juxtaglomerular cells. Homeostatic challenge to blood pressure causes release of active renin from the granules and recruitment of the renin lineage cells. We investigated the response to homeostatic challenge during late fetal development and following birth in a transgenic line expressing GFP under the renin promotor. Pregnant females were treated with water or captopril (30mg/kg/day), which inhibits angiotensin converting enzyme, from E15.5. We found an increase in renin transcription and expression by P1 following captopril treatment, with granulation increased at the glomerular poles and major arteries from E18.5. At P1, the granules showed a wide variation in electron density. Notably, rough endoplasmic reticulum was expanded in vascular smooth muscle cells (VSMCs) of captopril-treated pups at both time-points suggesting increased transcriptional activity. Paracrystalline material was observed in granules of captopril treated fetuses at E18.5 and in both treated and untreated pups at P1. Renin expression and some granules were confirmed in the kidney VSMCs by immuno-gold staining against GFP at E18.5. Importantly, we found no difference in active renin content between kidneys from treated and untreated pups at either age group. We therefore demonstrate a disconnect between granulation and active renin production in newborns when exposed to homeostatic challenge in utero.
Leishmaniainfection-derived extracellular vesicles drive transcription of genes involved in M2 polarization
Authors: Emerson Lisa , Gioseffi Anna , Barker Hailey , Sheppe Austin , Morrill Julianne K. , Edelmann Mariola , Kima Peter 
Published: May 2022

AbstractAlthough it is known that the composition of EVs is determined by the characteristics of the cell and its environment, the effects of intracellular infection on EV composition and functions are not well understood. We had previously shown that cultured macrophages infected withLeishmaniaparasites release EVs that contain parasite derived molecules (LiEVs). In this study we show that LdVash, a molecule previously identified in LiEVs fromL. donovaniinfected RAW264.7 macrophages is widely distributed in the liver ofL. donovaniinfected mice. This result shows for the first time that parasite molecules are released in EVs and distributed in infected tissues where they can be endocytosed by cells in the liver, including macrophages that undergo a significant increase in numbers as the infection progresses. To commence evaluating the potential impact of LiEVs on macrophage functions, we show that primary peritoneal exudate macrophages (PECs) express transcripts of signature molecules of M2 macrophages such as arginase 1, IL-10 and IL-4R when incubated with LiEVs. In comparative studies that illustrate how intracellular pathogens control the composition and functions of EVs released from macrophages, we show that EVs from RAW264.7 macrophages infected with Salmonella enterica serovar Typhimurium activate PECs to express transcripts of signature molecules of M1 macrophages such as iNOS, TNF alpha and IFN gamma and not M2 signature molecules. Finally, we show that in contrast to the polarized responses observed in in vitro studies of macrophages, both M1 and M2 signature molecules are detected inL. donovaniinfected livers although they exhibit differences in their spatial distribution in infected tissues.
Post-transcriptional control of SRSF9 promotes the epithelial-to-mesenchymal transition (EMT) in colorectal cancer cells
Authors: Rao Chaitra , Svoboda Robert A. , Southekal Siddesh , Vieira Heidi M. , Huisman Dianna H. , Chatterjee Deepan , Guda Chittibabu , Fisher Kurt W. , Anczuków Olga A , Lewis Robert E. 
Published: May 2022

AbstractIn human colorectal cancer (CRC) cells the Raf/MEK/ERK scaffold Kinase Suppressor of Ras 1 (KSR1)-dependent signaling is required for the epithelial-to-mesenchymal transition (EMT)-like phenotype. Here we show that KSR1 promotes the association of differentially spliced mRNA bearing recognition sites for the Serine/Arginine-Rich (SR) splicing factor SRSF9. CRISPR/Cas9 disruption of KSR1 destabilizes SRSF9 protein, which interacts preferentially with mRNA encoding Epithelial Stromal Interaction 1 (EPSTI1). EPSTI1 protein mediates Ras and KSR1-dependent induction of EMT. Analysis ofEPSTI1splice variants reveals that inclusion of exon 8 is critical to the ability of EPSTI1 to promote the E-to N-cadherin switch and CRC cell motile and invasive behavior. These data reveal a mechanism in CRC cells in which Ras-induced and KSR1-dependent signaling affects pre-mRNA splicing to control behaviors critical to cancer cell dissemination and metastasis.
Anaerobic degradation of acid red 73 by obligately aerobic Aspergillus tabacinus LZ-M though a self-redox mechanism
Authors: Yu Xuan , Zong Simin , Mao Chunlan , Khan Aman , Wang Wenxue , Yun Hui , Zhang Peng , Li Xiangkai 
Published: May 2022

AbstractFungi are potential biological resources for refractory organics degradation, but their anaerobic degradation of azo dyes are rarely reported. In this study, a fungus Aspergillus tabacinus LZ-M was isolated grown aerobically and degraded acid red 73 (AR73) with a decolorization rate of 90.28% in 5 days at 400 mg/L of concentration anaerobically. Metabolic pathway showed that AR73 was reduced into 2-hydroxynaphthalene and aniline then mineralized into CO2. The anaerobic self-redox process revealed electrons generated in carbon oxidation and transferred to -C-N= and -N=N, resulting in complete mineralization of AR73 in strain LZ-M. Data of transcriptome analysis showed that the benzene compounds produced from AR73 by declorizing reductase entered the catechol pathway and glycolysis process to mineralize. Enzymes involved in aromatics degradation, glycolysis processes, cytochrome C and quinone oxidoreductases were up-regulate, but the key reductase responsible to cleave AR73 to phenylhydrazine was not found. A novel enzyme Ord95 containing a glutamate S-transferase domain was identified in the unknown genes as a reductase which cleaving -C-N= in AR73 using NADH as electron donor, and three arginines key active sites. These observations reveal a new degradation mechanism of AR73 in strain LZ-M which would be potential candidate for treatment of azo dyes wastewater.Graphical abstract
Long-duration and non-invasive photoacoustic imaging of multiple anatomical structures in a live mouse using a single contrast agent
Authors: Khadria Anjul , Paavola Chad D. , Zhang Yang , Davis Samuel P. X. , Grealish Patrick , Maslov Konstantin , Shi Junhui , Beals John M. , Oladipupo Sunday S , Wang Lihong V. 
Published: May 2022

AbstractLong-durationin vivosimultaneous imaging of multiple anatomical structures is useful for understanding physiological aspects of diseases, informative for molecular optimization in preclinical models, and has potential applications in surgical settings to improve clinical outcomes. Previous studies involving simultaneous imaging of multiple anatomical structures, e.g., blood and lymphatic vessels as well as peripheral nerves and sebaceous glands, have used genetically engineered mice, which require expensive and time-consuming methods. Here, an IgG4 isotype control antibody is labeled with a near-infrared dye and injected into a mouse ear to enable simultaneous visualization of blood and lymphatic vessels, peripheral nerves, and sebaceous glands for up to 3 hours using photoacoustic microscopy. For multiple anatomical structure imaging, peripheral nerves and sebaceous glands are imaged inside the injected dye-labeled antibody mass while the lymphatic vessels are visualized outside the mass. The efficacy of the contrast agent to label and localize deep medial lymphatic vessels and lymph nodes using photoacoustic computed tomography is demonstrated. The capability of a single injectable contrast agent to image multiple structures for several hours will potentially improve preclinical therapeutic optimization, shorten discovery timelines, and enable clinical treatments.
ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology for video-rate super-resolution imaging
Authors: Lu Meng , Christensen Charles N. , Weber Jana M. , Konno Tasuku , Läubli Nino F. , Scherer Katharina M. , Avezov Edward , Lio Pietro , Lapkin Alexei A. , Kaminski Schierle Gabriele S. , Kaminski Clemens F. 
Published: May 2022

AbstractThe topology of endoplasmic reticulum (ER) network is highly regulated by various cellular and environmental stimuli and affects major functions such as protein quality control and the cell’s response to metabolic changes. The ability to quantify the dynamical changes of the ER structures in response to cellular perturbations is crucial for the development of novel therapeutic approaches against ER associated diseases, such as hereditary spastic paraplegias and Niemann Pick Disease type C. However, the rapid movement and small spatial dimension of ER networks make this task challenging. Here, we combine video-rate super-resolution imaging with a state-of-the-art semantic segmentation method capable of automatically classifying sheet and tubular ER domains inside individual cells. Data are skeletonised and represented by connectivity graphs to enable the precise and efficient quantification and comparison of the network connectivity from different complex ER phenotypes. The method, called ERnet, is powered by a Vision Transformer architecture, and integrates multi-head self-attention and channel attention into the model for adaptive weighting of frames in the time domain. We validated the performance of ERnet by measuring different ER morphology changes in response to genetic or metabolic manipulations. Finally, as a means to test the applicability and versatility of ERnet, we showed that ERnet can be applied to images from different cell types and also taken from different imaging setups. Our method can be deployed in an automatic, high-throughput, and unbiased fashion to identify subtle changes in cellular phenotypes that can be used as potential diagnostics for propensity to ER mediated disease, for disease progression, and for response to therapy.
Mathematical Characterization of Private and Public Immune Repertoire Sequences
Authors: Böttcher Lucas , Wald Sascha , Chou Tom 
Published: May 2022

AbstractDiverse T and B cell repertoires play an important role in mounting effective immune responses against a wide range of pathogens and malignant cells. The number of unique T and B cell clones is characterized by T and B cell receptors (TCRs and BCRs), respectively. Although receptor sequences are generated probabilistically by recombination processes, clinical studies found a high degree of sharing of TCRs and BCRs among different individuals. In this work, we formulate a mathematical and statistical framework to quantify receptor distributions. We define information-theoretic metrics for comparing the frequency of sampled sequences observed across different individuals. Using synthetic and empirical TCR amino acid sequence data, we perform simulations to compare theoretical predictions of this clonal commonality across individuals with corresponding observations. Thus, we quantify the concept of “publicness” or “privateness” of T cell and B cell clones. Our methods can also be used to study the effect of different sampling protocols on the expected commonality of clones and on the confidence levels of this overlap. We also quantify the information loss associated with grouping together certain receptor sequences, as is done in spectratyping.
Prenatal valproic acid-induced autism marmoset model exhibits higher salivary cortisol levels
Authors: Nakamura Madoka , Nakagami Akiko , Nakagaki Keiko , Yasue Miyuki , Kawai Nobuyuki , Ichinohe Noritaka 
Published: May 2022

AbstractIndividuals with autism spectrum disorder (ASD) are exposed to a variety of stressors owing to their behavioral traits. Cortisol is a hormone typically associated with stress, and its concentration and response to stress are higher in individuals with ASD than in controls. The mechanisms underlying cortisol dysregulation in ASD have been explored in rodents. Although rodent models have successfully replicated the major symptoms of autism (i.e., impaired vocal communication, social interaction deficits, and restricted/repetitive patterns of behavior), evidence suggests that the hypothalamic-pituitary-adrenal (HPA) axis system differs between rodents and primates. We developed an ASD model in the common marmoset (Callithrix jacchus), a New World monkey, utilizing prenatal exposure to valproic acid (VPA). In this study, we collected the salivary cortisol levels in VPA-exposed and unexposed marmosets in the morning and afternoon. Our results revealed that both VPA-exposed and unexposed marmosets showed similar diurnal changes in cortisol levels, which were lower in the afternoon than in the morning. However, heightened cortisol levels were observed in VPA-exposed marmosets in the morning, but not in the afternoon. These results are consistent with those of ASD in humans. Our results suggest that VPA-exposed marmosets show similarities not only in their behavioral patterns and brain pathologies, which we have reported previously but also in hormonal regulation, validating the usefulness of VPA-exposed marmosets also as a tool for ASD stress research.
Thermopriming-associated proteome and sugar content responses in Pinus radiata embryogenic tissue
Authors: Castander-Olarieta Ander , Pereira Cátia , Mendes Vera M. , Correia Sandra , Manadas Bruno , Canhoto Jorge , Montalbán Itziar A. , Moncaleán Paloma 
Published: May 2022

AbstractImproving the capacity of plants to face adverse environmental conditions requires a deep understanding of the molecular mechanisms governing stress response and adaptation. Proteomics, combined with metabolic analyses, offers a wide resource of information to be used in plant breeding programs. Previous studies have shown that somatic embryogenesis in Pinus spp. is a suitable tool not only to investigate stress response processes but also to modulate the behaviour of somatic plants. Based on this, the objective of this study was to analyse the protein and soluble sugar profiles of Pinus radiata embryonal masses after the application of high temperatures to unravel the mechanisms involved in thermopriming and memory acquisition at early stages of the somatic embryogenesis process. Results confirmed that heat provokes deep readjustments in the life-cycle of proteins, together with a significant reduction in the carbon-flux of central-metabolism pathways. Heat-priming also promotes the accumulation of proteins involved in oxidative stress defence, in the synthesis of specific amino acids such as isoleucine, influences cell division, the organization of the cytoskeleton and cell-walls, and modifies the levels of free soluble sugars like glucose or fructose. All this seems to be regulated by proteins linked with epigenetic, transcriptional and post-transcriptional mechanisms.