Strategies for Reducing Ruminant Methane Emissions

The paper studies the effect of additional administration of ultrafine particles on the cattle rumen microbiome composition. The in vitro method was used using the ANKOM Daisy II incubator according to a specialized method. Microflora analysis was performed using MiSeq (Illumina, USA) by a new generation sequencing method with a MiSeq reagent kit. After a detailed analysis of the structure and composition of the microbial community in the contents of the rumen sampled for different diets, it was found that no significant differences were observed in the bacterial communities, with the exception of a slight shift in the Bacteroidetes/Firmicutes ratio. However, we observed numerical differences in the abundance of some representatives, namely, with additional inclusion of Fe and Cr2O3, decrease in the abundance of the methane-forming species Methanobrevibacter, Methanobacterium, Methanosphaera, and Methnaomicrobium was noted regarding the control.

HOW ISO QUALITY MANAGEMENT STANDARDS CHANGE THE COMPANY LEVEL OF EXCELLENCE? STUDY CONDUCTED ON TWO COMPANIES OF POLISH DNA SEQUENCING INDUSTRY USING THE BUSINESS IMPROVEMENT MATRIX

This study examines the level of excellence of two companies, using Business Improvement Matrix (BIM), which is based on European Foundation of Quality Management’s Model of Excellence. It compares those organizations and shows how their quality management systems make an effect on BIM results. The researched companies are genXone S.A., which is in the process of implementing a quality management system compliant with ISO 13485: 2016, and Centrum Genetyki Medycznej GENESIS Sp. z o.o., certified with ISO 9001: 2015 since 2018. Both of them belong to sequencing industry in Poland, using new generation sequencing. This study shows that the company that has implemented its quality management system and has fully adopted its standards achieved a higher level of excellence than the company that just started the process of implementation of their quality management system.

RESEARCH OF THE MICROBIOM OF THE GASTROINTESTINAL TRACT OF THE ABERDIN-ANGUS BREED CATTLE

Целью исследования было определение таксономической структуры микробиома кишечника крупного рогатого скота породы Абердин-Ангус с помощью технологии секвенирования нового поколения. 16S метагеномный анализ, позволил определить микробный состав содержимого кишечника, минуя стадию культивирования на питательных средах. Проведена генетическая идентификация и получен таксономический профиль всех присутствующих бактерий, в том числе и некультивируемых форм. The aim of the study was to determine the taxonomic structure of the intestinal microbiome of Aberdeen Angus cattle using a new generation sequencing technology. 16S metagenomic analysis made it possible to determine the microbial composition of the intestinal contents bypassing the stage of cultivation on nutrient media. Genetic identification was carried out and a taxonomic profile of all bacteria present, including non-cultivated forms, was obtained. Key words: microbiome, cattle, Aberdeen Angus, next generation sequencing.

Complexity analysis of algorithms: A case study on bioinformatics tools

The data volume produced by the omic sciences nowadays was driven by the adoption of new generation sequencing platforms, popularly called NGS (Next Generation Sequencing). Among the analysis performed with this data, we can mention: mapping, genome assembly, genome annotation, pangenomic analysis, quality control, redundancy removal, among others. When it comes to redundancy removal analysis, it is worth noting the existence of several tools that perform this task, with proven accuracy through their scientific publications, but they lack criteria related to algorithmic complexity. Thus, this work aims to perform an algorithmic complexity analysis in computational tools for removing redundancy of raw reads from the DNA sequencing process, through empirical analysis. The analysis was performed with sixteen raw reads datasets. The datasets were processed with the following tools: MarDRe, NGSReadsTreatment, ParDRe, FastUniq, and BioSeqZip, and analyzed using the R statistical platform, through the GuessCompx package. The results demonstrate that the BioSeqZip and ParDRe tools present less complexity in this analysis

Sanger sequencing of SARS-CoV-2 Spike protein v1

The SARS-CoV-2 responsible for the ongoing COVID pandemic reveals particular evolutionary dynamics and an extensive polymorphism, mainly in Spike protein. Monitoring the S protein mutations is crucial for successful controlling measures and detect variants that can evade vaccine immunity. Even after the costs reduction imposed by the pandemic, the new generation sequencing methodologies remain unavailable to many scientific groups. Therefore, to support the urgent surveillance of SARS-CoV-2 S protein, this work describes a protocol for complete nucleotide sequencing of the S protein using the Sanger technique. Thus, any laboratory with experience in sequencing can adopt this protocol.

Characterization And Diversity of The Uterine Microbiota In Simmental And Simbrah Cows By Sequencing The V4 Region of The Gen rRNA-16s During An FTAI Protocol.

New generation sequencing techniques allow us to characterize the bacterial populations present in any organ or area. The knowledge of the uterine microbiota in bovines has grown in recent years as it has been shown that it influences fertility, however, there are very few studies in beef cattle. This work aims to contribute by generating information in beef cows, characterizing the uterine microbiome, determined by the sequencing of the hypervariate regions of gen 16S rRNA in samples obtained by the cytobrush technique in open cows prior to and during a standard synchronization, using an intravaginal device of progesterone, plus benzoate of estradiol and prostaglandins. The relative abundance in group I and II were very similar; Firmicutes, Proteobacteria, Bacteroidetes and Actinobacteria. Group III was Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria, and Fusobacteria, and Group IV, Proteobacteria, Firmicutes, Actinobacteria and Fusobacteria. The taxonomic composition in utero decreases throughout the synchronization protocol. There are internal and external factors that alter bacterial populations such as health status, hormones, pregnancy, medication administration, among others. To establish whether bacterial abundance has an influence on fertility, more robust studies are needed.

Multi-Technique Investigation of Grave Robes from 17th and 18th Century Crypts Using Combined Spectroscopic, Spectrometric Techniques, and New-Generation Sequencing

The textile fragments of the funeral clothes found in the 17th and 18th century crypts were subjected to spectroscopic, spectrometric, and microbial investigation. The next-generation sequencing enabled DNA identification of microorganisms at the genus and in five cases to the species level. The soft hydrofluoric acid extraction method was optimized to isolate different classes of dyes from samples that had direct contact with human remains. High-performance liquid chromatography coupled with diode matrix and tandem mass spectrometry detectors with electrospray ionization (HPLC-DAD-ESI-MS/MS) enabled the detection and identification of 34 colourants that are present in historical textiles. Some of them are thus far unknown and uncommon dyes. Indigo, madder, cochineal, turmeric, tannin-producing plant, and young fustic were identified as sources of dyes in textiles. Scanning electron microscopy with energy-dispersive X-ray detector (SEM-EDS) and Fourier transform infrared spectroscopy (FT-IR) were used to identify and characterize fibres and mordants in funeral gowns. Of the 23 textile samples tested, 19 were silk while the remaining four were recognized as wool. The presence of iron, aluminium, sodium, and calcium suggests that they were used as mordants. Traces of copper, silica, and magnesium might originate from the contaminants. The large amount of silver indicated the presence of metal wire in one of the dyed silk textiles. SEM images showed that textile fibres were highly degraded.

miRNAs of Aedes aegypti (Linnaeus 1762) conserved in six orders of the class Insecta

Aedesaegypti L. is the most important vector of arboviruses such as dengue, Zika, chikungunya, Mayaro, and yellow fever, which impact millions of people’s health per year. MicroRNA profile has been described in some mosquito species as being important for biological processes such as digestion of blood, oviposition, sexual differentiation, insecticide resistance, and pathogens dissemination. We identified the miRNAs of Ae.aegypti females, males and eggs of a reference insecticide susceptible strain New Orleans and compared them with those other insects to determine miRNA fingerprint by new-generation sequencing. The sequences were analyzed using data mining tools and categorization, followed by differential expression analysis and conservation with other insects. A total of 55 conserved miRNAs were identified, of which 34 were of holometabolous insects and 21 shared with hemimetabolous insects. Of these miRNAs, 32 had differential expression within the stages analyzed. Three predominant functions of miRNA were related to embryonic development regulation, metamorphosis, and basal functions. The findings of this research describe new information on Ae.aegypti physiology which could be useful for the development of new control strategies, particularly in mosquito development and metamorphosis processes.

Multilocus Sequence-Typing of Anthrax Microbe Strains Isolated in Russia and Neighboring Countries

Objective – genotyping by multilocus sequence-typing (MLST) and phylogenetic analysis of 40 Bacillus anthracis strains isolated in Russia and neighboring countries.Materials and methods. In this study, the sequences of seven housekeeping genes of B. anthracis strains were assembled based on the data of a whole genome new generation sequencing, after which the identified mutations and their coordinates were described. The obtained sequences were used for genotyping of the investigated sample using the MLST method. The results are compared with the data presented in PubMLST database. A phylogenetic analysis was performed for the in silico fused sequences of the seven loci of the identified sequence types. The MEGA 7.0 software package was used to build the dendrograms.Results and discussion. Two sequence types (ST) have been found in the examined sample: 35 strains belong to ST-1, and five strains that differed by one common mutation at the glpF locus – to ST-3 (according to PubMLST coding), which emphasizes the genetic separation of this group of strains. One strain has a unique mutation in the gmk gene located outside the region used for MLST.