scholarly journals Finally, Bulk Typing of Bacterial Species down to Strain Level using ON-rep-seq

2018 ◽  
Author(s):  
Łukasz Krych ◽  
Josué L. Castro-Mejía ◽  
Daniel N. Moesby ◽  
Morten B. Mikkelsen ◽  
Morten A. Rasmussen ◽  
...  
Keyword(s):  
High Speed ◽  
Bacterial Species ◽  
Cost Effective ◽  
Species Level ◽  
Strain Level ◽  
Read Length ◽  
High Quality ◽  
Sequencing Platform ◽  
Culture Independent ◽  
Single Flow

AbstractDespite the massive developments within culture-independent methods for detection and quantification of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (< 24h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation takes less than 5h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting the random error of reads within peaks of LCp generates a set (∼10 contigs per sample; 300bp - 3Kb) of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation. With benchmarked 288 isolates identified on a single flow cell and a theoretical throughput to evaluate over 1000 isolates, our method allows for detailed bacterial identification for less than 2$ per sample at very high speed.

scholarly journals DNA enrichment and tagmentation method for species-level identification and strain-level differentiation using ON-rep-seq

2019 ◽  
Vol 2 (1) ◽  
Author(s):  
Łukasz Krych ◽  
Josué L. Castro-Mejía ◽  
Laura M. Forero-Junco ◽  
Daniel N. Moesby ◽  
Morten B. Mikkelsen ◽  
...  
Keyword(s):  
Cost Effective ◽  
Species Level ◽  
Strain Level ◽  
Read Length ◽  
High Quality ◽  
Bacterial Dna ◽  
Sequencing Platform ◽  
Dna Library ◽  
Culture Independent ◽  
Level Identification

Abstract Despite the massive developments within culture-independent methods for detection of microorganisms during the last decade, culture-based methods remain a cornerstone in microbiology. Yet, the problem of rapid, accurate and inexpensive identification of bacterial isolates down to species/strain level remains unresolved. We have developed a new method for bacterial DNA enrichment and tagmentation allowing fast (<24 h) and cost-effective species level identification and strain level differentiation using the MinION portable sequencing platform (ON-rep-seq). DNA library preparation for 96 isolates takes less than 5 h and ensures highly reproducible distribution of reads that can be used to generate strain level specific read length counts profiles (LCp). We have developed a pipeline that by correcting reads error within peaks of LCp generates a set of high quality (>99%) consensus reads. Whereas, the information from high quality reads is used to retrieve species level taxonomy, comparison of LCp allows for strain level differentiation.

scholarly journals 2D-3D integration of hexagonal boron nitride and a high-κ dielectric for ultrafast graphene-based electro-absorption modulators

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hitesh Agarwal ◽  
Bernat Terrés ◽  
Lorenzo Orsini ◽  
Alberto Montanaro ◽  
Vito Sorianello ◽  
...  
Keyword(s):  
Boron Nitride ◽  
Hafnium Oxide ◽  
High Speed ◽  
Hexagonal Boron Nitride ◽  
Temperature Stability ◽  
Cost Effective ◽  
Fold Increase ◽  
Building Blocks ◽  
High Quality ◽  
New Device

AbstractElectro-absorption (EA) waveguide-coupled modulators are essential building blocks for on-chip optical communications. Compared to state-of-the-art silicon (Si) devices, graphene-based EA modulators promise smaller footprints, larger temperature stability, cost-effective integration and high speeds. However, combining high speed and large modulation efficiencies in a single graphene-based device has remained elusive so far. In this work, we overcome this fundamental trade-off by demonstrating the 2D-3D dielectric integration in a high-quality encapsulated graphene device. We integrated hafnium oxide (HfO2) and two-dimensional hexagonal boron nitride (hBN) within the insulating section of a double-layer (DL) graphene EA modulator. This combination of materials allows for a high-quality modulator device with high performances: a ~39 GHz bandwidth (BW) with a three-fold increase in modulation efficiency compared to previously reported high-speed modulators. This 2D-3D dielectric integration paves the way to a plethora of electronic and opto-electronic devices with enhanced performance and stability, while expanding the freedom for new device designs.

Dynamic Meta-Storms enables comprehensive taxonomic and phylogenetic comparison of shotgun metagenomes at the species level

2019 ◽  
Vol 36 (7) ◽  
pp. 2308-2310
Author(s):  
Gongchao Jing ◽  
Yufeng Zhang ◽  
Ming Yang ◽  
Lu Liu ◽  
Jian Xu ◽  
...  
Keyword(s):  
Beta Diversity ◽  
High Speed ◽  
Bacterial Species ◽  
Evolutionary Relationship ◽  
Pairwise Comparison ◽  
Species Level ◽  
Pairwise Distance ◽  
Supplementary Information ◽  
Phylogenic Tree ◽  
Diversity Pattern

Abstract Motivation An accurate and reliable distance (or dissimilarity) among shotgun metagenomes is fundamental to deducing the beta-diversity of microbiomes. To compute the distance at the species level, current methods either ignore the evolutionary relationship among species or fail to account for unclassified organisms that cannot be mapped to definite tip nodes in the phylogenic tree, thus can produce erroneous beta-diversity pattern. Results To solve these problems, we propose the Dynamic Meta-Storms (DMS) algorithm to enable the comprehensive comparison of metagenomes on the species level with both taxonomy and phylogeny profiles. It compares the identified species of metagenomes with phylogeny, and then dynamically places the unclassified species to the virtual nodes of the phylogeny tree via their higher-level taxonomy information. Its high speed and low memory consumption enable pairwise comparison of 100 000 metagenomes (synthesized from 3688 bacteria) within 6.4 h on a single computing node. Availability and implementation An optimized implementation of DMS is available on GitHub (https://github.com/qibebt-bioinfo/dynamic-meta-storms) under a GNU GPL license. It takes the species-level profiles of metagenomes as input, and generates their pairwise distance matrix. The bacterial species-level phylogeny tree and taxonomy information of MetaPhlAn2 have been integrated into this implementation, while customized tree and taxonomy are also supported. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals 2D-3D integration of hBN and a high-κ dielectric for ultrafast graphene-based electro-absorption modulators

2020 ◽  
Author(s):  
Hitesh Agarwal ◽  
Bernat Terrés ◽  
Lorenzo Orsini ◽  
Alberto Montanaro ◽  
Vito Sorianello ◽  
...  
Keyword(s):  
Hafnium Oxide ◽  
High Speed ◽  
Hexagonal Boron Nitride ◽  
Temperature Stability ◽  
Cost Effective ◽  
Fold Increase ◽  
Building Blocks ◽  
3D Integration ◽  
High Quality ◽  
New Device

Abstract Electro-absorption (EA) waveguide-coupled modulators are essential building blocks for on-chip optical communications. Compared to state-of-the-art silicon (Si) devices, graphene based EA modulators promise smaller footprints, larger temperature stability, cost-effective integration and high speeds. However, combining high speed and large modulation efficiencies in a single graphene-based device has remained elusive so far. In this work, we overcome this fundamental trade-off by demonstrating the first 2D-3D dielectric integration in a high-quality encapsulated graphene device. We integrated hafnium oxide (HfO2) and two-dimensional hexagonal boron nitride (hBN) within the insulating section of a double-layer (DL) graphene EA modulator. This novel combination of materials allows for a high-quality modulator device with record high performances: a ∼39GHz bandwidth (BW) with a three-fold increase in modulation efficiency compared to previously reported high speed modulators. This first demonstration of 2D-3D integration paves the way to a plethora of electronic and opto-electronic devices with enhanced performance and stability, while expanding the freedom for new device designs.

scholarly journals Strand-wise and bait-assisted assembly of nearly-full rrn operons applied to assess species engraftment after faecal microbiota transplantation

2020 ◽  
Author(s):  
Alfonso Benítez-Páez ◽  
Annick V. Hartstra ◽  
Max Nieuwdorp ◽  
Yolanda Sanz
Keyword(s):  
Gut Microbiota ◽  
Bacterial Species ◽  
Cost Effective ◽  
Strain Level ◽  
Level Variation ◽  
Faecal Microbiota ◽  
Single Nucleotide Variants ◽  
Single Nucleotide ◽  
Faecal Microbiota Transplantation ◽  
Effective Manner

AbstractBackgroundEffective methodologies to accurately identify members of the gut microbiota at the species and strain levels are necessary to unveiling more specific and detailed host-microbe interactions and associations with health and disease.MethodsMinION™ MkIb nanopore-based device and the R9.5 flowcell chemistry were used to sequence and assemble dozens of rrn regions (16S-ITS-23S) derived from the most prevalent bacterial species in the human gut microbiota. As a method proof-of-concept to disclose further strain-level variation, we performed a complementary analysis in a subset of samples derived from an faecal microbiota transplantation (FMT) trial aiming amelioration of glucose and lipid metabolism in overweight subjects with metabolic syndrome.ResultsThe resulting updated rrn database, the data processing pipeline, and the precise control of covariates (sequencing run, sex, age, BMI, donor) were pivotal to accurately estimate the changes in gut microbial species abundance in the recipients after FMT. Furthermore, the rrn methodology described here demonstrated the ability to detect strain-level variation, critical to evaluate the transference of bacteria from donors to recipients as a consequence of the FMT. At this regard, we showed that our FMT trial successfully induced donors’ strain engraftment of e.g. Parabacteroides merdae species in recipients by mapping and assessing their associated single nucleotide variants (SNV).ConclusionsWe developed a methodology that enables the identification of microbiota at species- and strain-level in a cost-effective manner. Despite its error-prone nature and its modest per-base accuracy, the nanopore data showed to have enough quality to estimate single-nucleotide variation. This methodology and data analysis represents a cost-effective manner to trace genetic variability needed for better understanding the health effects of the human microbiome.Trial registrationThe study was prospectively registered at the Dutch Trial registry - NTR4488 (https://www.trialregister.nl/trial/4488).

scholarly journals Comparison of three amplicon sequencing approaches to determine staphylococcal populations on human skin

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Charlotte Marie Ahle ◽  
Kristian Stødkilde-Jørgensen ◽  
Anja Poehlein ◽  
Wolfgang R. Streit ◽  
Jennifer Hüpeden ◽  
...  
Keyword(s):  
Human Skin ◽  
Skin Diseases ◽  
Cost Effective ◽  
Amplicon Sequencing ◽  
Species Level ◽  
Skin Microbiome ◽  
Staphylococcal Species ◽  
Culture Independent ◽  
Skin Samples ◽  
Mock Communities

Abstract Background Staphylococci are important members of the human skin microbiome. Many staphylococcal species and strains are commensals of the healthy skin microbiota, while few play essential roles in skin diseases such as atopic dermatitis. To study the involvement of staphylococci in health and disease, it is essential to determine staphylococcal populations in skin samples beyond the genus and species level. Culture-independent approaches such as amplicon next-generation sequencing (NGS) are time- and cost-effective options. However, their suitability depends on the power of resolution. Results Here we compare three amplicon NGS schemes that rely on different targets within the genes tuf and rpsK, designated tuf1, tuf2 and rpsK schemes. The schemes were tested on mock communities and on human skin samples. To obtain skin samples and build mock communities, skin swab samples of healthy volunteers were taken. In total, 254 staphylococcal strains were isolated and identified to the species level by MALDI-TOF mass spectrometry. A subset of ten strains belonging to different staphylococcal species were genome-sequenced. Two mock communities with nine and eighteen strains, respectively, as well as eight randomly selected skin samples were analysed with the three amplicon NGS methods. Our results imply that all three methods are suitable for species-level determination of staphylococcal populations. However, the novel tuf2-NGS scheme was superior in resolution power. It unambiguously allowed identification of Staphylococcus saccharolyticus and distinguish phylogenetically distinct clusters of Staphylococcus epidermidis. Conclusions Powerful amplicon NGS approaches for the detection and relative quantification of staphylococci in human samples exist that can resolve populations to the species and, to some extent, to the subspecies level. Our study highlights strengths, weaknesses and pitfalls of three currently available amplicon NGS approaches to determine staphylococcal populations. Applied to the analysis of healthy and diseased skin, these approaches can be useful to attribute host-beneficial and -detrimental roles to skin-resident staphylococcal species and subspecies.

Structural changes in silicon-on-insulator material during post-implantation annealing

1986 ◽  
Vol 44 ◽  
pp. 736-737
Author(s):  
C. O. Jung ◽  
S. J. Krause ◽  
S.R. Wilson
Keyword(s):  
Integrated Circuits ◽  
Oxide Layer ◽  
High Speed ◽  
Structural Changes ◽  
Device Fabrication ◽  
Silicon On Insulator ◽  
High Quality ◽  
Radiation Hardened ◽  
Post Implantation ◽  
Very High

Silicon-on-insulator (SOI) structures have excellent potential for future use in radiation hardened and high speed integrated circuits. For device fabrication in SOI material a high quality superficial Si layer above a buried oxide layer is required. Recently, Celler et al. reported that post-implantation annealing of oxygen implanted SOI at very high temperatures would eliminate virtually all defects and precipiates in the superficial Si layer. In this work we are reporting on the effect of three different post implantation annealing cycles on the structure of oxygen implanted SOI samples which were implanted under the same conditions.

The Formability and Elongation of Aluminum Alloys AA5083 and AA3003 for Micro-Truss Sandwiches Manufacturing

2020 ◽  
Vol 38 (9A) ◽  
pp. 1396-1405
Author(s):  
Arwa F. Tawfeeq ◽  
Matthew R. Barnett
Keyword(s):  
Aluminum Alloy ◽  
Strain Rate ◽  
Cost Effective ◽  
Tensile Tests ◽  
Truss Structures ◽  
High Quality ◽  
Trade Off ◽  
Clad Layer ◽  
Higher Temperature ◽  
Different Shapes

The development in the manufacturing of micro-truss structures has demonstrated the effectiveness of brazing for assembling these sandwiches, which opens new opportunities for cost-effective and high-quality truss manufacturing. An evolving idea in micro-truss manufacturing is the possibility of forming these structures in different shapes with the aid of elevated temperature. This work investigates the formability and elongation of aluminum alloy sheets typically used for micro-truss manufacturing, namely AA5083 and AA3003. Tensile tests were performed at a temperature in the range of 25-500 ○C and strain rate in the range of 2x10-4 -10-2 s-1. The results showed that the clad layer in AA3003 exhibited an insignificant effect on the formability and elongation of AA3003. The formability of the two alloys was improved significantly with values of m as high as 0.4 and 0.13 for AA5083 and AA3003 at 500 °C. While the elongation of both AA5083 and AA3003 was improved at a higher temperature, the elongation of AA5083 was inversely related to strain rate. It was concluded that the higher the temperature is the better the formability and elongation of the two alloys but at the expense of work hardening. This suggests a trade-off situation between formability and strength. 

The Radio Probe™: A New Measurement Tool for High Speed Integrated Circuits

2005 ◽  
Author(s):  
Mark Kimball
Keyword(s):  
Integrated Circuits ◽  
Integrated Circuit ◽  
High Speed ◽  
Attenuation Factor ◽  
Cost Effective ◽  
Frequency Measurement ◽  
Single Frequency ◽  
Measurement Tool ◽  
Probe Design ◽  
Differential Measurement

Abstract This article presents a novel tool designed to allow circuit node measurements in a radio frequency (RF) integrated circuit. The discussion covers RF circuit problems; provides details on the Radio Probe design, which achieves an input impedance of 50Kohms and an overall attenuation factor of 0 dB; and describes signal to noise issues in the output signal, along with their improvement techniques. This cost-effective solution incorporates features that make it well suited to the task of differential measurement of circuit nodes within an RF IC. The Radio Probe concept offers a number of advantages compared to active probes. It is a single frequency measurement tool, so it complements, rather than replaces, active probes.

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