scholarly journals An ”omic“ approach to Pyrocystis lunula: New insights related with this bioluminescent dinoflagellate

2019 ◽  
Author(s):  
Carlos Fajardo ◽  
Francisco Amil-Ruiz ◽  
Carlos Fuentes Almagro ◽  
Marcos De Donato ◽  
Almudena Escobar Niño ◽  
...  

Abstract Background: Pyrocystis lunula (Schutt) is a photoautotrophic dinoflagellate without armored, frequently found in marine environments. Today, there are several biotechnological applications derived from the bioluminescent system of this species. From a post-genomic perspective, in order to study the whole proteome of P. lunula, an ”omic“ approach (transcriptomic-proteomic analysis) was assessed using fresh microalgae samples. Results: A total of 80,874,825 raw reads were generated (11,292,087,505 pb; 55.82 % GC) by mRNA sequencing. Very high quality sequences were assembled into 414,295 contigs (219,203,407 pb; 55.38 % GC) by the Trinity software, generating a comprehensive reference transcriptome for this species. Then, a P. lunula proteome was predicted and further employed through the first proteomic analysis on this species. A total of 17,461 peptides were identified, yielding 3,182 protein identification hits. The identified proteins were further categorized according to functional description and gene ontology classification. Conclusions: The first comprehensive molecular analysis of the microalgae P. lunula using both, transcriptomic and proteomic approaches, has been reported. Proteomic results represent a valuable piece in the understanding of this microalgae regulation at molecular level, and shed light on the identification of important factors involved in gene expression regulation. Indeed, the presence of the luciferin-binding protein (LBP), which had not been described so far in the genus Pyrocystis has been highlighted.

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Francis Sahngun Nahm ◽  
Zee-Yong Park ◽  
Sang-Soep Nahm ◽  
Yong Chul Kim ◽  
Pyung Bok Lee

Background. Complex regional pain syndrome (CRPS) is a rare but debilitating pain disorder. Although the exact pathophysiology of CRPS is not fully understood, central and peripheral mechanisms might be involved in the development of this disorder. To reveal the central mechanism of CRPS, we conducted a proteomic analysis of rat cerebrum using the chronic postischemia pain (CPIP) model, a novel experimental model of CRPS.Materials and Methods. After generating the CPIP animal model, we performed a proteomic analysis of the rat cerebrum using a multidimensional protein identification technology, and screened the proteins differentially expressed between the CPIP and control groups.Results. A total of 155 proteins were differentially expressed between the CPIP and control groups: 125 increased and 30 decreased; expressions of proteins related to cell signaling, synaptic plasticity, regulation of cell proliferation, and cytoskeletal formation were increased in the CPIP group. However, proenkephalin A, cereblon, and neuroserpin were decreased in CPIP group.Conclusion. Altered expression of cerebral proteins in the CPIP model indicates cerebral involvement in the pathogenesis of CRPS. Further study is required to elucidate the roles of these proteins in the development and maintenance of CRPS.


2018 ◽  
Author(s):  
Dalit Engelhardt ◽  
Eugene I. Shakhnovich

Mutation rate is a key determinant of the pace as well as outcome of evolution, and variability in this rate has been shown in different scenarios to play a key role in evolutionary adaptation and resistance evolution under stress. Here we investigate the dynamics of resistance fixation in a bacterial population with variable mutation rates and show that evolutionary outcomes are most sensitive to mutation rate variations when the population is subject to environmental and demographic conditions that suppress the evolutionary advantage of high-fitness subpopulations. By directly mapping a molecular-level biophysical fitness function to the system-level dynamics of the population we show that both low and very high, but not intermediate, levels of stress result in a disproportionate effect of hypermutation on resistance fixation and that traditional definitions of the selection coefficient are insufficient to account for this effect. We demonstrate how this behavior is directly tied to the extent of genetic hitchhiking in the system, the propagation of high-mutation rate cells through association with high-fitness mutations. Our results indicate a substantial role for mutation rate flexibility in the evolution of antibiotic resistance under conditions that present a weak advantage over wildtype to resistant cells.


2016 ◽  
Vol 113 (11) ◽  
pp. 2827-2832 ◽  
Author(s):  
Pierre Ronceray ◽  
Chase P. Broedersz ◽  
Martin Lenz

Large-scale force generation is essential for biological functions such as cell motility, embryonic development, and muscle contraction. In these processes, forces generated at the molecular level by motor proteins are transmitted by disordered fiber networks, resulting in large-scale active stresses. Although these fiber networks are well characterized macroscopically, this stress generation by microscopic active units is not well understood. Here we theoretically study force transmission in these networks. We find that collective fiber buckling in the vicinity of a local active unit results in a rectification of stress towards strongly amplified isotropic contraction. This stress amplification is reinforced by the networks’ disordered nature, but saturates for high densities of active units. Our predictions are quantitatively consistent with experiments on reconstituted tissues and actomyosin networks and shed light on the role of the network microstructure in shaping active stresses in cells and tissue.


2006 ◽  
Vol 24 (18_suppl) ◽  
pp. 10524-10524
Author(s):  
G. Hudelist ◽  
C. Singer ◽  
K. Pischinger ◽  
K. Kaserer ◽  
M. Manavi ◽  
...  

10524 Background: Gene expression analysis has become a promising tool in predicting the clinical course of malignant disease and the response to antineoplastic therapy. Suprisingly, only little is known about the protein expression pattern of human tumors. Recent advances in proteomic analysis allow to identify proteins of interest by their expression and/or modification pattern in 2D-PAGE rather than using the traditional approach of translating gene expression data. Methods: In order to identify a proteomic pattern that is characteristic for malignant breast epithelium, we performed differential 2D-PAGE analysis in sets of microdissected malignant breast epithelia and corresponding adjacent normal breast epithelia from 5 patients with invasive breast carcinoma. Results: Thirty-two protein spots were found to be selectively regulated in malignant epithelium, and were subjected to MALDI-TOF and/or immunoblotting for protein identification. Thirteen of the identified proteins had previously not been associated with breast cancer. The validity of these findings was confirmed by literature review and immunohistochemistry for identified proteins in an independent cohort of 50 breast cancer specimens. Conclusions: We here describe a proteomic analysis of matched normal and malignant epithelia from invasive breast carcinomas. This strategy leads to a better understanding of oncogenesis at an operational level and helps to characterize the malignant phenotype of individual tumors and thereby to identify novel targets for antineoplastic therapy. No significant financial relationships to disclose.


1990 ◽  
Vol 180 ◽  
Author(s):  
P. C. Cagle ◽  
W. G. Klemperer ◽  
C. A. Simmons

ABSTRACTSol-gel polymerization of [Si8O12](OCH3)8 in CH3CN under neutral conditions yields very high surface area (SBET > 900 m2/g) xerogels. This property is seen to result from the structure of the gel on the molecular level. According to N2 adsorption studies, model studies, and TEM studies, the large size and rigidity of the cubic [Si8O12] core structure leads to polymers whose rigidity inhibits extensive crosslinking of the type observed in orthosilicate derived xerogels.


2018 ◽  
Vol 40 (1) ◽  
pp. 8-11
Author(s):  
Himadri S. Gupta ◽  
Greg Szulgit ◽  
Maurice R. Elphick ◽  
Jingyi Mo

The mutable collagenous tissue (MCT) of echinoderms (e.g. sea cucumbers, starfish and sea urchins) is unique because of its ability to ‘switch’ mechanical states rapidly and reversibly – from stiff to soft and vice versa. This kind of tissue in humans, for example, in skin, tendons and ligaments, does not have this property. So what are the molecular-level secrets by which MCT achieves this transformative ability? New real-time ultrastructural investigations are beginning to shed light on this question. Synchrotron X-ray measurements of dynamic molecular conformational changes point to the key factor being the gel-like matrix between the collagen fibrils. These findings could have applications for developing treatments for collagen-based disorders.


2006 ◽  
Vol 3 (2) ◽  
pp. 125-135
Author(s):  
Jayne Howell

That 40,000 women work as household workers in Oaxaca City (population 450,000) is deemed “very high for a country as developed as Mexico” (Selby, Murphy and Lorenzon 1991:48; INEGI 2001).  Ethnographic data collected among women currently and at one time working as either full-time or daily/hourly domestic workers shed light on the realities faced by unskilled women cityward migrants who find employment in the lowest paid, least prestigious jobs in the urban economy.  Two case studies are presented to illustrate ways that women's paid household labor can finance their own or their children's acquisition of the schooling requisite for more gainful, higher paid forms of urban formal sector employment. 


Blood ◽  
2013 ◽  
Vol 122 (21) ◽  
pp. 1871-1871 ◽  
Author(s):  
Anita D'Souza ◽  
Jason D Theis ◽  
Julie A Vrana ◽  
Ahmet Dogan

Abstract The amyloidoses are heterogeneous diseases associated with the deposition of insoluble proteins or peptides with a characteristic beta-diffraction pattern extracellularly. At the current time, over 27 different extracellular fibril proteins are known to cause disease in humans. Iatrogenic amyloidosis is a rare, often not sought diagnosis. On occasion, patients with drug induced amyloidosis can present with other systemic features reminiscent of systemic immunoglobulin-derived (AL) amyloidosis, and may present a diagnostic challenge. Treatment of the latter often involves chemotherapy and/or stem cell transplantation, while the former tends to remain localized and needs local therapy; thus accurate diagnosis is critical. To this end, proteomic analysis of amyloid tissue has proven to be an invaluable tool in amyloid typing. We have analyzed the biochemical composition of iatrogenic amyloid using laser capture/tandem mass spectrometry (LC-MS/MS)-based proteomic analysis in 52 cases of insulin and enfuvirtide (Fuzeon¨) associated amyloidosis. In brief, 10-μm-thick sections of formalin-fixed paraffin-embedded tissues were stained with Congo red. Congo red positively staining tissue as viewed with a fluorescent light source appeared bright red. Positive areas were dissected using laser microdissection to a volume of at least 60,000 μm2; three microdissections were analyzed for each case. The microdissected material was collected into 0.5-ml microcentrifuge tube caps containing 35 μL Tris/EDTA/0.002% Zwittergent buffer. Microdissected fragments were subjected to a heat-mediated antigen retrieval method (98C for 90minutes) before being denatured via sonication and subsequently digested into tryptic peptides overnight using 0.5ug of trypsin. The resulting digests were then analyzed with nanoflow LC-MS/MS. The MS/MS spectra of each case were matched against a composite protein sequence database using three different search algorithms (Sequest, X!Tandem, and Mascot). The composite database contained the human SwissProt entries but was also augmented with known immunoglobulin variant domains, known amyloidogenic mutations from literature, the enfuvirtide amino acid sequence, and common contaminants. Reversed protein sequences were appended to the database for estimating the false discovery rates of the identifications. The peptide identification results were filtered using Scaffold software (Proteome Software, Portland, OR) and then filtered peptides were assembled into protein identifications. Candidate proteins with at least one high-confident (probability of identification >90%) unique peptide identification and at least four MS/MS spectral matches were considered for clinical interpretation. For each case, we created a personalized proteomic profile that lists all the confident protein identifications in each of the microdissection along with their respective MS/MS spectral counts. The number of MS/MS spectra matching to a protein is considered as a semi-quantitative measure of its abundance. The most abundant amyloidogenic protein detected across all microdissections and as interpreted in the context of the clinical history is considered to be the amyloid subtype. Figure 1 shows the results of insulin amyloidosis. Figure 2 shows the results of enfuvirtide amyloidosis. Amyloid deposits are shown to be composed of the recombinant drug in addition to amyloid precursor proteins such as apolipoprotein A-I, A-IV, E and serum amyloid P (SAP).Figure 1. Insulin-associated amyloidosisFigure 1. Insulin-associated amyloidosisFigure 2Enfuvirtide (Fuzeon¨)-associated amyloidosisFigure 2. Enfuvirtide (Fuzeon¨)-associated amyloidosis In conclusion, we show the biochemical composition of all known drug-induced iatrogenic amyloidosis and provide the utility of proteomic analysis in elucidating amyloid subtyping for accurate diagnosis and management. Legend: A spectral count number of greater than 4 is significant. The green boxes denote protein identification at a probability of over 95%, and yellow 80-94%. In figure 1, insulin (# 2) and in figure 2, enfuvirtide (#5) are shown in abundance, additionally other amyloid precursors such as apolipoproteins A-IV, E, A-I and SAP are also seen. Disclosures: No relevant conflicts of interest to declare.


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