Search results for "Sequencing"

Ultradeep Sequencing Analysis of Population Dynamics of Virus Escape Mutants in RNAi-Mediated Resistant Plants

2012

Plant artificial micro-RNAs (amiRs) have been engineered to target viral genomes and induce their degradation. However, the exceptional evolutionary plasticity of RNA viruses threatens the durability of the resistance conferred by these amiRs. It has recently been shown that viral populations not experiencing strong selective pressure from an antiviral amiR may already contain enough genetic variability in the target sequence to escape plant resistance in an almost deterministic manner. Furthermore, it has also been shown that viral populations exposed to subinhibitory concentrations of the antiviral amiR speed up this process. In this article, we have characterized the molecular evolutiona…

Human factor policy testing in the sequencing of manual mixed model assembly lines

2004

In this paper the human resource management in manual mixed model assembly U-lines is considered. The objective is to minimise the total conveyor stoppage time to achieve the full efficiency of the line. A model, that includes effects of the human resource, was developed in order to evaluate human factor policies impact on the optimal solution of this line sequencing problem. Different human resource management policies are introduced to cope with the particular layout of the proposed line. Several examples have been proposed to investigate the effects of line dimensions on the proposed management policies. The examples have been solved through a genetic algorithm. The obtained results conf…

Evaluation of a new pooling strategy based on leukocyte count for rapid quantification of allele frequencies.

2007

Abstract Background: Allele frequencies of single-nucleotide polymorphisms (SNPs) can be quantified from DNA pools. The conventional preparation of DNA pools requires DNA isolation and quantification for each blood sample. We hypothesized that pooling of whole blood samples according to their leukocyte count, which determines DNA content, would be as reliable as the conventional pooling method but much less tedious to perform. Methods: We collected 100 whole blood samples and measured the leukocyte count. Samples were frozen until further use. After thawing, pools were generated by combining aliquots containing an equal number of leukocytes. In parallel, DNA was extracted from another aliqu…

The structure and biosynthesis of heinamides A1-A3 and B1-B5, antifungal members of the laxaphycin lipopeptide family.

2021

Laxaphycins are a family of cyclic lipopeptides with synergistic antifungal and antiproliferative activities. They are produced by multiple cyanobacterial genera and comprise two sets of structurally unrelated 11- and 12-residue macrocyclic lipopeptides. Here, we report the discovery of new antifungal laxaphycins from Nostoc sp. UHCC 0702, which we name heinamides, through antimicrobial bioactivity screening. We characterized the chemical structures of eight heinamide structural variants A1-A3 and B1-B5. These variants contain the rare non-proteinogenic amino acids 3-hydroxy-4-methylproline, 4-hydroxyproline, 3-hydroxy-d-leucine, dehydrobutyrine, 5-hydroxyl beta-amino octanoic acid, and O-c…

Evaluación del valor diagnóstico y pronóstico de las alteraciones moleculares en la leucemia mieloide aguda de novo mediante el empleo de técnicas de…

2020

La leucemia mieloide aguda (LMA) es una enfermedad muy heterogénea desde el punto de vista biológico con numerosas alteraciones moleculares implicadas en su patogenia. El análisis simultáneo de estas alteraciones génicas es imprescindible para conocer los mecanismos de leucemogénesis y evaluar sus implicaciones clínicas de manera individualizada en cada paciente. Las técnicas de next generation sequencing (NGS) han demostrado ser una herramienta eficaz para el análisis integrado de la complejidad de las neoplasias mieloides, por ello, el objetivo de este estudio es realizar una validación técnica y clínica de un panel de NGS dirigida a genes o regiones recurrentemente mutados en la enfermed…

Stimulated and unstimulated saliva samples have significantly different bacterial profiles

2018

Epidemiological studies use saliva on a regular basis as a non-invasive and easy-to-take sample, which is assumed to be a microbial representative of the oral cavity ecosystem. However, comparative studies between different kinds of saliva samples normally used in microbial studies are scarce. The aim of the current study was to compare oral microbiota composition between two different saliva samples collected simultaneously: non-stimulated saliva with paper points and stimulated saliva collected after chewing paraffin gum. DNA was extracted from saliva samples of ten individuals, then analyzed by 16S rRNA pyrosequencing to describe bacterial diversity. The results demonstrate significant d…

Comparison of pulsed-field gel electrophoresis and whole-genome-sequencing-based typing confirms the accuracy of pulsed-field gel electrophoresis for…

2020

Summary Aim To determine whether pulsed-field gel electrophoresis (PFGE) accurately recognizes isolates belonging to clusters defined by techniques based on whole-genome sequencing (WGS) using Pseudomonas aeruginosa as a model. Methods We selected 65 isolates of ST395 P. aeruginosa isolated in seven European hospitals between 1998 and 2012. Isolates were typed by PFGE and sequenced by WGS. A core genome multi-locus sequence typing (cgMLST) analysis based on 3831 genes was performed with a homemade pipeline. Findings PFGE identified eight pulsotypes and cgMLST differentiated nine clusters and nine singletons. Five cgMLST clusters and pulsotypes (31/65 isolates) coincided perfectly. Isolates …

Evolution of molluscan hemocyanins as deduced from DNA sequencing

2004

Identification of Novel Anthracycline Resistance Genes and Their Inhibitors

2021

Differentially expressed genes have been previously identified by us in multidrug-resistant tumor cells mainly resistant to doxorubicin. In the present study, we exemplarily focused on some of these genes to investigate their causative relationship with drug resistance. HMOX1, NEIL2, and PRKCA were overexpressed by lentiviral-plasmid-based transfection of HEK293 cells. An in silico drug repurposing approach was applied using virtual screening and molecular docking of FDA-approved drugs to identify inhibitors of these new drug-resistant genes. Overexpression of the selected genes conferred resistance to doxorubicin and daunorubicin but not to vincristine, docetaxel, and cisplatin, indicating…

Archaea in boreal Swedish lakes are diverse, dominated by Woesearchaeota and follow deterministic community assembly

2020

Despite their key role in biogeochemical processes, particularly the methane cycle, archaea are widely underrepresented in molecular surveys because of their lower abundance compared to bacteria and eukaryotes. Here, we use parallel high‐resolution small subunit rRNA gene sequencing to explore archaeal diversity in 109 Swedish lakes and correlate archaeal community assembly mechanisms to large‐scale latitudinal, climatic (nemoral to arctic), and nutrient (oligotrophic to eutrophic) gradients. Sequencing with universal primers showed the contribution of archaea was on average 0.8% but increased up to 1.5% of the three domains in forest lakes. Archaea‐specific sequencing revealed that freshwa…