Search

Owing to the complexities of bacterial RNA biology, the transcriptomes of even the best studied bacteria are not fully understood. To help elucidate the transcriptional landscape of E. coli, we compiled a compendium of 3,376 RNA-seq data sets composed of more than 7 trillion sequenced bases, which we evaluate with a transcript assembly pipeline. We report expression profiles for all annotated E. coli genes as well as 5,071 other transcripts. Additionally, we observe hundreds of instances of co-transcribed genes that are novel with respect to existing operon databases. By integrating data from a large number of sequencing experiments corresponding to a wide range of conditions, we are able to obtain a comprehensive view of the E. coli transcriptome.

Abstract Among the plant molecular mechanisms capable of effectively mitigating the effects of adverse weather conditions, the heat shock proteins (HSPs), a group of chaperones with multiple functions, stand out. At a time of full progress on the omic sciences, they look very promising in the genetic engineering field, especially in order to conceive superior genotypes, potentially tolerant to abiotic stresses (AbSts). Recently, some works concerning certain families of maize HSPs (ZmHSPs) were published. However, there was still a lack of a study that, with a high degree of criteria, would fully conglomerate them. Using distinct but complementary strategies, we have prospected as many ZmHSPs candidates as possible, gathering more than a thousand accessions. After detailed data mining, we accounted for 182 validated ones, belonging to seven families, which were subcategorized into classes with potential for functional parity. In them, we identified dozens of motifs with some degree of similarity with proteins from different kingdoms, which may help explain some of their still poorly understood means of action. Through in silico and in vitro approaches, we compared their expression levels after controlled exposure to several AbSts' sources, applied at diverse tissues, on varied phenological stages. Based on gene ontology concepts, we still analyzed them from different perspectives of term enrichment. We have also searched, in model plants and close species, for potentially orthologous genes. With all these new insights, which culminated in a plentiful supplementary material, rich in tables, we aim to constitute a fertile consultation source for those maize researchers attracted by these interesting stress proteins.

ABSTRACT Thousands of Pseudomonas aeruginosa RNA sequencing (RNA-seq) gene expression profiles are publicly available via the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). In this work, the transcriptional profiles from hundreds of studies performed by over 75 research groups were reanalyzed in aggregate to create a powerful tool for hypothesis generation and testing. Raw sequence data were uniformly processed using the Salmon pseudoaligner, and this read mapping method was validated by comparison to a direct alignment method. We developed filtering criteria to exclude samples with aberrant levels of housekeeping gene expression or an unexpected number of genes with no reported values and normalized the filtered compendia using the ratio-of-medians method. The filtering and normalization steps greatly improved gene expression correlations for genes within the same operon or regulon across the 2,333 samples. Since the RNA-seq data were generated using diverse strains, we report the effects of mapping samples to noncognate reference genomes by separately analyzing all samples mapped to cDNA reference genomes for strains PAO1 and PA14, two divergent strains that were used to generate most of the samples. Finally, we developed an algorithm to incorporate new data as they are deposited into the SRA. Our processing and quality control methods provide a scalable framework for taking advantage of the troves of biological information hibernating in the depths of microbial gene expression data and yield useful tools for P. aeruginosa RNA-seq data to be leveraged for diverse research goals. IMPORTANCE Pseudomonas aeruginosa is a causative agent of a wide range of infections, including chronic infections associated with cystic fibrosis. These P. aeruginosa infections are difficult to treat and often have negative outcomes. To aid in the study of this problematic pathogen, we mapped, filtered for quality, and normalized thousands of P. aeruginosa RNA-seq gene expression profiles that were publicly available via the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The resulting compendia facilitate analyses across experiments, strains, and conditions. Ultimately, the workflow that we present could be applied to analyses of other microbial species.

This review presents the work of an international team of researchers devoted to a thorough description of the problems of modern sociolinguistics. The developmental stages and basic concepts of sociolinguistics are analysed, and the trends and methods of modern sociolinguistic researches are presented. The mutual influences of language and society are demonstrated and the legal status of the state language in Ukraine is analysed.

Two new and two known species of the genus Paraoxydirus Jairajpuri and Ahmad, 1978 are described and illustrated from Western Ghats of India. P. vulvalpapillatus n. sp. is characterized by having large sized body (L = 4.6 – 4.8 mm); lip region continuous with completely amalgamated lips; amphidial fovea cup – shaped; 5 – 6 μm long odontostyle; 11 – 13 μm long odontophore; pharyngeal expansion about 28 – 36 % of neck length; transverse vulva; vulval papillae conspicuous; males with 46 – 54 μm long spicules; 11 – 14 continuous ventromedian supplements and long filiform tail similar in both sexes. P. indicus n. sp. is characterized by having large sized body (L = 4.0 – 4.8 mm); lip region poorly offset with amalgamated lips; amphidial fovea cup-shaped; 7 – 8 μm long, robust odontostyle; 17 – 18 μm long odontophore; pharyngeal expansion about 32 – 40 % of neck length; 21 – 26 μm long cardia; longitudinal vulva; 748 – 894 μm long filiform tail; males with 45 – 54 μm long spicules and 12 – 15 continuous ventromedian supplements. P. gigas Jairajpuri, 1964 and P. novus Jairajpuri, 1965 are redescribed based on specimens collected from several localities. A diagnostic Key and compendium to the identification of its eight valid species is provided.

Successfully integrating transcriptomic experiments is a challenging task with the ultimate goal of analyzing gene expression data in the broader context of all available measurements, all from a single point of access. In its second major release VESPUCCI, the integrated database of gene expression data for grapevine, has been updated to be FAIR-compliant, employing standards and created with open-source technologies. It includes all public grapevine gene expression experiments from both microarray and RNA-seq platforms. Transcriptomic data can be accessed in multiple ways through the newly developed COMPASS GraphQL interface, while the expression values are normalized using different methodologies to flexibly satisfy different analysis requirements. Sample annotations are manually curated and use standard formats and ontologies. The updated version of VESPUCCI provides easy querying and analyzing of integrated grapevine gene expression (meta)data and can be seamlessly embedded in any analysis workflow or tools. VESPUCCI is freely accessible and offers several ways of interaction, depending on the specific goals and purposes and/or user expertise; an overview can be found at https://vespucci.readthedocs.io/.

Blockchain technologies (BC) are immutable distributed systems of digital ledgers (i.e., without central repository) and, as rule, without central authority. Currently, there is a lot of excitement around the use of BC technology, although the technology itself, on the one hand, is still not quite clear to many ones, and on the other (and this is the main thing) is not new. Superficial understanding of the BC as a phenomenon with «magical properties» leads to numerous predictions about the possibility of revolutionary transformations based on its application to entire sectors of the economy and, above all, in the credit and financial sphere. In this regard, this article presents a systematized analysis, the history of the BC emergence, leading from the international standards ISO 7498-2 of 1989 and ITU-T X.800 of 1991, as well as a brief informal definition of BC and considered are the basic principles and components of this technology, including cryptographic one-way functions (hashes), transactions, addresses and their retrieval, «digital wallets», ledgers, blocks, blockchain in operations. Representation of the BC as a sequence of blocks bounded base on known mechanisms of the data integrity with using asymmetric cryptography allows us to conclude that only its evolutionary development is possible, although at a rapid pace in real time. This is a characteristic feature of establishing modern stage of and all other IT types. In conclusion, attention is drawn to the need for additional research to assess the security and reliability of the BC in terms of assessing the prospects for its use in specific business applications and critical information infrastructure systems.

Caveonchus siddiqii n. sp. is described and illustrated based on specimens collected from both India and Japan. It is characterized by having a medium sized body (L= 0.86 - 1.12 mm); labial disc present; amphideal fovea flask-shaped; lip region cap-like, offset by slight constriction; odontostyle 8 - 9 μm, odontophore 10 - 12 μm; pharynx with slender anterior part which expands abruptly into the saccate basal bulb, occupying about 16 - 21 % of total neck length; female genital system mono-opisthodelphic; anterior genital branch 70 - 100 μm or 1.9 - 2.8 times the midbody diameter long; tail short, rounded, hemispheroid, 0.5 - 0.7 anal body diameter long; spicules 30 - 38 μm long; and three spaced ventromedian supplements. Its relationship with all the known species of the genus is discussed. A diagnostic compendium and a key to identification of the species is also provided.

This paper deals with the morphological and molecular characterization of Kochinema farodai Baqri and Bohra, 2001, with an integrative approach. The finding of K. faroidai in California is a remarkable biogeographical novelty, as it is the first American record of the species. Molecular data herein obtained represent the first molecular study of the genus Kochinema. Furthermore, scanning electron microscopy (SEM) observations of a member of Kochinema are provided for the first time. Additionally, this contribution provides new insights into the phylogeny and taxonomy of the nematode genus Kochinema. A brief historical outline of the matter is presented. Then, the morphological pattern of the genus is revised and illustrated, the anterior position of amphids, whose opening is located on lateral lip, being its most relevant diagnostic feature. The phylogenetic analysis inferred from D2–D3 expansion segments of 28S rRNA gene shows that Kochinema clustered together with other dorylaimid species characterized by the absence of pars refringens vaginae and that it does not share a recent common ancestor with other members of the family Nordiidae. A likely polyphyly of the family Nordiidae is confirmed. Finally, an updated taxonomy of the genus is proposed, including a revised diagnosis, a list of species, a key to species identification, and a compendium of their main morphometrics and distribution data.

Large-scale transcriptional studies aim to decipher the dynamic cellular responses to a stimulus, like different environmental conditions. In the era of high-throughput omics biology, the most used technologies for these purposes are microarray and RNA-Seq, whose data are usually required to be deposited in public repositories upon publication. Such repositories have the enormous potential to provide a comprehensive view of how different experimental conditions lead to expression changes, by comparing gene expression across all possible measured conditions. Unfortunately, this task is greatly impaired by differences among experimental platforms that make direct comparisons difficult.In this paper we present the Vitis Expression Studies Platform Using COLOMBOS Compendia Instances (VESPUCCI), a gene expression compendium for grapevine which was built by adapting an approach originally developed for bacteria, and show how it can be used to investigate complex gene expression patterns. We integrated nearly all publicly available microarray and RNA-Seq expression data: 1608 gene expression samples from 10 different technological platforms. Each sample has been manually annotated using a controlled vocabulary developed ad hoc to ensure both human readability and computational tractability. Expression data in the compendium can be visually explored using several tools provided by the web interface or can be programmatically accessed using the REST interface. VESPUCCI is freely accessible at http://vespucci.colombos.fmach.it.

(francuski) Cet article a pour objet d'étude la voie romaine Naissus-Lissus, la station d'Ad Fines (Kuršumlija), le compendium (raccourci) dont fait état une inscription de Viminacium et une borne milliaire découverte récemment, entre autre matériel, sur le site d'Aquae Bas. (Kuršumlijska Banja). Il analyse les découvertes archéologiques et épigraphiques, et discute le tracé de cette voie de communication de l'antiquité romaine.

We present a new computing environment for authoring mixed natural and computer language documents. In this environment a single hierarchically-organized plain text source file may contain a variety of elements such as code in arbitrary programming languages, raw data, links to external resources, project management data, working notes, and text for publication. Code fragments may be executed in situ with graphical, numerical and textual output captured or linked in the le. Export to LATEX, HTML, LATEX beamer, DocBook and other formats permits working reports, presentations and manuscripts for publication to be generated from the file. In addition, functioning pure code files can be automatically extracted from the file. This environment is implemented as an extension to the Emacs text editor and provides a rich set of features for authoring both prose and code, as well as sophisticated project management capabilities.

In science and especially in medicine, ebooks have become more and more important during the last years. Having a cooperation with the author of one of the leading books of internal medicine in Germany, the idea came up to publish his book in a version for PDA. As by now, there is no satisfying solution for this. The existing products are either made for belletristic or they have no sufficient copy protection or both. This led to the decision of creating an own software to meet market needs. The result of this process is SciReader (short form for "scientific ebook reader"), a software for the technique of the new millennium.

Wild harvesting has taken place over millennia in Africa. However urbanization and cash economies have effectively altered harvesting from being cultural, traditional, and subsistence activities that are part of a rural norm, to being a subculture of commonly illicit activities located primarily within the urban, cash-based, informal economy. This paper focuses on Cape Town, South Africa where high levels of poverty and extensive population growth have led to a rapidly growing informal industry based on the cultural, subsistence, and entrepreneurial harvesting and consumption of products obtained from the local natural environment. Through a process of literature reviews, database analysis, and key informant interviews, a compendium of harvested species was developed, illustrating the breadth of illicit harvesting of products from nature reserves, public open space, and other commonage within the City. The compendium records 448 locally occurring species (198 animals and 250 plants) that are extracted for medicinal, energy, ornamental, sustenance, nursery, and other uses. The sustainability of harvesting is questionable; nearly 70% of all harvested flora and 100% of all collected fauna are either killed or reproductively harmed through the harvesting processes. Furthermore, for the 183 indigenous flora species currently recorded on the International Union for Conservation of Nature (IUCN) Red List, 28% (51) hold assessments ranging from Declining through to Critically Endangered. With respect to the more poorly assessed fauna (46 spp.), approximately 24% (11) have Declining or Threatened status.