Improving catchment runoff estimates by ameliorating the impacts of SILO pluviometer data discontinuities through expanding the SILO reference database

Background: Long noncoding RNAs (lncRNAs) are endogenous noncoding RNAs, arbitrarily longer than 200 nucleotides, that play critical roles in diverse biological processes. LncRNAs exist in different genomes ranging from animals to plants. Objective: PlncRNADB is a searchable database of lncRNA sequences and annotation in plants. Methods: We built a pipeline for lncRNA prediction in plants, providing a convenient utility for users to quickly distinguish potential noncoding RNAs from protein-coding transcripts. Results: More than five thousand lncRNAs are collected from four plant species (Arabidopsis thaliana, Arabidopsis lyrata, Populus trichocarpa and Zea mays) in PlncRNADB. Moreover, our database provides the relationship between lncRNAs and various RNA-binding proteins (RBPs), which can be displayed through a user-friendly web interface. Conclusion: PlncRNADB can serve as a reference database to investigate the lncRNAs and their interaction with RNA-binding proteins in plants. The PlncRNADB is freely available at http://bis.zju.edu.cn/PlncRNADB/.

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Reference Database of Lung Volumes and Capacities in Wistar Rats from 2 to 24 Months

Current Aging Science ◽

10.2174/1874609808666141229114508 ◽

2015 ◽

Vol 7 (3) ◽

pp. 220-228 ◽

Cited By ~ 5

Author(s):

Wilson Jacob Filho ◽

Renata Gabriel Fontinele ◽

Romeu Rodrigues de Souza

Keyword(s):

Wistar Rats ◽

Reference Database ◽

Lung Volumes

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Adaptability of Ultrasonic Lamb Wave Touchscreen to the Variations in Touch Force and Touch Area

Sensors ◽

10.3390/s21051736 ◽

2021 ◽

Vol 21 (5) ◽

pp. 1736

Author(s):

Zengchong Yang ◽

Xiucheng Liu ◽

Bin Wu ◽

Ren Liu

Keyword(s):

Lamb Wave ◽

Weight Coefficient ◽

The Self ◽

Reference Database ◽

Learning Method ◽

Improved Method ◽

Large Area ◽

Localization Model ◽

Reference Databases ◽

First Time

Previous studies on Lamb wave touchscreen (LWT) were carried out based on the assumption that the unknown touch had the consistent parameters with acoustic fingerprints in the reference database. The adaptability of LWT to the variations in touch force and touch area was investigated in this study for the first time. The automatic collection of the databases of acoustic fingerprints was realized with an experimental prototype of LWT employing three pairs of transmitter–receivers. The self-adaptive updated weight coefficient of the used transmitter–receiver pairs was employed to successfully improve the accuracy of the localization model established based on a learning method. The performance of the improved method in locating single- and two-touch actions with the reference database of different parameters was carefully evaluated. The robustness of the LWT to the variation of the touch force varied with the touch area. Moreover, it was feasible to locate touch actions of large area with reference databases of small touch areas as long as the unknown touch and the reference databases met the condition of equivalent averaged stress.

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Novel Soil-Derived Beta-Lactam, Chloramphenicol, Fosfomycin and Trimethoprim Resistance Genes Revealed by Functional Metagenomics

Antibiotics ◽

10.3390/antibiotics10040378 ◽

2021 ◽

Vol 10 (4) ◽

pp. 378

Author(s):

Inka Marie Willms ◽

Maja Grote ◽

Melissa Kocatürk ◽

Lukas Singhoff ◽

Alina Andrea Kraft ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Antibiotic Resistance Genes ◽

Reference Database ◽

Functional Metagenomics ◽

Beta Lactam ◽

Public Attention ◽

Soil Ecosystems ◽

High Level ◽

Antibiotic Efflux

Antibiotic resistance genes (ARGs) in soil are considered to represent one of the largest environmental resistomes on our planet. As these genes can potentially be disseminated among microorganisms via horizontal gene transfer (HGT) and in some cases are acquired by clinical pathogens, knowledge about their diversity, mobility and encoded resistance spectra gained increasing public attention. This knowledge offers opportunities with respect to improved risk prediction and development of strategies to tackle antibiotic resistance, and might help to direct the design of novel antibiotics, before further resistances reach hospital settings or the animal sector. Here, metagenomic libraries, which comprise genes of cultivated microorganisms, but, importantly, also those carried by the uncultured microbial majority, were screened for novel ARGs from forest and grassland soils. We detected three new beta-lactam, a so far unknown chloramphenicol, a novel fosfomycin, as well as three previously undiscovered trimethoprim resistance genes. These ARGs were derived from phylogenetically diverse soil bacteria and predicted to encode antibiotic inactivation, antibiotic efflux, or alternative variants of target enzymes. Moreover, deduced gene products show a minimum identity of ~21% to reference database entries and confer high-level resistance. This highlights the vast potential of functional metagenomics for the discovery of novel ARGs from soil ecosystems.

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Toward a global reference database of COI barcodes for marine zooplankton

Marine Biology ◽

10.1007/s00227-021-03887-y ◽

2021 ◽

Vol 168 (6) ◽

Author(s):

Ann Bucklin ◽

Katja T. C. A. Peijnenburg ◽

Ksenia N. Kosobokova ◽

Todd D. O’Brien ◽

Leocadio Blanco-Bercial ◽

...

Keyword(s):

Species Diversity ◽

Dna Sequences ◽

Reference Sequence ◽

Global Ocean ◽

Reference Database ◽

Data Repositories ◽

Marine Zooplankton ◽

The North ◽

Coi Sequences ◽

Taxonomic Groups

AbstractCharacterization of species diversity of zooplankton is key to understanding, assessing, and predicting the function and future of pelagic ecosystems throughout the global ocean. The marine zooplankton assemblage, including only metazoans, is highly diverse and taxonomically complex, with an estimated ~28,000 species of 41 major taxonomic groups. This review provides a comprehensive summary of DNA sequences for the barcode region of mitochondrial cytochrome oxidase I (COI) for identified specimens. The foundation of this summary is the MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data and metadata portal that is linked to NCBI GenBank and BOLD data repositories. The MZGdb provides enhanced quality control and tools for assembling COI reference sequence databases that are specific to selected taxonomic groups and/or ocean regions, with associated metadata (e.g., collection georeferencing, verification of species identification, molecular protocols), and tools for statistical analysis, mapping, and visualization. To date, over 150,000 COI sequences for ~ 5600 described species of marine metazoan plankton (including holo- and meroplankton) are available via the MZGdb portal. This review uses the MZGdb as a resource for summaries of COI barcode data and metadata for important taxonomic groups of marine zooplankton and selected regions, including the North Atlantic, Arctic, North Pacific, and Southern Oceans. The MZGdb is designed to provide a foundation for analysis of species diversity of marine zooplankton based on DNA barcoding and metabarcoding for assessment of marine ecosystems and rapid detection of the impacts of climate change.

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DXA Bone Mineral Density Reference Database for the Indonesia Population

Journal of Clinical Densitometry ◽

10.1016/j.jocd.2006.04.038 ◽

2006 ◽

Vol 9 (2) ◽

pp. 235 ◽

Cited By ~ 1

Author(s):

G. Tirtarahardja ◽

B. Setyohadi ◽

Q. Zhou ◽

L.S. Weynand

Keyword(s):

Bone Mineral Density ◽

Bone Mineral ◽

Reference Database ◽

Mineral Density

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Barcoding lichen-forming fungi using 454 pyrosequencing is challenged by artifactual and biological sequence variation

Genome ◽

10.1139/gen-2015-0189 ◽

2016 ◽

Vol 59 (9) ◽

pp. 685-704 ◽

Cited By ~ 16

Author(s):

Kristiina Mark ◽

Carolina Cornejo ◽

Christine Keller ◽

Daniela Flück ◽

Christoph Scheidegger

Keyword(s):

454 Pyrosequencing ◽

Ecological Integrity ◽

Common Species ◽

Sequencing Error ◽

Reference Database ◽

Biological Sequence ◽

Internal Transcribed Spacer Region ◽

Epiphytic Lichen ◽

Fungal Partner ◽

A Genome

Although lichens (lichen-forming fungi) play an important role in the ecological integrity of many vulnerable landscapes, only a minority of lichen-forming fungi have been barcoded out of the currently accepted ∼18 000 species. Regular Sanger sequencing can be problematic when analyzing lichens since saprophytic, endophytic, and parasitic fungi live intimately admixed, resulting in low-quality sequencing reads. Here, high-throughput, long-read 454 pyrosequencing in a GS FLX+ System was tested to barcode the fungal partner of 100 epiphytic lichen species from Switzerland using fungal-specific primers when amplifying the full internal transcribed spacer region (ITS). The present study shows the potential of DNA barcoding using pyrosequencing, in that the expected lichen fungus was successfully sequenced for all samples except one. Alignment solutions such as BLAST were found to be largely adequate for the generated long reads. In addition, the NCBI nucleotide database—currently the most complete database for lichen-forming fungi—can be used as a reference database when identifying common species, since the majority of analyzed lichens were identified correctly to the species or at least to the genus level. However, several issues were encountered, including a high sequencing error rate, multiple ITS versions in a genome (incomplete concerted evolution), and in some samples the presence of mixed lichen-forming fungi (possible lichen chimeras).

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