functional analysis
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2022 ◽  
Vol 22 ◽  
pp. 101009
Fangyan Pan ◽  
Yin Fu ◽  
Wenyi Zhang ◽  
Sufei Jiang ◽  
Yiwei Xiong ◽  

2022 ◽  
Vol 22 ◽  
pp. 100982
Wen-Ya Wei ◽  
Jian-Hua Huang ◽  
Qi-Bin Yang ◽  
Fa-Lin Zhou ◽  
Song Jiang ◽  

Cancers ◽  
2022 ◽  
Vol 14 (2) ◽  
pp. 421
Lide Alaña ◽  
Caroline E. Nunes-Xavier ◽  
Laura Zaldumbide ◽  
Idoia Martin-Guerrero ◽  
Lorena Mosteiro ◽  

Medulloblastoma is the primary malignant tumor of the Central Nervous System (CNS) most common in pediatrics. We present here, the histological, molecular, and functional analysis of a cohort of 88 pediatric medulloblastoma tumor samples. The WNT-activated subgroup comprised 10% of our cohort, and all WNT-activated patients had exon 3 CTNNB1 mutations and were immunostained for nuclear β-catenin. One novel heterozygous CTNNB1 mutation was found, which resulted in the deletion of β-catenin Ser37 residue (ΔS37). The ΔS37 β-catenin variant ectopically expressed in U2OS human osteosarcoma cells displayed higher protein expression levels than wild-type β-catenin, and functional analysis disclosed gain-of-function properties in terms of elevated TCF/LEF transcriptional activity in cells. Our results suggest that the stabilization and nuclear accumulation of ΔS37 β-catenin contributed to early medulloblastoma tumorigenesis.

2022 ◽  
Tommaso Mari ◽  
Kristin Moesbauer ◽  
Emanuel Wyler ◽  
Markus Landthaler ◽  
Christian Drosten ◽  

Phosphoproteomics routinely quantifies changes in the levels of thousands of phosphorylation sites, but functional analysis of such data remains a major challenge. While databases like PhosphoSitePlus contain information about many phosphorylation sites, the vast majority of known sites are not assigned to any protein kinase. Assigning changes in the phosphoproteome to the activity of individual kinases therefore remains a key challenge.. A recent large-scale study systematically identified in vitro substrates for most human protein kinases. Here, we reprocessed and filtered these data to generate an in vitro Kinase-to-Phosphosite database (iKiP-DB). We show that iKiP-DB can accurately predict changes in kinase activity in published phosphoproteomic datasets for both well-studied and poorly characterized kinases. We apply iKiP-DB to a newly generated phosphoproteomic analysis of SARS-CoV-2 infected human lung epithelial cells and provide evidence for coronavirus-induced changes in host cell kinase activity. In summary, we show that iKiP-DB is widely applicable to facilitate the functional analysis of phosphoproteomic datasets.

2022 ◽  
Vol 2022 ◽  
pp. 1-8
Xifeng Mi

With the continuous development of social economy, the expansion of cities often leads to the disorderly utilization of land resources and even waste. In view of these limitations and requirements, this paper introduces the automatic extraction algorithm of closed area boundary, combs the requirements of urban boundary extraction involved in urban planning and design, and uses the technology of geospatial analysis to carry out spatial analysis practice from three angles, so as to realize the expansion of functional analysis of urban planning and design and improve the efficiency and rationality of urban planning. The simulation results show that the automatic extraction algorithm of closed area boundary is effective and can support the functional analysis of urban planning and design expansion.

Sensors ◽  
2022 ◽  
Vol 22 (2) ◽  
pp. 600
Krzysztof Maniak ◽  
Remigiusz Mydlikowski

This paper analyses the function of an innovative integrated receiver for the measurement of electromagnetic field emissions. The autonomous receiver measures and registers the elevated emission levels of both components of the EM field originating from rocks subjected to increased mechanical stress. The receiver’s sensitivity of 60 µV/m, its dynamic range of 98 dB, and its impulse response of 0.23 V/µs were determined in laboratory conditions. Real EM field signals from hard coal samples subjected to crushing force were recorded using an autonomous receiver. The observed and recorded results confirm that the receiver operates in the full range of amplitudes of the EM field signal emitted from the rock. The results determine the band of characteristic signals for EM field emission from hard coal. The system created on the basis of autonomous EM receivers can support the existing seismic safety systems in real mine conditions by predicting the possibility of mine collapse hazards.

2022 ◽  
Martin W Lo ◽  
Alberto A Amarilla ◽  
John D Lee ◽  
Eduardo A Albornoz ◽  
Naphak Modhiran ◽  

The complement system has been heavily implicated in severe COVID-19 with clinical studies revealing widespread gene induction, deposition, and activation. However, the mechanism by which complement is activated in this disease remains incompletely understood. Herein we examined the relationship between SARS-CoV-2 and complement by inoculating the virus in lepirudin-anticoagulated human blood. This caused progressive C5a production after 30 minutes and 24 hours, which was blocked entirely by inhibitors for factor B, C3, C5, and heparan sulfate. However, this phenomenon could not be replicated in cell-free plasma, highlighting the requirement for cell surface deposition of complement and interactions with heparan sulfate. Additional functional analysis revealed that complement-dependent granulocyte and monocyte activation was delayed. Indeed, C5aR1 internalisation and CD11b upregulation on these cells only occurred after 24 hours. Thus, SARS-CoV-2 is a non-canonical complement activator that triggers the alternative pathway through interactions with heparan sulfate.

2022 ◽  
Lauren M Tom ◽  
Martina Aulitto ◽  
Yu-Wei Wu ◽  
Yu W Gao ◽  
Kai Deng ◽  

Plant cell walls are interwoven structures recalcitrant to degradation. Both native and adapted microbiomes are particularly effective at plant cell wall deconstruction. Studying these deconstructive microbiomes provides an opportunity to assess microbiome performance and relate it to specific microbial populations and enzymes. To establish a system assessing comparative microbiome performance, parallel microbiomes were cultivated on sorghum (Sorghum bicolor L. Moench) from compost inocula. Biomass loss and biochemical assays indicated that these microbiomes diverged in their ability to deconstruct biomass. Network reconstructions from time-dependent gene expression identified key deconstructive groups within the adapted sorghum-degrading communities, including Actinotalea, Filomicrobium, and Gemmanimonadetes populations. Functional analysis of gene expression demonstrated that the microbiomes proceeded through successional stages that are linked to enzymes that deconstruct plant cell wall polymers. This combination of network and functional analysis highlighted the importance of cellulose-active Actinobacteria in differentiating the performance of these microbiomes.

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