Computational methods for transcriptome annotation and quantification using RNA-seq

High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications

Characterization and classification of Turkish wines based on elemental composition

Commercial wines from 13 native and nonnative varieties in Turkey were analyzed for their elemental composition. Wines from four vintages (2006-2009) were analyzed by inductively coupled plasma with atomic emission spectrometry and mass spectroscopy (ICP-AES and ICP-MS) followed by multivariate statistics to study vintage, varietal, and regional differences. According to the partial least squares-discriminant analysis, wines from western regions could be discriminated with their higher Pb content. The red wines of two native grapes, Boǧazkere and Öküzgözü, were separated from the remaining varieties based on their high Ca and low B and Cu levels. Öküzgözü wines were different from Syrah and Cabernet Sauvignon wines. Similarly, native Emir wines showed differences from Muscat wines. The effective variables for discrimination analysis were natural minerals (Sr, Li, Al, Ba, and B) and minerals originating from agricultural activities, processing, or pollution (Ca, Cu, Mg, Co, Pb, and Ni). Characteristics of Turkish wines from native and nonnative grape varieties such as Cabernet Sauvignon, Merlot, Syrah, and Chardonnay were defined in terms of their mineral content for the first time.Scientific Research Project of Izmir Institute of Technology (IYTE-BAP-18-2008

Computational methods for transcriptome annotation and quantification using RNA-seq

High-throughput RNA sequencing (RNA-seq) promises a comprehensive picture of the transcriptome, allowing for the complete annotation and quantification of all genes and their isoforms across samples. Realizing this promise requires increasingly complex computational methods. These computational challenges fall into three main categories: (i) read mapping, (ii) transcriptome reconstruction and (iii) expression quantification. Here we explain the major conceptual and practical challenges, and the general classes of solutions for each category. Finally, we highlight the interdependence between these categories and discuss the benefits for different biological applications

Comparative Fungal Community Analyses Using Metatranscriptomics and Internal Transcribed Spacer Amplicon Sequencing from Norway Spruce

The health, growth, and fitness of boreal forest trees are impacted and improved by their associated microbiomes. Microbial gene expression and functional activity can be assayed with RNA sequencing (RNA-Seq) data from host samples. In contrast, phylogenetic marker gene amplicon sequencing data are used to assess taxonomic composition and community structure of the microbiome. Few studies have considered how much of this structural and taxonomic information is included in transcriptomic data from matched samples. Here, we described fungal communities using both host-derived RNA-Seq and fungal ITS1 DNA amplicon sequencing to compare the outcomes between the methods. We used a panel of root and needle samples from the coniferous tree species Picea abies (Norway spruce) growing in untreated (nutrient-deficient) and nutrient-enriched plots at the Flakaliden forest research site in boreal northern Sweden. We show that the relationship between samples and alpha and beta diversity indicated by the fungal transcriptome is in agreement with that generated by the ITS data, while also identifying a lack of taxonomic overlap due to limitations imposed by current database coverage. Furthermore, we demonstrate how metatranscriptomics data additionally provide biologically informative functional insights. At the community level, there were changes in starch and sucrose metabolism, biosynthesis of amino acids, and pentose and glucuronate interconversions, while processing of organic macromolecules, including aromatic and heterocyclic compounds, was enriched in transcripts assigned to the genus Cortinarius.IMPORTANCE A deeper understanding of microbial communities associated with plants is revealing their importance for plant health and productivity. RNA extracted from plant field samples represents the host and other organisms present. Typically, gene expression studies focus on the plant component or, in a limited number of studies, expression in one or more associated organisms. However, metatranscriptomic data are rarely used for taxonomic profiling, which is currently performed using amplicon approaches. We created an assembly-based, reproducible, and hardware-agnostic workflow to taxonomically and functionally annotate fungal RNA-Seq data obtained from Norway spruce roots, which we compared to matching ITS amplicon sequencing data. While we identified some limitations and caveats, we show that functional, taxonomic, and compositional insights can all be obtained from RNA-Seq data. These findings highlight the potential of metatranscriptomics to advance our understanding of interaction, response, and effect between host plants and their associated microbial communities

Information Systems of Ostrava City Magistrate

Import 04/11/2015Resumé Tato práce se zabývá analýzou informačních systémů veřejné správy a informačních systémů Magistrátu města Ostravy. Cílem práce bylo zhodnotit činnosti a služby informačních systémů Magistrátu města Ostravy. V diplomové práci byly stanoveny hypotézy, které se potvrdily. V první hypotéze jsme se zabývali tím, zda Magistrát města Ostravy zajišťuje činnosti informačních systémů a služeb převážně externí firmou. Tato hypotéza se potvrdila. Druhá hypotéza, kterou jsme zjišťovali, byla, zda jsou služby Informačních technologií poskytovány Magistrátem města Ostravy v největší míře právě pro občany – fyzické osoby. I tato hypotéza se nám potvrdila. V diplomové práci byla stanovena také kritéria, kterými jsme dospěli k závěrům hypotézy. Kritéria jsou tato: Zhodnocení činností Informačních systémů, jaký je jejich obsah, náplň, jaké systémy Magistrát města Ostravy využívá a jakým způsobem jsou zajišťovány. V diplomové práci jsme dospěli ke zjištění, že informační systémy jsou zajišťovány z 96 % externí, outsourcingovou společností a nejvíce informační služby využívají občané – fyzické osoby, ze 43%. Přínosem práce je pak zjištění, že outsourcingová společnost, kterou využívá Magistrát města Ostravy pro správu informačních systémů, je ve 100% vlastnictví města Ostravy. Takto řízená správa se jeví jako neefektivní. I když zisk ve veřejném sektoru není hlavním cílem.Resume This thesis deals with the analysis of information systems of the public administration and information systems in the Municipality of Ostrava City. The aim of the thesis was to evaluate the activities and services of information systems in the Municipality of Ostrava City. In this thesis have been determined the hypotheses, which have been confirmed. In the first hypothesis, we have been dealing with the fact, if the Municipality of Ostrava City provides the business information systems and services mainly by the external company. This hypothesis has been confirmed. The second hypothesis, we have been investigated with was the fact, if the information technology services provided by the Municipality of Ostrava City are in the greatest rate for citizens - individuals. Also this hypothesis has been confirmed. In the thesis have been also determined the criteria, by which we came to the conclusions of the hypothesis. The criteria are as follows: the evaluation of information systems, what the content is, and what system the Municipality of Ostrava City uses and how they are provided. In this thesis we came to the finding that information systems are provided from 96 % by the external outsourcing company and the information services are mostly used by citizens - individuals, namely from 43 %. The contribution of this thesis is the finding that the outsourcing company, used by the Municipality of Ostrava City for the management of information systems, is by 100 % owned by the Ostrava City. In this way controlled management seems to be ineffective. Although the profit is not in the public sector the primary aim.153 - Katedra veřejné ekonomikydobř

Comparative omics and feeding manipulations in chicken indicate a shift of the endocrine role of visceral fat towards reproduction.

BACKGROUND: The mammalian adipose tissue plays a central role in energy-balance control, whereas the avian visceral fat hardly expresses leptin, the key adipokine in mammals. Therefore, to assess the endocrine role of adipose tissue in birds, we compared the transcriptome and proteome between two metabolically different types of chickens, broilers and layers, bred towards efficient meat and egg production, respectively. RESULTS: Broilers and layer hens, grown up to sexual maturation under free-feeding conditions, differed 4.0-fold in weight and 1.6-fold in ovarian-follicle counts, yet the relative accumulation of visceral fat was comparable. RNA-seq and mass-spectrometry (MS) analyses of visceral fat revealed differentially expressed genes between broilers and layers, 1106 at the mRNA level (FDR ≤ 0.05), and 203 at the protein level (P ≤ 0.05). In broilers, Ingenuity Pathway Analysis revealed activation of the PTEN-pathway, and in layers increased response to external signals. The expression pattern of genes encoding fat-secreted proteins in broilers and layers was characterized in the RNA-seq and MS data, as well as by qPCR on visceral fat under free feeding and 24 h-feed deprivation. This characterization was expanded using available RNA-seq data of tissues from red junglefowl, and of visceral fat from broilers of different types. These comparisons revealed expression of new adipokines and secreted proteins (LCAT, LECT2, SERPINE2, SFTP1, ZP1, ZP3, APOV1, VTG1 and VTG2) at the mRNA and/or protein levels, with dynamic gene expression patterns in the selected chicken lines (except for ZP1; FDR/P ≤ 0.05) and feed deprivation (NAMPT, SFTPA1 and ZP3) (P ≤ 0.05). In contrast, some of the most prominent adipokines in mammals, leptin, TNF, IFNG, and IL6 were expressed at a low level (FPKM/RPKM< 1) and did not show differential mRNA expression neither between broiler and layer lines nor between fed vs. feed-deprived chickens. CONCLUSIONS: Our study revealed that RNA and protein expression in visceral fat changes with selective breeding, suggesting endocrine roles of visceral fat in the selected phenotypes. In comparison to gene expression in visceral fat of mammals, our findings points to a more direct cross talk of the chicken visceral fat with the reproductive system and lower involvement in the regulation of appetite, inflammation and insulin resistance.The study was supported by the Israel Academy of Sciences grants no. 876/ 14 and 1294/17, and Chief Scientist of the Israeli Ministry of Agriculture 0469/14 (to MFE and ES)

Metatranscriptomics captures dynamic shifts in mycorrhizal coordination in boreal forests

Carbon storage and cycling in boreal forests—the largest terrestrial carbon store—ismoderated by complex interactions between trees and soil microorganisms. However,existing methods limit our ability to predict how changes in environmental conditionswill alter these associations and the essential ecosystem services they provide. To addressthis, we developed a metatranscriptomic approach to analyze the impact of nutrientenrichment on Norway sprucefine roots and the community structure, function, andtree–microbe coordination of over 350 root-associated fungal species. In response toaltered nutrient status, host trees redefined their relationship with the fungal commu-nity by reducing sugar efflux carriers and enhancing defense processes. This resulted ina profound restructuring of the fungal community and a collapse in functional coordi-nation between the tree and the dominant Basidiomycete species, and an increase infunctional coordination with versatile Ascomycete species. As such, there was a func-tional  shift  in  community  dominance  from  Basidiomycetes  species,  with  importantroles in enzymatically cycling recalcitrant carbon, to Ascomycete species that have mela-nized cell walls that are highly resistant to degradation. These changes were accompa-nied  by  prominent  shifts  in  transcriptional  coordination  between  over  60  predictedfungal effectors, with more than 5,000 Norway spruce transcripts, providing mechanis-tic insight into the complex molecular dialogue coordinating host trees and their fungalpartners. The host–microbe dynamics captured by this study functionally inform howthese complex and  sensitive biological  relationships may mediate  the carbon  storagepotential of boreal soils under changing nutrient conditions

The genome of the green anole lizard and a comparative analysis with birds and mammals

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments1. Among amniotes, genome sequences are available for mammals2 and birds3–5, but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes3. Also, A. carolinensis mobile elements are very young and diverse – more so than in any other sequenced amniote genome. This lizard genome’s GC content is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds6. We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations