scholarly journals The MG-RAST API explorer: an on-ramp for RESTful query composition

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Tobias Paczian ◽  
William L. Trimble ◽  
Wolfgang Gerlach ◽  
Travis Harrison ◽  
Andreas Wilke ◽  
...  

Abstract Background The MG-RAST API provides search capabilities and delivers organism and function data as well as raw or annotated sequence data via the web interface and its RESTful API. For casual users, however, RESTful APIs are hard to learn and work with. Results We created the graphical MG-RAST API explorer to help researchers more easily build and export API queries; understand the data abstractions and indices available in MG-RAST; and use the results presented in-browser for exploration, development, and debugging. Conclusions The API explorer lowers the barrier to entry for occasional or first-time MG-RAST API users.

2019 ◽  
Vol 16 (3) ◽  
Author(s):  
Yaoyong Li ◽  
Elisa Aguilar-Martinez ◽  
Andrew D. Sharrocks

AbstractThe interconversion of sequences that constitute the genome and the proteome is becoming increasingly important due to the generation of large amounts of DNA sequence data. Following mapping of DNA segments to the genome, one fundamentally important task is to find the amino acid sequences which are coded within a list of genomic sections. Conversely, given a series of protein segments, an important task is to find the genomic loci which code for a list of protein regions. To perform these tasks on a region by region basis is extremely laborious when a large number of regions are being studied. We have therefore implemented an R package geno2proteo which performs the two mapping tasks and subsequent sequence retrieval in a batch fashion. In order to make the tool more accessible to users, we have created a web interface of the R package which allows the users to perform the mapping tasks by going to the web page http://sharrocksresources.manchester.ac.uk/tofigaps and using the web service.


1982 ◽  
Vol 60 (4) ◽  
pp. 475-479 ◽  
Author(s):  
R. J. Cedergren

Extensive sequence data on mitochondrial (mt) tRNAs give for the first time an opportunity to evaluate tRNA gene evolution in this organelle. Deductions from these gene structures relate to the evolution of tRNA genes in other cellular systems and to the origin of the genetic code. Mt tRNAs, in contrast to the prokaryotic nature of chloroplastic tRNA structure, can not at the present time be definitely related to either prokaryotic or eukaryotic tRNAs, probably because of a higher mutation rate in mitochondria.Fungal mt tRNAs having the same anticodon and function are generally similar enough to be considered homologous. Comparisons of all mt tRNA sequences contained in the same mitochondrion indicate that some tRNAs originated by duplication of a prototypic gene which, after divergence, led to tRNAs having different amino acid specificities. The deviant mt genetic code, although admittedly permitting a simpler decoding mechanism, is not useful in determining whether the origin of mitochondria had preceded or was derived from prokaryotes or eukaryotes, since the genetic code is variable even among mitochondria. Variants of the mt genetic code lead to speculation on the nature of die primordial code and its relation to the present "universal" code.


2019 ◽  
Vol 20 (11) ◽  
pp. 1046-1051 ◽  
Author(s):  
Przemysław Gajda-Morszewski ◽  
Klaudyna Śpiewak-Wojtyła ◽  
Maria Oszajca ◽  
Małgorzata Brindell

Lactoferrin was isolated and purified for the first time over 50-years ago. Since then, extensive studies on the structure and function of this protein have been performed and the research is still being continued. In this mini-review we focus on presenting recent scientific efforts towards the elucidation of the role and therapeutic potential of lactoferrin saturated with iron(III) or manganese(III) ions. The difference in biological activity of metal-saturated lactoferrin vs. the unmetalated one is emphasized. The strategies for oral delivery of lactoferrin, are also reviewed, with particular attention to the metalated protein.


2021 ◽  
Vol 13 (3) ◽  
pp. 80
Author(s):  
Lazaros Vrysis ◽  
Nikolaos Vryzas ◽  
Rigas Kotsakis ◽  
Theodora Saridou ◽  
Maria Matsiola ◽  
...  

Social media services make it possible for an increasing number of people to express their opinion publicly. In this context, large amounts of hateful comments are published daily. The PHARM project aims at monitoring and modeling hate speech against refugees and migrants in Greece, Italy, and Spain. In this direction, a web interface for the creation and the query of a multi-source database containing hate speech-related content is implemented and evaluated. The selected sources include Twitter, YouTube, and Facebook comments and posts, as well as comments and articles from a selected list of websites. The interface allows users to search in the existing database, scrape social media using keywords, annotate records through a dedicated platform and contribute new content to the database. Furthermore, the functionality for hate speech detection and sentiment analysis of texts is provided, making use of novel methods and machine learning models. The interface can be accessed online with a graphical user interface compatible with modern internet browsers. For the evaluation of the interface, a multifactor questionnaire was formulated, targeting to record the users’ opinions about the web interface and the corresponding functionality.


2008 ◽  
Vol 74 (24) ◽  
pp. 7821-7823 ◽  
Author(s):  
Kai Linke ◽  
Nagarajan Periasamy ◽  
Matthias Ehrmann ◽  
Roland Winter ◽  
Rudi F. Vogel

ABSTRACT High hydrostatic pressure (HHP) is suggested to influence the structure and function of membranes and/or integrated proteins. We demonstrate for the first time HHP-induced dimer dissociation of membrane proteins in vivo with Vibrio cholerae ToxR variants in Escherichia coli reporter strains carrying ctx::lacZ fusions. Dimerization ceased at 20 to 50 MPa depending on the nature of the transmembrane segments rather than on changes in the ToxR lipid bilayer environment.


2021 ◽  
Vol 16 ◽  
Author(s):  
Jinghao Peng ◽  
Jiajie Peng ◽  
Haiyin Piao ◽  
Zhang Luo ◽  
Kelin Xia ◽  
...  

Background: The open and accessible regions of the chromosome are more likely to be bound by transcription factors which are important for nuclear processes and biological functions. Studying the change of chromosome flexibility can help to discover and analyze disease markers and improve the efficiency of clinical diagnosis. Current methods for predicting chromosome flexibility based on Hi-C data include the flexibility-rigidity index (FRI) and the Gaussian network model (GNM), which have been proposed to characterize chromosome flexibility. However, these methods require the chromosome structure data based on 3D biological experiments, which is time-consuming and expensive. Objective: Generally, the folding and curling of the double helix sequence of DNA have a great impact on chromosome flexibility and function. Motivated by the success of genomic sequence analysis in biomolecular function analysis, we hope to propose a method to predict chromosome flexibility only based on genomic sequence data. Method: We propose a new method (named "DeepCFP") using deep learning models to predict chromosome flexibility based on only genomic sequence features. The model has been tested in the GM12878 cell line. Results: The maximum accuracy of our model has reached 91%. The performance of DeepCFP is close to FRI and GNM. Conclusion: The DeepCFP can achieve high performance only based on genomic sequence.


2019 ◽  
Author(s):  
Tilman Venzl

In the 18th century, as many as 300 German-language plays were produced with the military and its contact and friction with civil society serving as focus of the dramatic events. The immense public interest these plays attracted feeds not least on the fundamental social structural change that was brought about by the establishment of standing armies. In his historico-cultural literary study, Tilman Venzl shows how these military dramas literarily depict complex social processes and discuss the new problems in an affirmative or critical manner. For the first time, the findings of the New Military History are comprehensively included in the literary history of the 18th century. Thus, the example of selected military dramas – including Lessing's Minna von Barnhelm and Lenz's Die Soldaten – reveals the entire range of variety characterizing the history of both form and function of the subject.


2021 ◽  
Author(s):  
Bo Galle ◽  

<p>We present a detailed global data-set of volcanic sulphur dioxide (SO2) emissions during the period 2005-2017. Measurements were obtained by scanning-DOAS instruments of the NOVAC network at 32 volcanoes, and processed using a standardized procedure. We reveal the daily statistics of volcanic gas emissions under a variety of volcanological and meteorological conditions. Data from several volcanoes are presented for the first time. Our results  are compared with yearly averages derived from measurements from space by the Aura/OMI instrument and with historical inventories of GEIA. This comparison shows some interesting differences which reasons are briefly discussed. Data is openly available through the web repository at https://novac.chalmers.se/.</p>


Hypertension ◽  
2014 ◽  
Vol 64 (suppl_1) ◽  
Author(s):  
Hongmei Peng ◽  
Oscar Carretero ◽  
Xiao-Ping Yang ◽  
Pablo Nakagawa ◽  
Jiang Xu ◽  
...  

Elevated interleukin-4 (IL-4) levels are positively related to cardiac fibrosis in heart failure and hypertension. Using Balb/c exhibiting high circulating IL-4, Balb/c- Il4 tm2Nnt (IL-4 knockout with Balb/c background, IL-4 -/- ) and C57BL/6 mice, as well as cultured cardiac fibroblasts (CFs), we hypothesized that 1) high levels of IL-4 result in cardiac fibrosis, making the heart susceptible to angiotensin II (Ang II)-induced damage, and 2) IL-4 potently stimulates collagen production by CFs. Each strain (9- to 12-week old male) received vehicle or Ang II (1.4 mg/kg/day, s.c. via osmotic mini-pump) for 8 weeks. Cardiac fibrosis and function were determined by histology and echocardiography, respectively. Compared to C57BL/6, Balb/c mice had doubled interstitial collagen in the heart, enlarged left ventricle and decreased cardiac function along with elevated cardiac IL-4 protein (1.00±0.08 in C57BL/6 vs 2.61±0.46 in Balb/c, p <0.05); all those changes were significantly attenuated in IL-4 -/- (Table 1). Ang II further deteriorated cardiac fibrosis and dysfunction in Balb/c; these detrimental effects were attenuated in IL-4 -/- , although the three strains had a similar level of hypertension. In vitro study revealed that IL-4Rα was constitutively expressed in CFs (Western blot), and IL-4 potently stimulated collagen production by CFs (hydroxproline assay, from 18.89±0.85 to 38.81±3.61 μg/mg at 10 ng/ml, p <0.01). Our study demonstrates for the first time that IL-4, as a potent pro-fibrotic cytokine in the heart, contributes to cardiac fibrotic remodeling and dysfunction. Thus IL-4 may be a potential therapeutic target for cardiac fibrosis and dysfunction.


2007 ◽  
Vol 44 (2) ◽  
pp. 43-46 ◽  
Author(s):  
D. Kuznetsov ◽  
N. Kuznetsova

AbstractFor the first time, DNA sequence data were obtained for three species of Trichostrongylus from Russia. Internal transcribed spacer (ITS-2) of ribosomal DNA was sequenced for T. axei, T. colubriformis and T. probolurus from sheep from the Moscow region. ITS-2 rDNA length was estimated as 238 nucleotides for T. colubriformis and T. probolurus and 237 nucleotides for T. axei. The G+C content of the ITS-2 sequences of T. colubriformis, T. axei and T. probolurus were 31 %, 32 % and 34 % respectively. The level of interspecific differences in ITS-2 of rDNA of T. axei, T. probolurus and T. colubriformis ranged from 3 to 4 %. The ITS-2 sequences from the Russian specimens were compared with those of T. axei, T. probolurus and T. colubriformis from Australia and Germany. Intraspecific variation ranged from 0 % in T. colubriformis to 3.0 % in T. axei.


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