scholarly journals Are there systematic biases in RNA-seq data analysis? A case study for Amphimedon queenslandica sponge as a model object

2020 ◽  
Author(s):  
Sergey Feranchuk
Keyword(s):  
Functional Annotation ◽  
Rna Seq ◽  
Expression Levels ◽  
Model Object ◽  
Wide Range ◽  
Amphimedon Queenslandica ◽  
Systematic Biases ◽  
Series Of Experiments ◽  
Notch Pathways

AbstractBACKGROUNDThe performance of a functional annotation approach for RNA-seq bioinformatics pipelines was to be compared with the method where groups of genes are generated with no relation to ontologes. Three publicly available RNA-Seq experiments for Amphimedon queenslandica sponge were used for the designed comparison. One of these experiments was referred in the publication where stages of embryo development were compared for a wide range of animal species.METHODSThe expression levels were re-calculated here for three independent series of experiments. The functional annotation of differential expression levels was than conducted. This allow to compare an applicability of the two approaches, and to re-evaluate the interpretation provided in the mentioned publication.RESULTSIt was confirmed by the conventional approach that Wnt and Notch pathways do operate in a development of a sponge embryo. The method of annotation which uses unbounded grouping of genes was effective in an ability to separate development stages of sponge embryo. In addition, the published results were by a suggestion distorted by an artifact, caused by a positive feedback in the stage of data processing.

scholarly journals RDBMS and NOSQL Based Hybrid Technology for Transcriptome Data Structuring and Processing

2020 ◽  
Vol 15 (2) ◽  
pp. 455-470
Author(s):  
A.M. Mukhin ◽  
M.A. Genaev ◽  
D.A. Rasskazov ◽  
S.A. Lashin ◽  
D.A. Afonnikov
Keyword(s):  
Functional Annotation ◽  
Molecular Genetic ◽  
Hybrid Approach ◽  
Heterogeneous Data ◽  
Amino Acid Sequences ◽  
Model Organisms ◽  
Rna Seq ◽  
Wide Range ◽  
Sequencing Experiment ◽  
Agricultural Plants

The transcriptome sequencing experiment (RNA-seq) has become almost a routine procedure for studying both model organisms and crops. As a result of bioinformatics processing of such experimental output, huge heterogeneous data are obtained, representing nucleotide sequences of transcripts, amino acid sequences, and their structural and functional annotation. It is important to present the data obtained to a wide range of researchers in the form of databases. This article proposes a hybrid approach to creating molecular genetic databases that contain information about transcript sequences and their structural and functional annotation. The essence of the approach consists in the simultaneous storing both structured and weakly structured data in the database. The technology was used to implement a database of transcriptomes of agricultural plants. This paper discusses the features of implementing this approach and examples of generating both simple and complex queries to such a database in the SQL language. The OORT database is freely available at https://oort.cytogen.ru/.

scholarly journals Narrow Substrate Requirements Alongside Rapid Substrate Turnover for Wood-Inhabiting Fungi: A Case Study of Pleurotus Calyptratus (Agaricales, Basidiomycota) in Ukraine

2020 ◽  
Author(s):  
Oleh Prylutskyi ◽  
Iryna Yatsiuk ◽  
Anton Savchenko ◽  
Maryna Kit ◽  
Oleksii Solodiankin ◽  
...  
Keyword(s):  
Fruit Body ◽  
Tree Age ◽  
Model Object ◽  
Host Trees ◽  
Dead Trees ◽  
Wide Range ◽  
Species Specific ◽  
Living Tissues ◽  
Body Production

Abstract BackgroundPleurotus calyptratus is a wood-inhabiting oyster mushroom which produces fruiting bodies on logs, stumps and branches of both dead and living Populus tremula and P. alba. Easily recognisable in the field fruit bodies and strict and steady fruiting period make this species an attractive model object for investigations of ecology of wood-inhabiting fungi. This fungus is rather common in Ukraine, but considered rare in many other European countries.To explore species biology in relation to its rarity issues, we analyzed substrate requirements and habitat supply for P. calyptratus in two sites in Eastern Ukraine, as well as monitored patterns of fruit body production in three large aspen stands over 6 years. In addition, patterns of mycelial presence of P. calyptratus mycelia were studied in living aspen trees using custom species-specific primers.ResultsStudy demonstrates potential suitability of a wide range of life / decomposition stages of aspen or white poplar tree trunks for P. calyptratus. This window of suitability, however, is rather short: dying of freshly dead trees, rarely exceeding two years) regardless of tree age, volume, position or other parameters. Moreover, mycelium presence of P. calyptratus was detected in the living tissues of host trees. These findings supported hypotheses of early substrate colonization and latent mycelial development of P. calyptratus before the substrate reached a stage suitable for fructification.ConclusionsConfirmed by a combination of fruit body survey and detection of mycelial DNA, P. calyptratus demonstrates an ecological strategy which combines both strict substrate requirements and rapid substrate turnover. We suppose that such a strategy may be widely distributed among wood-inhabiting agarics.

Site specific agricultural soil management with the use of new technologies

2013 ◽  
Vol 16 (1) ◽  
pp. 59-67
Keyword(s):  
New Technologies ◽  
Digital Interface ◽  
Appropriate Treatment ◽  
Wide Range ◽  
Soil Variation ◽  
Soil Information ◽  
Remote Sensing Techniques ◽  
Agricultural Areas

<p>The Soil Science Institute of Thessaloniki produces new digitized Soil Maps that provide a useful electronic database for the spatial representation of the soil variation within a region, based on in situ soil sampling, laboratory analyses, GIS techniques and plant nutrition mathematical models, coupled with the local land cadastre. The novelty of these studies is that local agronomists have immediate access to a wide range of soil information by clicking on a field parcel shown in this digital interface and, therefore, can suggest an appropriate treatment (e.g. liming, manure incorporation, desalination, application of proper type and quantity of fertilizer) depending on the field conditions and cultivated crops. A specific case study is presented in the current work with regards to the construction of the digitized Soil Map of the regional unit of Kastoria. The potential of this map can easily be realized by the fact that the mapping of the physicochemical properties of the soils in this region provided delineation zones for differential fertilization management. An experiment was also conducted using remote sensing techniques for the enhancement of the fertilization advisory software database, which is a component of the digitized map, and the optimization of nitrogen management in agricultural areas.</p>

Research of the activity and viability of spermatozoa at different concentrations and proportions of diluents after incubation

2020 ◽  
pp. 88-95
Author(s):  
Svitlana Lobchenko ◽  
Tetiana Husar ◽  
Viktor Lobchenko
Keyword(s):  
Plasma Concentration ◽  
Incubation Time ◽  
Coefficient Of Variation ◽  
Incubation Medium ◽  
Wide Range ◽  
Series Of Experiments ◽  
The Subject ◽  
Boar Spermatozoa ◽  
Native Plasma ◽  
Better Than

The results of studies of the viability of spermatozoa with different incubation time at different concentrations and using different diluents are highlighted in the article. (Un) concentrated spermatozoa were diluented: 1) with their native plasma; 2) medium 199; 3) a mixture of equal volumes of plasma and medium 199. The experiment was designed to generate experimental samples with spermatozoa concentrations prepared according to the method, namely: 0.2; 0.1; 0.05; 0.025 billion / ml. The sperm was evaluated after 2, 4, 6 and 8 hours. The perspective of such a study is significant and makes it possible to research various aspects of the subject in a wide range. In this regard, a series of experiments were conducted in this area. The data obtained are statistically processed and allow us to highlight the results that relate to each stage of the study. In particular, in this article it was found out some regularities between the viability of sperm, the type of diluent and the rate of rarefaction, as evidenced by the data presented in the tables. As a result of sperm incubation, the viability of spermatozoa remains at least the highest trend when sperm are diluted to a concentration of 0.1 billion / ml, regardless of the type of diluent used. To maintain the viability of sperm using this concentration of medium 199 is not better than its native plasma, and its mixture with an equal volume of plasma through any length of time incubation of such sperm. Most often it is at this concentration of sperm that their viability is characterized by the lowest coefficient of variation, regardless of the type of diluent used, which may indicate the greatest stability of the result under these conditions. The viability of spermatozoa with a concentration of 0.1 billion / ml is statistically significantly reduced only after 6 or even 8 hours of incubation. If the sperm are incubated for only 2 hours, regardless of the type of diluent used, the sperm concentrations tested do not affect the viability of the sperm. Key words: boar, spermatozoa, sperm plasma, concentration, incubation, medium 199, activity, viability, rarefaction.

Oxford Studies in Ancient Philosophy, Volume 55

2018 ◽  
Keyword(s):  
Middle Ages ◽  
Ancient Philosophy ◽  
Recent Book ◽  
Loss Of Control ◽  
Ancient Greek ◽  
Original Essays ◽  
Constant Change ◽  
Wide Range ◽  
Metaphysical Principle

Oxford Studies in Ancient Philosophy provides, twice each year, a collection of the best current work in the field of ancient philosophy. Each volume features original essays that contribute to an understanding of a wide range of themes and problems in all periods of ancient Greek and Roman philosophy, from the beginnings to the threshold of the Middle Ages. From its first volume in 1983, OSAP has been a highly influential venue for work in the field, and has often featured essays of substantial length as well as critical essays on books of distinctive importance. Volume LV contains: a methodological examination on how the evidence for Presocratic thought is shaped through its reception by later thinkers, using discussions of a world soul as a case study; an article on Plato’s conception of flux and the way in which sensible particulars maintain a kind of continuity while undergoing constant change; a discussion of J. L. Austin’s unpublished lecture notes on Aristotle’s Nicomachean Ethics and his treatment of loss of control (akrasia); an article on the Stoics’ theory of time and in particular Chrysippus’ conception of the present and of events; and two articles on Plotinus, one that identifies a distinct argument to show that there is a single, ultimate metaphysical principle; and a review essay discussing E. K. Emilsson’s recent book, Plotinus.

scholarly journals A Comprehensive Bioinformatics Analysis of Notch Pathways in Bladder Cancer

Cancers ◽  
2021 ◽  
Vol 13 (12) ◽  
pp. 3089
Author(s):  
Chuan Zhang ◽  
Mandy Berndt-Paetz ◽  
Jochen Neuhaus
Keyword(s):  
Cell Cycle ◽  
Bladder Cancer ◽  
Notch Signaling ◽  
Epithelial Mesenchymal Transition ◽  
Tumor Biology ◽  
Disease Free Survival ◽  
Mesenchymal Transition ◽  
Expression Levels ◽  
Notch Receptors ◽  
Notch Pathways

Background: A hallmark of Notch signaling is its variable role in tumor biology, ranging from tumor-suppressive to oncogenic effects. Until now, the mechanisms and functions of Notch pathways in bladder cancer (BCa) are still unclear. Methods: We used publicly available data from the GTEx and TCGA-BLCA databases to explore the role of the canonical Notch pathways in BCa on the basis of the RNA expression levels of Notch receptors, ligands, and downstream genes. For statistical analyses of cancer and non-cancerous samples, we used R software packages and public databases/webservers. Results: We found differential expression between control and BCa samples for all Notch receptors (NOTCH1, 2, 3, 4), the delta-like Notch ligands (DLL1, 3, 4), and the typical downstream gene hairy and enhancer of split 1 (HES1). NOTCH2/3 and DLL4 can significantly differentiate non-cancerous samples from cancers and were broadly altered in subgroups. High expression levels of NOTCH2/3 receptors correlated with worse overall survival (OS) and shorter disease-free survival (DFS). However, at long-term (>8 years) follow-up, NOTCH2 expression was associated with a better OS and DFS. Furthermore, the cases with the high levels of DLL4 were associated with worse OS but improved DFS. Pathway network analysis revealed that NOTCH2/3 in particular correlated with cell cycle, epithelial–mesenchymal transition (EMT), numbers of lymphocyte subtypes, and modulation of the immune system. Conclusions: NOTCH2/3 and DLL4 are potential drivers of Notch signaling in BCa, indicating that Notch and associated pathways play an essential role in the progression and prognosis of BCa through directly modulating immune cells or through interaction with cell cycle and EMT.

scholarly journals Intravitreal brimonidine inhibits form-deprivation myopia in guinea pigs

2021 ◽  
Vol 8 (1) ◽  
Author(s):  
Yifang Yang ◽  
Junshu Wu ◽  
Defu Wu ◽  
Qi Wei ◽  
Tan Zhong ◽  
...  
Keyword(s):  
Guinea Pig ◽  
Intravitreal Injection ◽  
Guinea Pigs ◽  
Intravitreal Injections ◽  
Eye Drops ◽  
Rna Seq ◽  
Myopia Progression ◽  
Expression Levels ◽  
Guinea Pig Model ◽  
Administration Methods

Abstract Background The use of ocular hypotensive drugs has been reported to attenuate myopia progression. This study explores whether brimonidine can slow myopia progression in the guinea pig form-deprivation (FD) model. Methods Three-week-old pigmented male guinea pigs (Cavia porcellus) underwent monocular FD and were treated with 3 different methods of brimonidine administration (eye drops, subconjunctival or intravitreal injections). Four different concentrations of brimonidine were tested for intravitreal injection (2 μg/μL, 4 μg/μL, 20 μg/μL, 40 μg/μL). All treatments continued for a period of 21 days. Tonometry, retinoscopy, and A-scan ultrasonography were used to monitor intraocular pressure (IOP), refractive error and axial length (AL), respectively. On day 21, guinea pigs were sacrificed for RNA sequencing (RNA-seq) to screen for associated transcriptomic changes. Results The myopia model was successfully established in FD animals (control eye vs. FD eye, respectively: refraction at day 20, 0.97 ± 0.18 D vs. − 0.13 ± 0.38 D, F = 6.921, P = 0.02; AL difference between day 0 and day 21, 0.29 ± 0.04 mm vs. 0.45 ± 0.03 mm, F = 11.655, P = 0.004). Among the 3 different brimonidine administration methods, intravitreal injection was the most effective in slowing myopia progression, and 4 μg/μL was the most effective among the four different concentrations of brimonidine intravitreal injection tested. The AL and the refraction of the brimonidine intravitreal injection group was significantly shorter or more hyperopic than those of other 2 groups. Four μg/μL produced the smallest difference in AL and spherical equivalent difference values. FD treatment significantly increased the IOP. IOP was significantly lower at 1 day after intravitreal injections which was the lowest in FD eye of intravitreal injection of brimonidine. At day 21, gene expression analyses using RNA-seq showed upregulation of Col1a1 and Mmp2 expression levels by intravitreal brimonidine. Conclusions Among the 3 different administration methods, intravitreal injection of brimonidine was the most effective in slowing myopia progression in the FD guinea pig model. Intravitreal brimonidine at 4 μg/μL significantly reduced the development of FD myopia in guinea pigs. Expression levels of the Col1a1 and Mmp2 genes were significantly increased in the retinal tissues of the FD-Inj-Br group.

scholarly journals SAUTE: sequence assembly using target enrichment

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Alexandre Souvorov ◽  
Richa Agarwala
Keyword(s):  
De Bruijn Graph ◽  
Challenging Problem ◽  
Target Enrichment ◽  
Rna Seq ◽  
Sequencing Technology ◽  
Insert Size ◽  
Systematic Biases ◽  
Target Sequences ◽  
Genomic Regions ◽  
Higher Sensitivity

Abstract Background Illumina is the dominant sequencing technology at this time. Short length, short insert size, some systematic biases, and low-level carryover contamination in Illumina reads continue to make assembly of repeated regions a challenging problem. Some applications also require finding multiple well supported variants for assembled regions. Results To facilitate assembly of repeat regions and to report multiple well supported variants when a user can provide target sequences to assist the assembly, we propose SAUTE and SAUTE_PROT assemblers. Both assemblers use de Bruijn graph on reads. Targets can be transcripts or proteins for RNA-seq reads and transcripts, proteins, or genomic regions for genomic reads. Target sequences are nucleotide and protein sequences for SAUTE and SAUTE_PROT, respectively. Conclusions For RNA-seq, comparisons with Trinity, rnaSPAdes, SPAligner, and SPAdes assembly of reads aligned to target proteins by DIAMOND show that SAUTE_PROT finds more coding sequences that translate to benchmark proteins. Using AMRFinderPlus calls, we find SAUTE has higher sensitivity and precision than SPAdes, plasmidSPAdes, SPAligner, and SPAdes assembly of reads aligned to target regions by HISAT2. It also has better sensitivity than SKESA but worse precision.

scholarly journals Clustering Single-Cell RNA-Seq Data with Regularized Gaussian Graphical Model

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 311
Author(s):  
Zhenqiu Liu
Keyword(s):  
Single Cell ◽  
Free Parameter ◽  
Graphical Model ◽  
Expression Patterns ◽  
Information Criterion ◽  
Log P ◽  
Rna Seq ◽  
Clustering Methods ◽  
Wide Range ◽  
Free Parameters

Single-cell RNA-seq (scRNA-seq) is a powerful tool to measure the expression patterns of individual cells and discover heterogeneity and functional diversity among cell populations. Due to variability, it is challenging to analyze such data efficiently. Many clustering methods have been developed using at least one free parameter. Different choices for free parameters may lead to substantially different visualizations and clusters. Tuning free parameters is also time consuming. Thus there is need for a simple, robust, and efficient clustering method. In this paper, we propose a new regularized Gaussian graphical clustering (RGGC) method for scRNA-seq data. RGGC is based on high-order (partial) correlations and subspace learning, and is robust over a wide-range of a regularized parameter λ. Therefore, we can simply set λ=2 or λ=log(p) for AIC (Akaike information criterion) or BIC (Bayesian information criterion) without cross-validation. Cell subpopulations are discovered by the Louvain community detection algorithm that determines the number of clusters automatically. There is no free parameter to be tuned with RGGC. When evaluated with simulated and benchmark scRNA-seq data sets against widely used methods, RGGC is computationally efficient and one of the top performers. It can detect inter-sample cell heterogeneity, when applied to glioblastoma scRNA-seq data.

scholarly journals Assessing the Relation between Mud Components and Rheology for Loss Circulation Prevention Using Polymeric Gels: A Machine Learning Approach

Energies ◽  
2021 ◽  
Vol 14 (5) ◽  
pp. 1377
Author(s):  
Musaab I. Magzoub ◽  
Raj Kiran ◽  
Saeed Salehi ◽  
Ibnelwaleed A. Hussein ◽  
Mustafa S. Nasser
Keyword(s):  
Machine Learning ◽  
Rheological Properties ◽  
Nearest Neighbor ◽  
Drilling Fluid ◽  
Gradient Boosting ◽  
K Nearest Neighbor ◽  
Wide Range ◽  
Machine Learning Approach ◽  
Drilling Operations

The traditional way to mitigate loss circulation in drilling operations is to use preventative and curative materials. However, it is difficult to quantify the amount of materials from every possible combination to produce customized rheological properties. In this study, machine learning (ML) is used to develop a framework to identify material composition for loss circulation applications based on the desired rheological characteristics. The relation between the rheological properties and the mud components for polyacrylamide/polyethyleneimine (PAM/PEI)-based mud is assessed experimentally. Four different ML algorithms were implemented to model the rheological data for various mud components at different concentrations and testing conditions. These four algorithms include (a) k-Nearest Neighbor, (b) Random Forest, (c) Gradient Boosting, and (d) AdaBoosting. The Gradient Boosting model showed the highest accuracy (91 and 74% for plastic and apparent viscosity, respectively), which can be further used for hydraulic calculations. Overall, the experimental study presented in this paper, together with the proposed ML-based framework, adds valuable information to the design of PAM/PEI-based mud. The ML models allowed a wide range of rheology assessments for various drilling fluid formulations with a mean accuracy of up to 91%. The case study has shown that with the appropriate combination of materials, reasonable rheological properties could be achieved to prevent loss circulation by managing the equivalent circulating density (ECD).

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