MGcount: a total RNA-seq quantification tool to address multi-mapping and multi-overlapping alignments ambiguity in non-coding transcripts

Background Total-RNA sequencing (total-RNA-seq) allows the simultaneous study of both the coding and the non-coding transcriptome. Yet, computational pipelines have traditionally focused on particular biotypes, making assumptions that are not fullfilled by total-RNA-seq datasets. Transcripts from distinct RNA biotypes vary in length, biogenesis, and function, can overlap in a genomic region, and may be present in the genome with a high copy number. Consequently, reads from total-RNA-seq libraries may cause ambiguous genomic alignments, demanding for flexible quantification approaches. Results Here we present Multi-Graph count (MGcount), a total-RNA-seq quantification tool combining two strategies for handling ambiguous alignments. First, MGcount assigns reads hierarchically to small-RNA and long-RNA features to account for length disparity when transcripts overlap in the same genomic position. Next, MGcount aggregates RNA products with similar sequences where reads systematically multi-map using a graph-based approach. MGcount outputs a transcriptomic count matrix compatible with RNA-sequencing downstream analysis pipelines, with both bulk and single-cell resolution, and the graphs that model repeated transcript structures for different biotypes. The software can be used as a python module or as a single-file executable program. Conclusions MGcount is a flexible total-RNA-seq quantification tool that successfully integrates reads that align to multiple genomic locations or that overlap with multiple gene features. Its approach is suitable for the simultaneous estimation of protein-coding, long non-coding and small non-coding transcript concentration, in both precursor and processed forms. Both source code and compiled software are available at https://github.com/hitaandrea/MGcount.

Spectropolarimetry as a tool for understanding the diversity of planetary atmospheres

The polarization state of starlight reflected by a planetary atmosphere uniquely reveals coverage, particle size, and composition of aerosols as well as changing cloud patterns. It is not possible to obtain a comparable level of detail from flux-only observations. It is therefore a powerful tool to better understand the crucial role played by clouds and aerosols in the chemistry, dynamics, and radiative balance of a planet. Furthermore, polarization observations can probe the atmosphere of planets independently of the orbital geometry (hence it applies to both transiting and non-transiting exoplanets). A high-resolution spectropolarimeter with a broad wavelength coverage, particularly if attached to a large space telescope, would enable simultaneous study of the polarimetric planetary properties of the continuum and to look for and characterize the polarimetric signal due to scattering from single molecules, providing detailed information about the composition and vertical structure of the atmosphere.

Utilizing high-p⊥ theory and data to constrain the initial stages of quark-gluon plasma

The scarce knowledge of the initial stages of quark-gluon plasma before the thermalization is mostly inferred through the low-[Formula: see text] sector. We propose a complementary approach in this report — the use of high-[Formula: see text] probes’ energy loss. We study the effects of four commonly assumed initial stages, whose temperature profiles differ only before the thermalization, on high-[Formula: see text][Formula: see text] and [Formula: see text] predictions. The predictions are based on our Dynamical Radiative and Elastic ENergy-loss Approach (DREENA) framework. We report insensitivity of [Formula: see text] to the initial stages, making it unable to distinguish between different cases. [Formula: see text] displays sensitivity to the presumed initial stages, but current experimental precision does not allow resolution between these cases. We further revise the commonly accepted procedure of fitting the energy loss parameters, for each individual initial stage, to the measured [Formula: see text]. We show that the sensitivity of [Formula: see text] to various initial stages obtained through such procedure is mostly a consequence of fitting procedure, which may obscure the physical interpretations. Overall, the simultaneous study of high-[Formula: see text] observables, with unchanged energy loss parametrization and restrained temperature profiles, is crucial for future constraints on initial stages.

Bacterial, phytoplankton, and viral dynamics of meromictic Lake Cadagno offer insights into the Proterozoic ocean microbial loop

Meromictic Lake Cadagno, with its permanent stratification and persistent microbial bloom within the anoxic chemocline, serves as an ancient ocean analogue. Although the lake has been studied for over 25 years, the absence of simultaneous study of the bacteria, phytoplankton, and viruses, together with primary and secondary productivity, has hindered a comprehensive understanding of its microbial food web. This study evaluated the identities, abundances, and productivity of microbes in the context of nutrient biogeochemical cycling across the stratified depths of Lake Cadagno. Photosynthetic pigments and chloroplast 16S rRNA gene phylogenies suggested high abundances of eukaryotic phytoplankton, primarily Chlorophyta, through the water column. Of these, a close relative of Ankyra judayi, a high-alpine adapted chlorophyte, peaked with oxygen in the mixolimnion, while Closteriopsis-related chlorophytes peaked in the chemocline and monimolimnion. Chromatium, a genus of anoxygenic phototrophic sulfur bacteria, dominated the chemocline along with Lentimicrobium, a genus of known fermenters whose abundance was newly reported in Lake Cadagno. Secondary production peaked in the chemocline, suggesting anoxygenic primary producers depended on heterotrophic nutrient remineralization. Virus-to-microbe ratios (VMR) peaked in the zone of high phytoplankton abundances, yet were at a minimum at the peak of Chromatium, dynamic trends that suggest viruses may play a role in the modulation of oxygenic and anoxygenic photo- and chemosynthesis in Lake Cadagno. Through the combined analysis of bacterial, eukaryotic, viral, and biogeochemical dynamics of Lake Cadagno, this study provides a new perspective on the biological and geochemical connections that comprised the food webs of the Proterozoic ocean.

“Lesões de células gigantes” dos maxilares: possibilidades e limitações do diagnóstico histológico

The authors studied the «giant cell lesions» calling attention for the necessity of submit X rays and a good clinic history to the patologist. They believe not in the diferencial diagnosis, in histologic level, between giant cell reparative granuloma and Done manifestations of hyperparatireoidism. In such cases blood chemistry has the last word. They believe in the histologic identification of the true giant cell tumor. Also in the histologic identification of cherubism, but consider easy in this case, the simultaneous study of the x rays and clinical history.

The use of interactive methods in teaching the Russian language in technical universities of Kazakhstan

The relevance of the research is determined by the introduction of the CLIL trilingual system, which includes a simultaneous study of Russian, Kazakh, and English in accordance with the language policy of Kazakhstan. The research is based upon the authors’ own pedagogical experience, official law documents, and state guidelines regarding the language policy in Kazakhstan, and the analysis of the scientific literature on the matter. The paper reveals the features of the educational system of Kazakhstan as the result of recent state policy changes: orientation towards European standards, foreign language learning for professional communication as a priority, the digitalization of education, and its practical focus.

The relationship between the simultaneity present of cagA and hopQI genes in Helicobacter pylori and the risk of gastric cancer

Helicobacter pylori is a bacterium that causes infections in the gastrointestinal tract. This type of bacterium is very common and contagious at the same time. H. pylori enters the mouth and continues its course along the gastrointestinal tract. H. pylori infection induces an inflammatory response that leads to the activity of neutrophils, lymphocytes, plasma cells, and macrophages. In addition to the bacterial role in gastric mucosa, the host's inflammatory response may also play a role in disease outcome. In inflammation, the risk of carcinogenesis increases due to DNA damage increased proliferation and the creation of an environment rich in cytokines and growth factors. Genetic methods and diagnosis of H. pylori genes are used to identify healthy and healthy gastric cancer patients infected with H. pylori. In relation to the genes associated with H. pylori pathogenesis, the presence of genes such as cagA, hopQI, hopQII and so on is used, and PCR of a part of these genes amplified fragments of different lengths. One of the less-studied cases is the association of two or more pathogenic genes simultaneously with H. pylori. In this research, the frequency of disease and healthy individuals who are infected with H. pylori and have two genotypes cagA and hopQI at the same time, was examined. In order to diagnose H. pylori-infected individuals in healthy and gastric cancer patients, after PCR of glmM gene, PCR product electrophoresis on agarose gel was used. For this purpose, gastric tissue biopsy was used in patients and saliva was used in healthy individuals. For this purpose, 100 gastric biopsy samples were collected from patients with gastric cancer and 100 saliva samples from healthy individuals. According to the data, there is a significant relationship between the simultaneous presence of two genes cagA and hopQI and gastric cancer. In patients, 45.3% showed both genotypes, while in healthy individuals only 10.5% have this genotype and other healthy but infected with H. pylori (90.8%) do not have this genotype. To be. No report was observed on the simultaneous study of cagA and hopQI genes. No report was observed regarding the simultaneous study of cagA and hopQI genes.

Integrating multi-taxon palaeogenomes and sedimentary ancient DNA to study past ecosystem dynamics

Ancient DNA (aDNA) has played a major role in our understanding of the past. Important advances in the sequencing and analysis of aDNA from a range of organisms have enabled a detailed understanding of processes such as past demography, introgression, domestication, adaptation and speciation. However, to date and with the notable exception of microbiomes and sediments, most aDNA studies have focused on single taxa or taxonomic groups, making the study of changes at the community level challenging. This is rather surprising because current sequencing and analytical approaches allow us to obtain and analyse aDNA from multiple source materials. When combined, these data can enable the simultaneous study of multiple taxa through space and time, and could thus provide a more comprehensive understanding of ecosystem-wide changes. It is therefore timely to develop an integrative approach to aDNA studies by combining data from multiple taxa and substrates. In this review, we discuss the various applications, associated challenges and future prospects of such an approach.