scholarly journals Combined transcriptome and proteome profiling reveals specific molecular brain signatures for sex, maturation and circalunar clock phase

eLife ◽  
2019 ◽  
Vol 8 ◽  
Author(s):  
Sven Schenk ◽  
Stephanie C Bannister ◽  
Fritz J Sedlazeck ◽  
Dorothea Anrather ◽  
Bui Quang Minh ◽  
...  
Keyword(s):  
Sexual Differentiation ◽  
Circadian Clocks ◽  
Proteomic Profiling ◽  
Marine Animals ◽  
Lunar Cycles ◽  
Platynereis Dumerilii ◽  
Related Proteins ◽  
Molecular Brain ◽  
Sex Maturation ◽  
Insight Into

Many marine animals, ranging from corals to fishes, synchronise reproduction to lunar cycles. In the annelid Platynereis dumerilii, this timing is orchestrated by an endogenous monthly (circalunar) clock entrained by moonlight. Whereas daily (circadian) clocks cause extensive transcriptomic and proteomic changes, the quality and quantity of regulations by circalunar clocks have remained largely elusive. By establishing a combined transcriptomic and proteomic profiling approach, we provide first systematic insight into the molecular changes in Platynereis heads between circalunar phases, and across sexual differentiation and maturation. Whereas maturation elicits large transcriptomic and proteomic changes, the circalunar clock exhibits only minor transcriptomic, but strong proteomic regulation. Our study provides a versatile extraction technique and comprehensive resources. It corroborates that circadian and circalunar clock effects are likely distinct and identifies key molecular brain signatures for reproduction, sex and circalunar clock phase. Examples include prepro-whitnin/proctolin and ependymin-related proteins as circalunar clock targets.

scholarly journals Single Extracellular Vesicles (EV) Proteomic Profiling Altered and Identifies Co-Localization of SARS-CoV-2 Nucleocapsid Protein with CD81/Integrin-Rich EV Subpopulation in Sputum Samples of COVID-19 Patients

2021 ◽  
Author(s):  
Ruiting Sun ◽  
Yanling Cai ◽  
Yumin Zhou ◽  
Ge Bai ◽  
Airu Zhu ◽  
...  
Keyword(s):  
Nucleocapsid Protein ◽  
Proteomic Profiling ◽  
N Protein ◽  
Transmission Electron ◽  
Highly Correlated ◽  
Related Proteins ◽  
First Time ◽  
The Relationship ◽  
Differential Contribution ◽  
Insight Into

Abstract Understanding the pathogenesis of SARS-CoV-2 is crucial to respond to the current coronavirus disease 2019 (COVID-19) pandemic. Sputum samples from 20 COVID-19 patients and healthy controls were collected, respectively. During the isolation of infectious SARS-CoV-2 virus, EV-like vesicles were associated with virions under a transmission electron microscope. Next, the expression of IL6 and TGF-β increased in EVs derived from the sputum of patients, and these were highly correlated with the expression of the SARS-CoV-2 N protein. Further, proximity barcoding assay (PBA) was used to investigate the immune-related proteins in the EVs, and the relationship between EVs and SARS-CoV-2 N protein in COVID-19 patients’ samples. Particularly, to investigate the differential contribution of the specific EV subsets, the protein expression of a single EV was detected and analyzed for the first time. Among the 40 EV subpopulations, 18 were found to have significant differences. The EV subpopulation regulated by CD81 were most likely to correlate with the changes in the pulmonary microenvironment after SARS-CoV-2 infection. This study provides evidence on the association between EVs and the SARS-CoV-2 virus, give a deep insight into the possible pathogenesis of SARS-CoV-2 infection and the possibility of nanoparticles drug intervention in viral infection.

scholarly journals Converging physiological roles of the anthrax toxin receptors

F1000Research ◽  
2019 ◽  
Vol 8 ◽  
pp. 1415
Author(s):  
Oksana A. Sergeeva ◽  
F. Gisou van der Goot
Keyword(s):  
Anthrax Toxin ◽  
Loss Of Function ◽  
Disease Symptoms ◽  
Hyaline Fibromatosis Syndrome ◽  
Anthrax Toxins ◽  
The Difference ◽  
Related Proteins ◽  
Tumor Endothelial Marker 8 ◽  
Insight Into ◽  
Shed Light

The anthrax toxin receptors—capillary morphogenesis gene 2 (CMG2) and tumor endothelial marker 8 (TEM8)—were identified almost 20 years ago, although few studies have moved beyond their roles as receptors for the anthrax toxins to address their physiological functions. In the last few years, insight into their endogenous roles has come from two rare diseases: hyaline fibromatosis syndrome, caused by mutations in CMG2, and growth retardation, alopecia, pseudo-anodontia, and optic atrophy (GAPO) syndrome, caused by loss-of-function mutations in TEM8. Although CMG2 and TEM8 are highly homologous at the protein level, the difference in disease symptoms points to variations in the physiological roles of the two anthrax receptors. Here, we focus on the similarities between these receptors in their ability to regulate extracellular matrix homeostasis, angiogenesis, cell migration, and skin elasticity. In this way, we shed light on how mutations in these two related proteins cause such seemingly different diseases and we highlight the existing knowledge gaps that could form the focus of future studies.

Protocadherins and diversity of the cadherin superfamily

1996 ◽  
Vol 109 (11) ◽  
pp. 2609-2611 ◽  
Author(s):  
S.T. Suzuki
Keyword(s):  
Cell Adhesion ◽  
Circumstantial Evidence ◽  
Biological Role ◽  
Classical Cadherins ◽  
Adhesion Role ◽  
Multicellular Organisms ◽  
Related Proteins ◽  
Insight Into ◽  
Cadherin Superfamily

Recent cadherin studies have revealed that many cadherins and cadherin-related proteins are expressed in various tissues of different multicellular organisms. These proteins are characterized by the multiple repeats of the cadherin motif in their extracellular domains. The members of the cadherin superfamily are divided into two groups: classical cadherin type and protocadherin type. The current cadherins appear to have evolved from a protocadherin type. Recent studies have proved the cell adhesion role of classical cadherins in embryogenesis. In contrast, the biological role of protocadherins is elusive. Circumstantial evidence, however, suggests that protocadherins are involved in a variety of cell-cell interactions. Since protocadherins, and many other new cadherins as well, have unique properties, studies of these cadherins may provide insight into the structure and biological role of the cadherin superfamily.

DAX1 and SF1 Mutations Provide Insight into Sexual Differentiation

2002 ◽  
pp. 151-171
Author(s):  
G. Ozisik ◽  
J. C. Achermann ◽  
J. J. Meeks ◽  
J. L. Jameson
Keyword(s):  
Sexual Differentiation ◽  
Insight Into

scholarly journals Proteomic Profiling Reveals the Ambivalent Character of the Mesenchymal Stem Cell Secretome: Assessing the Effect of Preconditioned Media on Isolated Human Islets

2020 ◽  
Vol 29 ◽  
pp. 096368972095233
Author(s):  
Heide Brandhorst ◽  
Daniel Brandhorst ◽  
Anju Abraham ◽  
Samuel Acreman ◽  
Simen W. Schive ◽  
...  
Keyword(s):  
Culture Media ◽  
Human Islets ◽  
Human Islet ◽  
Physical Contact ◽  
Proteomic Profiling ◽  
Protective Capacity ◽  
Islet Culture ◽  
Proinflammatory Mediators ◽  
Related Proteins

Previous studies in rodents have indicated that function and survival of transplanted islets can be substantially improved by mesenchymal stem cells (MSC). The few human islet studies to date have confirmed these findings but have not determined whether physical contact between MSC and islets is required or whether the benefit to islets results from MSC-secreted proteins. This study aimed to investigate the protective capacity of MSC-preconditioned media for human islets. MSC were cultured for 2 or 5 days in normoxia or hypoxia before harvesting the cell-depleted media for human islet culture in normoxia or hypoxia for 6–8 or 3–4 days, respectively. To characterize MSC-preconditioned media, proteomic secretome profiling was performed to identify angiogenesis- and inflammation-related proteins. A protective effect of MSC-preconditioned media on survival and in vitro function of hypoxic human islets was observed irrespective of the atmosphere used for MSC preconditioning. Islet morphology changed markedly when media from hypoxic MSC were used for culture. However, PDX-1 and insulin gene expression did not confirm a change in the genetic phenotype of these islets. Proteomic profiling of preconditioned media revealed the heterogenicity of the secretome comprising angiogenic and antiapoptotic as well as angiostatic or proinflammatory mediators released at an identical pattern regardless whether MSC had been cultured in normoxic or hypoxic atmosphere. These findings do not allow a clear discrimination between normoxia and hypoxia as stimulus for protective MSC capabilities but indicate an ambivalent character of the MSC angiogenesis- and inflammation-related secretome. Nevertheless, culture of human islets in acellular MSC-preconditioned media resulted in improved morphological and functional islet integrity suggesting a disbalance in favor of protective factors. Further approaches should aim to eliminate potentially detrimental factors to enable the production of advanced clinical grade islet culture media with higher protective qualities.

scholarly journals In Silico Investigation of the Anti-Tumor Mechanisms of Epigallocatechin-3-Gallate

Molecules ◽  
2019 ◽  
Vol 24 (7) ◽  
pp. 1445 ◽  
Author(s):  
Wang Wang ◽  
Xiuhong Xiong ◽  
Xue Li ◽  
Qinyang Zhang ◽  
Wentao Yang ◽  
...  
Keyword(s):  
Green Tea ◽  
Molecular Mechanisms ◽  
Protein Database ◽  
Tumor Target ◽  
Target Proteins ◽  
Pharmacological Mechanism ◽  
Putative Target ◽  
Docking Method ◽  
Related Proteins ◽  
Insight Into

The EGCG, an important component of polyphenol in green tea, is well known due to its numerous health benefits. We employed the reverse docking method for the identification of the putative targets of EGCG in the anti-tumor target protein database and these targets were further uploaded to public databases in order to understand the underlying pharmacological mechanisms and search for novel EGCG-associated targets. Similarly, the pharmacological linkage between tumor-related proteins and EGCG was manually constructed in order to provide greater insight into the molecular mechanisms through a systematic integration with applicable bioinformatics. The results indicated that the anti-tumor mechanisms of EGCG may involve 12 signaling transduction pathways and 33 vital target proteins. Moreover, we also discovered four novel putative target proteins of EGCG, including IKBKB, KRAS, WEE1 and NTRK1, which are significantly related to tumorigenesis. In conclusion, this work may provide a useful perspective that will improve our understanding of the pharmacological mechanism of EGCG and identify novel potential therapeutic targets.

scholarly journals Using a Simple Cellular Assay to Map NES Motifs in Cancer-Related Proteins, Gain Insight into CRM1-Mediated NES Export, and Search for NES-Harboring Micropeptides

2020 ◽  
Vol 21 (17) ◽  
pp. 6341
Author(s):  
Maria Sendino ◽  
Miren Josu Omaetxebarria ◽  
Gorka Prieto ◽  
Jose Antonio Rodriguez
Keyword(s):  
Nuclear Export ◽  
Relevant Information ◽  
Sequence Motifs ◽  
Specific Sequence ◽  
Cellular Assay ◽  
Small Proteins ◽  
Binding Groove ◽  
Related Proteins ◽  
Insight Into

The nuclear export receptor CRM1 (XPO1) recognizes and binds specific sequence motifs termed nuclear export signals (NESs) in cargo proteins. About 200 NES motifs have been identified, but over a thousand human proteins are potential CRM1 cargos, and most of their NESs remain to be identified. On the other hand, the interaction of NES peptides with the “NES-binding groove” of CRM1 was studied in detail using structural and biochemical analyses, but a better understanding of CRM1 function requires further investigation of how the results from these in vitro studies translate into actual NES export in a cellular context. Here we show that a simple cellular assay, based on a recently described reporter (SRVB/A), can be applied to identify novel potential NESs motifs, and to obtain relevant information on different aspects of CRM1-mediated NES export. Using cellular assays, we first map 19 new sequence motifs with nuclear export activity in 14 cancer-related proteins that are potential CRM1 cargos. Next, we investigate the effect of mutations in individual NES-binding groove residues, providing further insight into CRM1-mediated NES export. Finally, we extend the search for CRM1-dependent NESs to a recently uncovered, but potentially vast, set of small proteins called micropeptides. By doing so, we report the first NES-harboring human micropeptides.

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