scholarly journals Rapid succession drives spring community dynamics of small protists at Helgoland Roads, North Sea

2020 ◽  
Vol 42 (3) ◽  
pp. 305-319 ◽  
Author(s):  
Laura Käse ◽  
Alexandra C Kraberg ◽  
Katja Metfies ◽  
Stefan Neuhaus ◽  
Pim A A Sprong ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Community Dynamics ◽  
Sampling Period ◽  
Next Generation ◽  
Helgoland Roads ◽  
Long Term Ecological Research ◽  
Eukaryotic Microbes ◽  
Five Phases ◽  
Generation Sequencing

Abstract The dynamics of diatoms and dinoflagellates have been monitored for many decades at the Helgoland Roads Long-Term Ecological Research site and are relatively well understood. In contrast, small-sized eukaryotic microbes and their community changes are still much more elusive, mainly due to their small size and uniform morphology, which makes them difficult to identify microscopically. By using next-generation sequencing, we wanted to shed light on the Helgoland planktonic community dynamics, including nano- and picoplankton, during a spring bloom. We took samples from March to May 2016 and sequenced the V4 region of the 18S rDNA. Our results showed that mixotrophic and heterotrophic taxa were more abundant than autotrophic diatoms. Dinoflagellates dominated the sequence assemblage, and several small-sized eukaryotic microbes like Haptophyta, Choanoflagellata, Marine Stramenopiles and Syndiniales were identified. A diverse background community including taxa from all size classes was present during the whole sampling period. Five phases with several communities were distinguished. The fastest changes in community composition took place in phase 3, while the communities from phases 1 to 5 were more similar to each other despite contrasting environmental conditions. Synergy effects of next-generation sequencing and traditional methods may be exploited in future long-term observations.

scholarly journals Next Generation Sequencing Discoveries of the Nitrate-Responsive Oral Microbiome and Its Effect on Vascular Responses

2019 ◽  
Vol 8 (8) ◽  
pp. 1110 ◽  
Author(s):  
Melissa M. Grant ◽  
Daniel Jönsson
Keyword(s):  
Nitric Oxide ◽  
Next Generation Sequencing ◽  
Human Condition ◽  
Oral Microbiome ◽  
Oral Microbiota ◽  
Next Generation ◽  
Contributing Factors ◽  
Future Directions ◽  
Generation Sequencing

Cardiovascular disease is a worldwide human condition which has multiple underlying contributing factors: one of these is long-term increased blood pressure—hypertension. Nitric oxide (NO) is a small nitrogenous radical species that has a number of physiological functions including vasodilation. It can be produced enzymatically through host nitric oxide synthases and by an alternative nitrate–nitrite–NO pathway from ingested inorganic nitrate. It was discovered that this route relies on the ability of the oral microbiota to reduce nitrate to nitrite and NO. Next generation sequencing has been used over the past two decades to gain deeper insight into the microbes involved, their location and the effect of their removal from the oral cavity. This review article presents this research and comments briefly on future directions.

scholarly journals Correlation of Long-term Results of Imatinib in Advanced Gastrointestinal Stromal Tumors With Next-Generation Sequencing Results

JAMA Oncology ◽  
2017 ◽  
Vol 3 (7) ◽  
pp. 944 ◽  
Author(s):  
Michael C. Heinrich ◽  
Cathryn Rankin ◽  
Charles D. Blanke ◽  
George D. Demetri ◽  
Ernest C. Borden ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Gastrointestinal Stromal Tumors ◽  
Long Term Results ◽  
Next Generation ◽  
Stromal Tumors ◽  
Generation Sequencing

scholarly journals Case Report: Metagenomics Next-Generation Sequencing Can Help Define the Best Therapeutic Strategy for Brain Abscesses Caused by Oral Pathogens

2021 ◽  
Vol 8 ◽  
Author(s):  
Zhonghui Ma ◽  
Su Yan ◽  
Haoxin Dong ◽  
Huifen Wang ◽  
Yonggang Luo ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Brain Abscess ◽  
Genomic Analysis ◽  
Critical Factor ◽  
Oral Microbiome ◽  
Next Generation ◽  
Gram Staining ◽  
Brain Abscesses ◽  
Generation Sequencing

Brain abscesses are associated with an increased long-term risk of new seizures and increased mortality within several years after infection. Common microorganisms that cause brain abscesses include bacteria, fungi, and mycoplasma. We report a 75-year-old man with a brain abscess caused by Prevotella denticola, an oral pathogen. Based on the clinical condition, we suspected that the patient had a blood-borne brain abscess, and he received antibiotics and systemic supportive treatment. The patient developed shock for the second time after negative Gram-staining results. Metagenomics next-generation sequencing showed one strain from the oral microbiome, confirming our hypothesis, and targeted antibiotic treatment was administered quickly. Thus, we report a case in which genomic analysis was the critical factor in determining the best antimicrobial therapy for administration.

scholarly journals Next‐Generation Sequencing Reveals Differential Responses to Acute versus Long‐Term Exposures to Graphene Oxide in Human Lung Cells

Small ◽  
2020 ◽  
Vol 16 (21) ◽  
pp. 1907686 ◽  
Author(s):  
Sourav P. Mukherjee ◽  
Govind Gupta ◽  
Katharina Klöditz ◽  
Jun Wang ◽  
Artur Filipe Rodrigues ◽  
...  
Keyword(s):  
Graphene Oxide ◽  
Next Generation Sequencing ◽  
Human Lung ◽  
Lung Cells ◽  
Next Generation ◽  
Human Lung Cells ◽  
Differential Responses ◽  
Generation Sequencing

scholarly journals Molecular Study of Long-Term Survivors of Glioblastoma by Gene-Targeted Next-Generation Sequencing

2018 ◽  
Vol 77 (8) ◽  
pp. 710-716 ◽  
Author(s):  
Diana Cantero ◽  
Ángel Rodríguez de Lope ◽  
Raquel Moreno de la Presa ◽  
Juan M Sepúlveda ◽  
José M Borrás ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Molecular Study ◽  
Next Generation ◽  
Targeted Next Generation Sequencing ◽  
Long Term Survivors ◽  
Generation Sequencing

Hepatitis B virus resistance substitutions: long-term analysis by next-generation sequencing

2016 ◽  
Vol 161 (10) ◽  
pp. 2885-2891 ◽  
Author(s):  
Leandro R. Jones ◽  
Mariano Sede ◽  
Julieta M. Manrique ◽  
Jorge Quarleri
Keyword(s):  
Next Generation Sequencing ◽  
Hepatitis B Virus ◽  
Hepatitis B ◽  
Virus Resistance ◽  
Next Generation ◽  
B Virus ◽  
Term Analysis ◽  
Generation Sequencing

scholarly journals Next-generation sequencing-based molecular genetic profiling in adults with acute myeloid leukaemia

2020 ◽  
Vol 65 (4) ◽  
pp. 444-459
Author(s):  
A. I. Kashlakova ◽  
E. N. Parovichnikova ◽  
B. V. Biderman ◽  
Y. V. Sidorova ◽  
Y. A. Chabaeva ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Acute Myeloid Leukaemia ◽  
Myeloid Leukaemia ◽  
Molecular Genetic ◽  
Driver Mutations ◽  
Next Generation ◽  
Old Patients ◽  
Generation Sequencing ◽  
Acute Myeloid

Introduction. Acute myeloid leukaemia (AML) is associated with multiple driver mutations, which prognostic value remains understudied.Aim. Assessment of the frequency of mutations in various genes and their impact on acute myeloid leukaemia outcome in adults.Materials and methods. The study included 90 adult patients with newly diagnosed AML; 76 were aged under 60, 14 were 60 and more years old. Patients under 60 had chemotherapy (CT) “7+3” as induction, the elder cohort had variant low-dose CT with hypomethylating agents. The molecular genetic status of patients was determined using next-generation sequencing; the in-house gene panel included ASXL1, BCOR, DNMT3, FLT3, IDH1, IDH2, PIGA, RUNX1, SETBP1, SF3B1, SRSF2, TET2, TP53 and U2AF2.Results. Nucleotide substitutions were identified in genes DNMT3, TET2, TP53, SETBP1, BCOR, RUNX1, IDH2, IDH1, FLT3, U2AF2, SF3B1 in 57.8 % of the patients (n = 52), with 17.8 % (n = 16) having compound mutations in two or three genes. Treatment efficacy and long-term outcomes were assessed against age, ELN-2017 risk groups and mutations in genes TP53, RUNX1, IDH1, IDH2 and DNMT3. In the long term, a reliable variation was revealed in the overall survival (OS) rate with respect to mutations in genes TP53 and RUNX1. Patients with mutant TP53 had 30 % OS, those with the intact gene — 53.4 % (p = 0.0037). Similar results were obtained with RUNX1: mutations marked 20 % OS, intact patients had 54% OS (p = 0.0466).Conclusion. Mutations in genes FLT3-ITD, NPM1 and CEBPA are proxy to AML. However, a more accurate prognosis and optimal choice of therapy require detailed molecular profiling due to genetic heterogeneity of AML patients.

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