bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of CRISPR/Cas9 RANKL knockout mesenchymal stem cell clones based on single-cell printing technology and emulsion coupling assay as a low-cellularity workflow for single-cell cloning
Authors: Groß Tobias , Jeney Csaba , Halm Darius , Finkenzeller Günter , Stark G. Björn , Zengerle Roland , Kolaty Peter , Zimmermann Stefan 
Published: August 2020

AbstractThe homogeneity of the genetically modified single-cells is a necessity for many applications such as cell line development, gene therapy, and tissue engineering and in particular for regenerative medical applications. The lack of tools to effectively isolate and characterize CRISPR/Cas9 engineered cells is considered as a significant bottleneck in these applications. Especially the incompatibility of protein detection technologies to confirm protein expression changes without a preconditional large-scale clonal expansion, creates a gridlock in many applications. To ameliorate the characterization of engineered cells, we propose an improved workflow, including single-cell printing/isolation technology based on fluorescent properties with high yield, a genomic edit screen (surveyor assay), mRNA rtPCR assessing altered gene expression and a versatile protein detection tool called emulsion-coupling to deliver a high-content, unified single-cell workflow. The workflow was exemplified by engineering and functionally validating RANKL knockout immortalized mesenchymal stem cells showing altered bone formation capacity of these cells. The resulting workflow is economical, without the requirement of large-scale clonal expansions of the cells with overall cloning efficiency above 30% of CRISPR/Cas9 edited cells. Nevertheless, as the single-cell clones are comprehensively characterized at an early, highly parallel phase of the development of cells including DNA, RNA, and protein levels, the workflow delivers a higher number of successfully edited cells for further characterization, lowering the chance of late failures in the development process.Author summaryI completed my undergraduate degree in biochemistry at the University of Ulm and finished my master's degree in pharmaceutical biotechnology at the University of Ulm and University of applied science of Biberach with a focus on biotechnology, toxicology and molecular biology. For my master thesis, I went to the University of Freiburg to the department of microsystems engineering, where I developed a novel workflow for cell line development. I stayed at the institute for my doctorate, but changed my scientific focus to the development of the emulsion coupling technology, which is a powerful tool for the quantitative and highly parallel measurement of protein and protein interactions. I am generally interested in being involved in the development of innovative molecular biological methods that can be used to gain new insights about biological issues. I am particularly curious to unravel the complex and often poorly understood protein interaction pathways that are the cornerstone of understanding cellular functionality and are a fundamental necessity to describe life mechanistically.
Role of neutrophil extracellular traps in regulation of lung cancer invasion and metastasis: Structural Insights from a Computational Model
Authors: Lee Junho , Lee Donggu , Lawler Sean , Kim Yangjin 
Published: August 2020

AbstractLung cancer is one of the leading causes of cancer-related deaths worldwide and is characterized by hijacking immune system for active growth and aggressive metastasis. Neutrophils, which in their original form should establish immune activities to the tumor as a first line of defense, are undermined by tumor cells to promote tumor invasion in several ways. In this study, we investigate the mutual interactions between the tumor cells and the neutrophils that facilitate tumor invasion by developing a mathematical model that involves taxis-reaction-diffusion equations for the critical components in the interaction. These include the densities of tumor and neutrophils, and the concentrations of signaling molecules and structure such as neutrophil extracellular traps (NETs). We apply the mathematical model to a Boyden invasion assay used in the experiments to demonstrate that the tumor-associated neutrophils can enhance tumor cell invasion by secreting the neutrophil elastase. We show that the model can both reproduce the major experimental observation on NET-mediated cancer invasion and make several important predictions to guide future experiments with the goal of the development of new anti-tumor strategies. Moreover, using this model, we investigate the fundamental mechanism of NET-mediated invasion of cancer cells and the impact of internal and external heterogeneity on the migration patterning of tumour cells and their response to different treatment schedules.Author summaryWhen cancer patients are diagnosed with tumours at a primary site, the cancer cells are often found in the blood or already metastasized to the secondary sites in other organs. These metastatic cancer cells are more resistant to major anti-cancer therapies, and lead to the low survival probability. Until recently, the role of neutrophils, specifically tumor-associated neutrophils as a member of complex tumor microenvironment, has been ignored for a long time due to technical difficulties in tumor biology but these neutrophils are emerging as an important player in regulation of tumor invasion and metastasis. The mutual interaction between a tumor and neutrophils from bone marrow or in blood induces the critical transition of the naive form, called the N1 type, to the more aggressive phenotype, called the N2 TANs, which then promotes tumor invasion. In this article, we investigate how stimulated neutrophils with different N1 and N2 landscapes shape the metastatic potential of the lung cancers. Our simulation framework is designed for boyden invasion chamber in experiments and based on a mathematical model that describes how tumor cells interact with neutrophils and N2 TANs can promote tumor cell invasion. We demonstrate that the efficacy of anti-tumor (anti-invasion) drugs depend on this critical communication and N1 → N2 landscapes of stimulated neutrophils.
Multi-environment phenotyping ofC. elegansfor robust evaluation of physical performance
Authors: Hewitt Jennifer E. , Laranjeiro Ricardo , Norouzi Masoud , Ellwood Rebecca , Antebi Adam , Szewczyk Nathaniel J. , Driscoll Monica , Vanapalli Siva A. 
Published: August 2020

ABSTRACTDetermining the physical performance of humans using several measures is essential to evaluating the severity of diseases, understanding the role of environmental factors, and developing therapeutic interventions. Development of analogous measures of physical performance in model organisms can help in identifying conserved signaling pathways and prioritizing drug candidates. In this study, we propose a multi-environment phenotyping (MEP) approach that generates a comprehensive set of measures indicative of physical performance inC. elegans. We challengeC. elegansin different mechanical environments of burrowing, swimming, and crawling, each of which places different physiological demands on the animals to generate locomotory forces. Implementation of the MEP approach is done using three established assays corresponding to each environment–a hydrogel-based burrowing assay, the CeleST swim assay, and the NemaFlex crawling strength assay. Using this approach, we study individuals and show that these three assays report on unique aspects of nematode physiology, as phenotypic measures obtained from different environments do not correlate with one another. Analysis of a subset of genes representative of oxidative stress, glucose metabolism, and fat metabolism show differential expression depending on the animal’s environment, suggesting that each environment evokes a response with distinct genetic requirements. To demonstrate the utility of the MEP platform, we evaluate the response of a muscular dystrophy model ofC. elegans dys-1to drug interventions of prednisone, melatonin and serotonin. We find that prednisone, which is the current treatment standard for human Duchenne muscular dystrophy, confers benefits in all three assays. Furthermore, while the tested compounds improve the physical performance ofdys-1, these compounds are not able to fully restore the measures to wild-type levels, suggesting the need for discovery efforts to identify more efficacious compounds that could be aided using the MEP platform. In summary, the MEP platform’s ability to robustly defineC. eleganslocomotory phenotypes demonstrates the utility of the MEP approach toward identification of candidates for therapeutic intervention, especially in disease models in which the neuromuscular performance is impaired.
Two forms of isometric muscle function: Interpersonal motor task supports a distinction between a holding and a pushing isometric muscle action
Authors: Schaefer Laura V , Bittmann Frank N 
Published: August 2020

AbstractIn sports and movement sciences isometric muscle function is measured by pushing against a stable resistance. However, subjectively one can hold or push isometrically. Several investigations suggest a distinction of those forms. The aim of this study was to investigate, whether or not these two forms of isometric muscle action can be distinguished by objective parameters in an interpersonal setting. 20 subjects were grouped in 10 same sex pairs, in which one partner should perform the pushing isometric muscle action (PIMA) and the other partner executed the holding isometric muscle action (HIMA). The partners were coupled by an interface including a strain gauge and an acceleration sensor. The mechanical oscillations of the triceps brachii (MMGtri) muscle, its tendon (MTGtri) and the abdominal muscle (MMGobl) were recorded by piezoelectric-sensor-based measurement system (mechanomyography (MMG); mechanotendography (MTG)). Each partner performed three 15s (80% MVIC) and two fatiguing trials (90% MVIC) during PIMA and HIMA, respectively (tasks changed in the couple). Regarded parameters to compare PIMA and HIMA were (1) the mean frequency, (2) the normalized mean amplitude, (3) the amplitude variation, (4) the power in the frequency range of 8 to 15 Hz and (5) a special power-frequency ratio and the number of task failures during HIMA or PIMA (partner who quit the task).A “HIMA failure” occurred in 87.5% of trials (p<0.000). No significant differences between PIMA and HIMA were found for the mean frequency and normalized amplitude. The MMGobl showed a significantly higher values of the amplitude variation (15s:p0.013; fatigue:p=0.007) and of the power-frequency-ratio (15s:p= 0.040; fatigue:p= 0.002) during HIMA and a higher power in the range of 8 to 15 Hz during PIMA (15s:p=0.001; fatigue:p=0.011). MMGtri and MTGtri showed no significant differences.Based on the findings it is suggested that a holding and a pushing isometric muscle action can be distinguished objectively, whereby a more complex neural control is assumed for HIMA.
Acoustic niche partitioning in two tropical wet forest bird communities
Authors: Hart Patrick J. , Paxton Kristina , Ibanez Thomas , Tredinnick Grace , Sebastián-González Esther , Tanimoto-Johnson Ann 
Published: August 2020

AbstractWhen acoustic signals sent from individuals overlap in frequency and time, acoustic interference and signal masking may occur. Under the acoustic niche hypothesis (ANH), signaling behavior has evolved to minimize overlap with other calling individuals through selection on signal structure and the sender’s ability to adjust the timing of signals. In this study, we examine the fine-scale use of acoustic space and the relevance of the acoustic niche hypothesis in two montane tropical wet forest bird communities (Costa Rica and Hawai’i) that vary in bird species richness. We used a null model approach to test the prediction that there are differences between observed and expected signal overlap in both communities. As predicted under ANH, we found much lower overlap of acoustic signals than expected by chance. In addition, spectral and temporal overlap between different signals was far more common in Hawaii than Costa Rica. These findings constitute strong support that there is competition for acoustic space in signaling communities, and this has resulted in temporal and spectral partitioning of the soundscape.
Influenza virus inhibits respiratory syncytial virus (RSV) infection via a two-wave expression of interferon-induced protein with tetratricopeptide (IFIT) proteins
Authors: Drori Yaron , Jacob-Hirsch Jasmine , Pando Rakefet , Glatman-Freedman Aharona , Friedman Nehemya , Mendelson Ella , Mandelboim Michal 
Published: August 2020

AbstractInfluenza viruses and respiratory syncytial virus (RSV) are respiratory viruses that primarily circulate worldwide during the autumn and winter seasons. Seasonal surveillance shows that RSV infection generally precedes influenza. However, in the last four winter seasons (2016-2020) an overlap of the morbidity peaks of both viruses was observed in Israel, and was paralleled by significantly lower RSV infection rates. To investigate whether the influenza virus inhibits RSV we performed coinfection of Human cervical carcinoma (HEp2) cells or mice with influenza and RSV and we observed that the influenza inhibited RSV growth, both in vitro and in vivo. Mass spectrometry analysis of mouse lungs infected with influenza identified a two-wave pattern of protein expression upregulation, which included members of the interferon-induced protein with tetratricopeptide (IFITs) family. Interestingly, in the second peak of upregulation, influenza viruses were no longer detectable in mouse lungs. We also observed that knockdown and overexpression of IFITs in HEp2 cells affected RSV multiplicity. In conclusion, influenza infection inhibits RSV infectivity via upregulation of IFIT proteins in a two-wave modality. Understanding of the interaction between influenza and RSV viruses and immune system involvement will contribute to the development and optimization of future treatment strategies against these viruses.Author SummaryRespiratory syncytial virus (RSV) and influenza viruses are both respiratory viruses associated with morbidity and mortality worldwide. RSV is usually detected in October, with a clear peak in December, whereas influenza virus arrives in November and peaks in January. In the last four seasons, influenza infection overlapped with that of RSV in Israel, which resulted in decreased morbidity of RSV suggesting that influenza virus inhibits RSV infection. To identify the mechanism responsible for the influenza inhibition of RSV we performed experiments in culture and in mice. We observed that influenza infection results in two wave modality of inhibition of RSV infection. Using mass spectrometry perfornmed on lungs from infected mice we show that influenza infection induces the expression of (IFIT) family of proteins which also showed a two-wave modality. Using knockdown and overexpression experiments we showed that indeed the IFTIs inhibits RSV infection. Our study provides new insights on the interaction between influenza and RSV viruses and immune system involvement and contribute to the development of future treatment strategies against these viruses.
Physiological, Biochemical and Microstructural Changes in Rice (Oryza sativaL.) under Varying pH Levels
Authors: Ekta  , Singh Anil Kumar , Pandey Dev Mani 
Published: August 2020

AbstractSoil acidification exerts detrimental effects on rice plant leading to severe reduction in its yield. In the present study, we investigated the physiological, biochemical and microstructural changes in the leaves of rice cultivars, namely, Jhilli Dhan (JD) and Gora Dhan (GD), under varying pH conditions (pH 6.5, 5.5, 4.5 and 3.5). Seedlings were grown at varying pH levels for 14 days under controlled conditions. Root and shoot growth and chlorophyll content were found to be decreased with increasing acidity, whereas electrolyte leakage was increased with increasing acidity. Overall, seedling growth was significantly reduced at pH 3.5, while, it was maximum at pH 6.5 treatment, which might be the result of cumulative altered physiological parameters. Further, biochemical parameters, namely total soluble sugar (TSS), proline content and lipid peroxidation were found to be positively correlated with acidity. Microstructural changes were observed through Swept-Source Optical Coherence Tomography (SS-OCT) and Field Emission Scanning Electron Microscope (FESEM). The thickness between different layers of leaves was found to be disintegrating at low pH conditions and the thickness of parenchyma cells was reduced significantly. FESEM analysis revealed changes in characteristics of stomata under acidic stress. The understanding of physiological, biochemical and microstructural changes in rice leaves under varying pH conditions may help in developing rice with improved tolerance towards soil acidity stress.
Characterization of Onion Seedlots into Different Storability Groups with 4 Parameter Hill Function (4-PHF)
Authors: Kumar Sunil , Basu Sudipta , Anand Anjali , Aravind J. 
Published: August 2020

AbstractOnion varieties were classified into different storability groups by comparing two approaches (i)germination and vigor indices (conventional germination parameters) (ii)variables extracted from 4 Parameter Hill Function (4-PHF), after mimicking ageing conditions with accelerated ageing (42 °C and 100% RH). The study revealed that in comparison to evaluation using conventional germination parameters, the parameters extracted using 4-PHF provided realistic characterization of varieties as good, medium and poor storers. Time related parameters like time to maximum germination rate (TMGR), time to 50% germination (T50), difference between time at germination onset (lag) and 50% germination (Dlag-50), uniformity (U) along with germination percent (a) and area under curve (AUC) were decisive in identification of the varieties to a storage category which was misinterpreted with exclusive use of conventional approach. The distinction between good and medium storers was not of much significance but shift of varieties like Bhima Super, Pusa Red and Agrifound Light Red from poor to good performance cluster could be detected exclusively through 4-PHF analysis. Curve fittings highlightedAUCas the most crucial parameter contributing towards clustering of the varieties in different storability groups. Our study is the first reported research of using 4-PHF mathematical function for seedlot characterization into different storability groups.
Unveiling sex-based differences in the effects of alcohol abuse: a comprehensive functional meta-analysis of transcriptomic studies
Authors: Ferrer Franc Casanova , Pascual María , Hidalgo Marta R. , Malmierca-Merlo Pablo , Guerri Consuelo , García-García Francisco 
Published: August 2020

AbstractThe abuse of alcohol, one of the most popular psychoactive substances, can cause several pathological and psychological consequences, including alcohol use disorder (AUD). An impaired ability to stop or control alcohol intake despite adverse health or social consequences characterize AUD. While AUDs predominantly occur in men, growing evidence suggests the existence of distinct cognitive and biological consequences of alcohol dependence in women. The molecular and physiological mechanisms participating in these differential effects remain unknown. Transcriptomic technology permits the detection of the biological mechanisms responsible for such sex-based differences, which supports the subsequent development of novel personalized therapeutics to treat AUD. We conducted a systematic review and meta-analysis of transcriptomics studies regarding alcohol dependence in humans with representation from both sexes. For each study, we processed and analyzed transcriptomic data to obtain a functional profile of pathways and biological functions and then integrated the resulting data by meta-analysis to characterize any sex-based transcriptomic differences associated with AUD. Global results of the transcriptomic analysis revealed the association of decreased tissue regeneration, embryo malformations, altered intracellular transport, and increased rate of RNA and protein replacement with female AUD patients. Meanwhile, our analysis indicated that increased inflammatory response and blood pressure and a reduction in DNA repair capabilities associated with male AUD patients. In summary, our functional meta-analysis of transcriptomic studies provides evidence for differential biological mechanisms that AUD patients of differing sex.Abstract Figure
Continued topographical learning- and relearning-dependent activity in the resting state after post-training sleep and wake
Authors: Deantoni Michele , Villemonteix Thomas , Balteau Evelyne , Schmidt Christina , Peigneux Philippe 
Published: August 2020

AbstractContinuation of experience-dependent neural activity during offline periods of sleep and wakefulness is a critical element of memory consolidation. Using functional magnetic resonance imaging (fMRI), offline consolidation effects have been evidenced probing behavioral and neurophysiological changes during memory retrieval, i.e. in the context of task practice. Resting state fMRI (rfMRI) further allows investigating the offline evolution of recently learned information, without confounding task-related effects. In the present study, we used rfMRI to investigate offline changes in functional connectivity (FC) and Amplitude of Low Frequency Fluctuation (ALFF) associated with learning and relearning in a spatial navigation task, following an episode of post-training wake or sleep, respectively. Resting state activity was measured immediately (i) before and (ii) after topographical learning in a virtual town, (iii) 4 days later after regular sleep (RS) vs. sleep deprivation (SD) on the first post-learning night, and (iv) after topographical re-learning in an extended town encompassing the initial map. Task (navigation)-based fMRI activity was also recorded on Day 1 and Day 4 during target retrieval. Our results highlight the continuation of navigation-related activity in the subsequent resting state, as evidenced by changes in FC and ALFF in task-related neural networks. Behavioural performance was not modulated by post-training SD vs RS. However, in line with prior reports, post-training SD was associated with increased FC between navigation-related brain structures when faced to the task of learning a novel but related environment in the extended version of the city at Day 4. These results suggest the use of compensatory resources to link novel information with SD-related less efficiently consolidated memory traces.