scholarly journals HIGH-THROUGHPUT SEQUENCING ANALYSIS OF MICROBIAL POPULATIONS IN ARCTIC ROCK SAMPLE

2019 ◽  
Vol 1 (2) ◽  
pp. 29-38
Author(s):  
Piyush Kumar Gupta ◽  
Rama Shanker Verma ◽  
Maria Frolova ◽  
Arkady Ayzenshtadt
Keyword(s):  
Microbial Diversity ◽  
Human Health ◽  
High Throughput ◽  
Raw Material ◽  
Severe Toxicity ◽  
Sequencing Analysis ◽  
Dependent Manner ◽  
Taxonomic Level ◽  
Microbial Species ◽  
Metagenomic Study

Recent developments in the existing molecular genetic tools have augmented our current understanding towards the deleterious effects of nanoparticles on human health. During building construction, the rapid generation of nanoparticles has greatly affected to human with severe toxicity by generating free radicals inside their body as potential health hazards. However, there is still need of analyzing nanoparticle toxicity based on the type of microbial diversity present on surface and its potential impacts on human health. In this study, we used rocks as raw material collected from Arkhangelsk (arctic) region of Russia and fabricated into particles of nanometer range in size by planetary ball milling. The paper presents data of the elemental composition on the basis of which the value of the specific mass energy of atomization of the raw material of the rock was calculated. The energy parameters of the micro- and nanosystems of the sample were calculated: free surface energy and surface activity. These nanoparticles were showing minimal cytotoxicity to human embryonic kidney cells in a dose-dependent manner. The high-throughput next-generation sequencing (NGS) was used to perform 16S rRNA metagenomic study for determining the type of microbial diversity present on nanoparticle’s surface. The first highest abundance was found for actinobacteria at phylum taxonomic level indicating a population of gram + ve bacteria having economic importance to human. The second highest abundance was seen for proteobacteria at similar taxonomic level exhibiting population of gram - ve bacteria causing pathogenicity in human. The highest abundance of top 25 microbial species was also discussed in this study. In future, this metagenomic study will also identify other microbial species based on 18S rRNA sequencing.

scholarly journals Statistical models and computational algorithms for discovering relationships in microbiome data

2017 ◽  
Vol 16 (1) ◽  
pp. 1-12
Author(s):  
Mateen R. Shaikh ◽  
Joseph Beyene
Keyword(s):  
Human Health ◽  
High Throughput ◽  
Statistical Models ◽  
Computational Algorithms ◽  
Data Sets ◽  
Taxonomic Level ◽  
High Throughput Technology ◽  
Stool Samples ◽  
Microbiome Data ◽  
Human Stool

AbstractMicrobiomes, populations of microscopic organisms, have been found to be related to human health and it is expected further investigations will lead to novel perspectives of disease. The data used to analyze microbiomes is one of the newest types (the result of high-throughput technology) and the means to analyze these data is still rapidly evolving. One of the distributions that have been introduced into the microbiome literature, the Dirichlet-Multinomial, has received considerable attention. We extend this distribution’s use uncover compositional relationships between organisms at a taxonomic level. We apply our new method in two real microbiome data sets: one from human nasal passages and another from human stool samples.

PEAS AND PRODUCTS OF ITS PROCESSING OF - NONCONVENTIONAL RAW MATERIAL RESOURCES

2020 ◽  
Author(s):  
D.Y. Bolgova ◽  
◽  
N.A. Tarasenko ◽  
Z.S. Mukhametova ◽  
◽  
...  
Keyword(s):  
Chemical Composition ◽  
Human Health ◽  
Food Production ◽  
Food Industry ◽  
Raw Material ◽  
Plant Proteins ◽  
Material Resources ◽  
The Rich

Nutrition is an important factor that affects human health. The use of plant proteins as various additives in food production has now been actively developed. The rich chemical composition of pea grains determines the possibility of application in the food industry. Peas are characterized by good assimilability and degree of digestion.

scholarly journals Repurposing cabozantinib with therapeutic potential in KIT-driven t(8;21) acute myeloid leukaemias

2021 ◽  
Author(s):  
Kuan-Wei Su ◽  
Da-Liang Ou ◽  
Yu-Hsuan Fu ◽  
Hwei-Fang Tien ◽  
Hsin-An Hou ◽  
...  
Keyword(s):  
Tyrosine Kinase ◽  
Ribosome Biogenesis ◽  
Kinase Inhibitor ◽  
Therapeutic Potential ◽  
Xenograft Model ◽  
Sequencing Analysis ◽  
Dependent Manner ◽  
Leukocyte Activation ◽  
Mouse Xenograft Model ◽  
Acute Myeloid

AbstractCabozantinib is an orally available, multi-target tyrosine kinase inhibitor approved for the treatment of several solid tumours and known to inhibit KIT tyrosine kinase. In acute myeloid leukaemia (AML), aberrant KIT tyrosine kinase often coexists with t(8;21) to drive leukaemogenesis. Here we evaluated the potential therapeutic effect of cabozantinib on a selected AML subtype characterised by t(8;21) coupled with KIT mutation. Cabozantinib exerted substantial cytotoxicity in Kasumi-1 cells with an IC50 of 88.06 ± 4.32 nM, which was well within clinically achievable plasma levels. The suppression of KIT phosphorylation and its downstream signals, including AKT/mTOR, STAT3, and ERK1/2, was elicited by cabozantinib treatment and associated with subsequent alterations of cell cycle- and apoptosis-related molecules. Cabozantinib also disrupted the synthesis of an AML1-ETO fusion protein in a dose- and time-dependent manner. In a mouse xenograft model, cabozantinib suppressed tumourigenesis at 10 mg/kg and significantly prolonged survival of the mice. Further RNA-sequencing analysis revealed that mTOR-mediated signalling pathways were substantially inactivated by cabozantinib treatment, causing the downregulation of ribosome biogenesis and glycolysis, along with myeloid leukocyte activation. We suggest that cabozantinib may be effective in the treatment of AML with t(8;21) and KIT mutation. Relevant clinical trials are warranted.

scholarly journals Environmental Sequencing Provides Reasonable Estimates of the Relative Abundance of Specific Picoeukaryotes

2016 ◽  
Vol 82 (15) ◽  
pp. 4757-4766 ◽  
Author(s):  
Caterina R. Giner ◽  
Irene Forn ◽  
Sarah Romac ◽  
Ramiro Logares ◽  
Colomban de Vargas ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
High Throughput ◽  
Relative Abundance ◽  
Ribosomal Dna ◽  
18S Rdna ◽  
High Throughput Sequencing ◽  
454 Sequencing ◽  
Epifluorescence Microscopy ◽  
Environmental Sequencing

ABSTRACTHigh-throughput sequencing (HTS) is revolutionizing environmental surveys of microbial diversity in the three domains of life by providing detailed information on which taxa are present in microbial assemblages. However, it is still unclear how the relative abundance of specific taxa gathered by HTS correlates with cell abundances. Here, we quantified the relative cell abundance of 6 picoeukaryotic taxa in 13 planktonic samples from 6 European coastal sites using epifluorescence microscopy on tyramide signal amplification-fluorescencein situhybridization preparations. These relative abundance values were then compared with HTS data obtained in three separate molecular surveys: 454 sequencing of the V4 region of the 18S ribosomal DNA (rDNA) using DNA and RNA extracts (DNA-V4 and cDNA-V4) and Illumina sequencing of the V9 region (cDNA-V9). The microscopic and molecular signals were generally correlated, indicating that a relative increase in specific 18S rDNA was the result of a large proportion of cells in the given taxa. Despite these positive correlations, the slopes often deviated from 1, precluding a direct translation of sequences to cells. Our data highlighted clear differences depending on the nucleic acid template or the 18S rDNA region targeted. Thus, the molecular signal obtained using cDNA templates was always closer to relative cell abundances, while the V4 and V9 regions gave better results depending on the taxa. Our data support the quantitative use of HTS data but warn about considering it as a direct proxy of cell abundances.IMPORTANCEDirect studies on marine picoeukaryotes by epifluorescence microscopy are problematic due to the lack of morphological features and due to the limited number and poor resolution of specific phylogenetic probes used in fluorescencein situhybridization (FISH) routines. As a consequence, there is an increasing use of molecular methods, including high-throughput sequencing (HTS), to study marine microbial diversity. HTS can provide a detailed picture of the taxa present in a community and can reveal diversity not evident using other methods, but it is still unclear what the meaning of the sequence abundance in a given taxon is. Our aim is to investigate the correspondence between the relative HTS signal and relative cell abundances in selected picoeukaryotic taxa. Environmental sequencing provides reasonable estimates of the relative abundance of specific taxa. Better results are obtained when using RNA extracts as the templates, while the region of 18S ribosomal DNA had different influences depending on the taxa assayed.

scholarly journals High-Throughput Sequencing Analysis of the Actinobacterial Spatial Diversity in Moonmilk Deposits

Antibiotics ◽  
2018 ◽  
Vol 7 (2) ◽  
pp. 27 ◽  
Author(s):  
Marta Maciejewska ◽  
Magdalena Całusińska ◽  
Luc Cornet ◽  
Delphine Adam ◽  
Igor Pessi ◽  
...  
Keyword(s):  
High Throughput ◽  
High Throughput Sequencing ◽  
Spatial Diversity ◽  
Sequencing Analysis

scholarly journals Spatiotemporal dynamics of OCT4 protein localization during preimplantation development in mice

Reproduction ◽  
2016 ◽  
Vol 152 (5) ◽  
pp. 417-430 ◽  
Author(s):  
Atsushi Fukuda ◽  
Atsushi Mitani ◽  
Toshiyuki Miyashita ◽  
Hisato Kobayashi ◽  
Akihiro Umezawa ◽  
...  
Keyword(s):  
Nuclear Localization ◽  
Splice Variants ◽  
Protein Localization ◽  
Preimplantation Development ◽  
Preimplantation Embryos ◽  
Sequencing Analysis ◽  
Dependent Manner ◽  
Cell Stage ◽  
Protein Levels ◽  
Oct4 Protein

Spatiotemporal expression of transcription factors is crucial for genomic reprogramming. Pou5f1 (Oct4) is an essential transcription factor for reprogramming. A recent study reported that OCT4A, which is crucial for establishment and maintenance of pluripotent cells, is expressed in oocytes, but maternal OCT4A is dispensable for totipotency induction. Whereas another study reported that OCT4B, which is not related to pluripotency, is predominantly expressed instead of OCT4A during early preimplantation phases in mice. To determine the expression states of OCT4 in murine preimplantation embryos, we conducted in-depth expression and functional analyses. We found that pluripotency-related OCT4 mainly localizes to the cytoplasm in early preimplantation phases, with no major nuclear localization until the 8–16-cell stage despite high expression in both oocytes and early embryos. RNA-sequencing analysis using oocytes and early preimplantation embryos could not identify the splice variants creating alternative forms of OCT4 protein. Forced expression of OCT4 in zygotes by the injection of polyadenylated mRNA clearly showed nuclear localization of OCT4 protein around 3–5-fold greater than physiological levels and impaired developmental competency in a dose-dependent manner. Embryos with modest overexpression of OCT4 could develop to the 16-cell stage; however, more than 50% of the embryos were arrested at this stage, similar to the results for OCT4 depletion. In contrast, extensive overexpression of OCT4 resulted in complete arrest at the 2-cell stage accompanied by downregulation of zygotically activated genes and repetitive elements related to the totipotent state. These results demonstrated that OCT4 protein localization was spatiotemporally altered during preimplantation development, and strict control of Oct4 protein levels was essential for proper totipotential reprogramming.

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