scholarly journals Expression of Wnt and TGF-Beta Pathway Components during Whole-Body Regeneration from Cell Aggregates in Demosponge Halisarca dujardinii

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 944
Author(s):  
Ilya Borisenko ◽  
Fyodor V. Bolshakov ◽  
Alexander Ereskovsky ◽  
Andrey I. Lavrov
Keyword(s):  
Signaling Pathways ◽  
In Silico Analysis ◽  
Signaling Cascades ◽  
Whole Body ◽  
Cell Aggregates ◽  
Rna Seq ◽  
Tgf Beta ◽  
Axial Patterning ◽  
Silico Analysis

The phenomenon of whole-body regeneration means rebuilding of the whole body of an animal from a small fragment or even a group of cells. In this process, the old axial relationships are often lost, and new ones are established. An amazing model for studying this process is sponges, some of which are able to regenerate into a definitive organism after dissociation into cells. We hypothesized that during the development of cell aggregates, primmorphs, new axes are established due to the activation of the Wnt and TGF-beta signaling pathways. Using in silico analysis, RNA-seq, and whole-mount in situ hybridization, we identified the participants in these signaling pathways and determined the spatiotemporal changes in their expression in demosponge Halisarca dujardinii. It was shown that Wnt and TGF-beta ligands are differentially expressed during primmorph development, and transcripts of several genes are localized at the poles of primmorphs, in the form of a gradient. We suppose that the Wnt and TGF-beta signaling cascades are involved in the initial axial patterning of the sponge body, which develops from cells after dissociation.

scholarly journals Clinicopathologic features of TDO2 overexpression in renal cell carcinoma

BMC Cancer ◽  
2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Quoc Thang Pham ◽  
Daiki Taniyama ◽  
Yohei Sekino ◽  
Shintaro Akabane ◽  
Takashi Babasaki ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
In Silico Analysis ◽  
Immunohistochemical Analysis ◽  
Rna Seq ◽  
Anoikis Resistance ◽  
Silico Analysis ◽  
Proliferation And Invasion

Abstract Background Tryptophan 2,3-dioxygenase (TDO2) is the primary enzyme catabolizing tryptophan. Several lines of evidence revealed that overexpression of TDO2 is involved in anoikis resistance, spheroid formation, proliferation, and invasion and correlates with poor prognosis in some cancers. The aim of this research was to uncover the expression and biofunction of TDO2 in renal cell carcinoma (RCC). Methods To show the expression of TDO2 in RCC, we performed qRT-PCR and immunohistochemistry in integration with TCGA data analysis. The interaction of TDO2 with PD-L1, CD44, PTEN, and TDO2 expression was evaluated. We explored proliferation, colony formation, and invasion in RCC cells line affected by knockdown of TDO2. Results RNA-Seq and immunohistochemical analysis showed that TDO2 expression was upregulated in RCC tissues and was associated with advanced disease and poor survival of RCC patients. Furthermore, TDO2 was co-expressed with PD-L1 and CD44. In silico analysis and in vitro knockout of PTEN in RCC cell lines revealed the ability of PTEN to regulate the expression of TDO2. Knockdown of TDO2 suppressed the proliferation and invasion of RCC cells. Conclusion Our results suggest that TDO2 might have an important role in disease progression and could be a promising marker for targeted therapy in RCC. (199 words)

scholarly journals Utilisation of 2,2DCP by Staphyloccocus aureus ZT and In Silico Analysis of Putative Dehalogenase

2021 ◽  
Vol 13 (1) ◽  
pp. 1-8
Author(s):  
Zatty Zawani Zaidi ◽  
Fahrul Huyop
Keyword(s):  
In Silico ◽  
Culture Media ◽  
Enrichment Culture ◽  
In Silico Analysis ◽  
In Situ Bioremediation ◽  
Isolation And Characterization ◽  
Halogenated Compound ◽  
Silico Analysis ◽  
Dehalogenase Gene

Halogenated compound such as 2,2-dichloropropionic acid is known for its toxicity and polluted many areas especially with agricultural activities. This study focused on the isolation and characterization of the bacterium that can utilise 2,2-dichloropropionic acid from palm oil plantation in Lenga, Johor and in silico analysis of putative dehalogenase obtained from NCBI database of the same genus and species. The bacterium was isolated using an enrichment culture media supplemented with 20 mM 2,2-dicholoropropionic acid as a carbon source.  The cells were grown at 30˚C with cells doubling time of 2.00±0.005 hours with the maximum growth at A680nm of 1.047 overnight. The partial biochemical tests and morphological examination concluded that the bacterium belongs to the genus Staphylococcus sp.. This is the first reported studies of  Staphylococcus sp. with the ability to grow on 2,2-dichloropropionic acid. The genomic DNA from NCBI database of the same species was analysed assuming the same genus and has identical genomic sequence.  The full genome of Staphylococcus sp. was screened for dehalogenase gene and  haloacid dehalogenase gene was detected in the mobile genetic element of the species revealed that the dehalogenase sequence has little identities to the previously reported dehalogenases.The main outcome of the studies suggesting an in situ bioremediation can be regarded as a natural process to detoxify the contaminated sites provided that the microorganisms contained a specialised gene sequence within its genome that served the nature for many long years. Whether microorganisms will be successful in destroying man-made contaminants entirely rely on what types of organisms play a role in in situ bioremediation and which contaminants are most susceptible to bioremediation. 

scholarly journals Identifying new COVID-19 receptor Neuropilin-1 in severe Alzheimer’s diseases patients group brain using genome-wide association study approach

2021 ◽  
Author(s):  
Key-Hwan Lim ◽  
Sumin Yang ◽  
Sung-Hyun Kim ◽  
Jae-Yeol Joo
Keyword(s):  
In Silico ◽  
Genome Wide Association Study ◽  
Transmembrane Protein ◽  
In Silico Analysis ◽  
Therapeutic Drug ◽  
Rna Seq ◽  
Total Rna ◽  
Neuropilin 1 ◽  
Silico Analysis ◽  
Brain Tissues

Abstract Background Numerous studies have been conducted on different aspects of the COVID-19 (coronavirus disease 2019) pandemic, which is caused by SARS-CoV-2, since its emergence in late 2019. Mutual relations among SARS-CoV-2 and neuro-pathophysiological phenomena are continuously being demonstrated, and several underlying diseases, such as those in the elderly, are positively correlated with susceptibility to SARS-CoV-2 infection. The expression of angiotensin converting enzyme 2 (ACE2), which is required for SARS-CoV-2 infection, was recently demonstrated to be increased in Alzheimer’s disease (AD) patients. Methods Recent preclinical studies have shown that Neuropilin-1 (NRP1), which is a transmembrane protein with roles in neuronal development, axonal outgrowth, and angiogenesis, also plays a role in the infectivity of SARS-CoV-2. Thus, we hypothesized that NRP1 may be upregulated in AD patients and that a correlation between AD and SARS-CoV-2 NRP1-mediated infectivity may exist. We used an AD mouse model that mimics AD and performed high throughput total RNA-seq with brain tissue and whole blood. For quantification of NPR1 in AD, brain tissues and blood were subjected to western blotting and RT-qPCR analysis. In silico analysis for NRP1 expression in AD patients has been performed on the human hippocampus data sets (GSE4226, GSE1297). Results Many cases of severe symptom of COVID-19 are concentrated in elderly group who have complications such as diabetes, degenerative disease, and brain disorders. Total RNA-seq analysis showed that Nrp1 gene was commonly overexpressed in AD model. Similar to ACE2, NRP1 protein also strongly expressed in the AD brain tissues. Interestingly, in silico analysis revealed that the level of expression for NRP1 was distinct at age and AD progression. Conclusions Given that the NRP1 is highly expressed in AD, it will be important to understand and predict that NRP1 may a risk factor for SARS-CoV-2 infection in AD patients. This will support to development of potential therapeutic drug to reduce SARS-CoV-2 transmission.

scholarly journals Peroxide sensing and signaling in the Sporothrix schenckii complex: an in silico analysis to uncover putative mechanisms regulating the Hog1 and AP-1 like signaling pathways

2014 ◽  
Vol 53 (1) ◽  
pp. 51-59 ◽  
Author(s):  
I. Ortega ◽  
M. S. Soares Felipe ◽  
A. T. R. Vasconcelos ◽  
L. M. Lopes Bezerra ◽  
A. Da Silva Dantas
Keyword(s):  
Signaling Pathways ◽  
In Silico ◽  
Sporothrix Schenckii ◽  
In Silico Analysis ◽  
Silico Analysis

scholarly journals Integrated Analysis Identifies Key lncRNA-mRNA Network in Atrial Fibrillation

2021 ◽  
Author(s):  
Rou-Mu Hu ◽  
Tao Song ◽  
Zheng Liu ◽  
Xiandong Yin ◽  
Xinchun Yang
Keyword(s):  
Atrial Fibrillation ◽  
Pearson Correlation ◽  
In Silico Analysis ◽  
Integrated Analysis ◽  
Rna Seq ◽  
Tissue Samples ◽  
Diagnostic Biomarkers ◽  
Precise Diagnosis ◽  
Mirna Sponges ◽  
Silico Analysis

Abstract Background: Atrial fibrillation (AF), the most common cardiac arrhythmias, is associated with the risk of stroke and pronounced morbidity and mortality. The application of biomarkers in the management of AF has been grown as an interesting topic. Long non-coding RNAs (lncRNAs) have been reported to participate in the pathogenesis of cardiovascular diseases by regulating mRNA networks. Results: In this study, we firstly used two AF cohorts to identify circulating lncRNAs and mRNAs with potential diagnostic prediction value. The expression of 8,164 lncRNAs and 14,508 mRNAs were quantified in these two cohorts with lncRNA microarray. By using a stringent threshold (P < 0.01, fold change > 2.0 or < 0.5), we identified 10 lncRNAs and 7 mRNAs were significantly differentially expressed in AF in both cohorts. To further explore the function of these significantly dysregulated lncRNA and mRNA, we performed co-expression analysis by using RNA-seq data of 429 atrial appendage tissue samples. Interestingly, we found a significant lncRNA-mRNA network for 5 lncRNAs (AC109460.1, AL031123.1, MIAT, PTPRG-AS1 and ZNF815P) and 4 mRNAs (D2HGDH, SPNS1, KCND2 and TNFAIP8L3) with Pearson correlation r > 0.3 (all P < 10-8). Moreover, in silico analysis showed that the lncRNA MIAT and PTPRG-AS1 may serve as miRNA sponges to regulate D2HGDH, SPNS1, KCND2 and TNFAIP8L3.Conclusions: Our study suggested that the circulating lncRNA-mRNA network of MIAT and PTPRG-AS1 play an important role in AF and may be considerable diagnostic biomarkers. These results may contribute to the precise diagnosis and early detection of this disease.

Sponge Behavior and the Chemical Basis of Responses: A Post-Genomic View

2019 ◽  
Vol 59 (4) ◽  
pp. 751-764 ◽  
Author(s):  
Sally P Leys ◽  
Jasmine L Mah ◽  
Paul R McGill ◽  
Laura Hamonic ◽  
Fabio C De Leo ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Atmospheric Pressure ◽  
Water Movement ◽  
Whole Body ◽  
Signal Pathways ◽  
Chemical Signaling ◽  
Electrical Signaling ◽  
Complex Signaling

Abstract Sponges perceive and respond to a range of stimuli. How they do this is still difficult to pin down despite now having transcriptomes and genomes of an array of species. Here we evaluate the current understanding of sponge behavior and present new observations on sponge activity in situ. We also explore biosynthesis pathways available to sponges from data in genomes/transcriptomes of sponges and other non-bilaterians with a focus on exploring the role of chemical signaling pathways mediating sponge behavior and how such chemical signal pathways may have evolved. Sponge larvae respond to light but opsins are not used, nor is there a common photoreceptor molecule or mechanism used across sponge groups. Other cues are gravity and chemicals. In situ recordings of behavior show that both shallow and deep-water sponges move a lot over minutes and hours, and correlation of behavior with temperature, pressure, oxygen, and water movement suggests that at least one sponge responds to changes in atmospheric pressure. The sensors for these cues as far as we know are individual cells and, except in the case of electrical signaling in Hexactinellida, these most likely act as independent effectors, generating a whole-body reaction by the global reach of the stimulus to all parts of the animal. We found no evidence for use of conventional neurotransmitters such as serotonin and dopamine. Intriguingly, some chemicals synthesized by symbiont microbes could mean other more complex signaling occurs, but how that interplay might happen is not understood. Our review suggests chemical signaling pathways found in sponges do not reflect loss of a more complex set.

Reconstruction and in silico analysis of the MAPK signaling pathways in the human blood fluke,Schistosoma japonicum

FEBS Letters ◽  
2006 ◽  
Vol 580 (15) ◽  
pp. 3677-3686 ◽  
Author(s):  
Lili Wang ◽  
Zhong Yang ◽  
Yuanyuan Li ◽  
Fudong Yu ◽  
Paul J. Brindley ◽  
...  
Keyword(s):  
Signaling Pathways ◽  
Schistosoma Japonicum ◽  
Human Blood ◽  
In Silico ◽  
In Silico Analysis ◽  
Mapk Signaling ◽  
Blood Fluke ◽  
Silico Analysis ◽  
Mapk Signaling Pathways

scholarly journals Identifying new COVID-19 receptor Neuropilin-1 in severe Alzheimer’s diseases patients group brain using genome-wide association study approach

2021 ◽  
Author(s):  
Key-Hwan Lim ◽  
Sumin Yang ◽  
Sung-Hyun Kim ◽  
Jae-Yeol Joo
Keyword(s):  
In Silico ◽  
Genome Wide Association Study ◽  
Transmembrane Protein ◽  
In Silico Analysis ◽  
Therapeutic Drug ◽  
Rna Seq ◽  
Total Rna ◽  
Neuropilin 1 ◽  
Silico Analysis ◽  
Brain Tissues

Abstract Background Numerous studies have been conducted on different aspects of the COVID-19 (coronavirus disease 2019) pandemic, which is caused by SARS-CoV-2, since its emergence in late 2019. Mutual relations among SARS-CoV-2 and neuro-pathophysiological phenomena are continuously being demonstrated, and several underlying diseases, such as those in the elderly, are positively correlated with susceptibility to SARS-CoV-2 infection. The expression of angiotensin converting enzyme 2 (ACE2), which is required for SARS-CoV-2 infection, was recently demonstrated to be increased in Alzheimer’s disease (AD) patients.Methods Recent preclinical studies have shown that Neuropilin-1 (NRP1), which is a transmembrane protein with roles in neuronal development, axonal outgrowth, and angiogenesis, also plays a role in the infectivity of SARS-CoV-2. Thus, we hypothesized that NRP1 may be upregulated in AD patients and that a correlation between AD and SARS-CoV-2 NRP1-mediated infectivity may exist. We used an AD mouse model that mimics AD and performed high throughput total RNA-seq with brain tissue and whole blood. For quantification of NPR1 in AD, brain tissues and blood were subjected to western blotting and RT-qPCR analysis. In silico analysis for NRP1 expression in AD patients has been performed on the human hippocampus data sets (GSE4226, GSE1297).Results Many cases of severe symptom of COVID-19 are concentrated in elderly group who have complications such as diabetes, degenerative disease, and brain disorders. Total RNA-seq analysis showed that Nrp1 gene was commonly overexpressed in AD model. Similar to ACE2, NRP1 protein also strongly expressed in the AD brain tissues. Interestingly, in silico analysis revealed that the level of expression for NRP1 was distinct at age and AD progression.Conclusions Given that the NRP1 is highly expressed in AD, it will be important to understand and predict that NRP1 may a risk factor for SARS-CoV-2 infection in AD patients. This will support to development of potential therapeutic drug to reduce SARS-CoV-2 transmission.

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