Menu

Auto Tag: by Pacific

July 7, 2019  |  

Complete genome of Halomonas aestuarii Hb3, isolated from tidal flat

Halomonas aestuarii Hb3, a moderately halophilic bacterium belonging to the class Gammaproteobacteria, was isolated from a tidal flat. Herein, we report the complete genome sequence of its strain Hb3. Its size is estimated at 3.54Mbp with a mean G+C content of 67.9%. The genome includes 3238 open reading frames, 65 transfer RNAs, and four ribosomal RNA gene operons. Genes related to the degradation of monoaromatic compounds, detoxification of arsenic, and production of polymers were identified. These features indicate that this strain may be important for ecological and industrial application.

Read more
July 7, 2019  |  

Complete genome sequence of “Thiodictyon syntrophicum” sp. nov. strain Cad16T, a photolithoautotrophic purple sulfur bacterium isolated from the alpine meromictic Lake Cadagno.

Thiodictyon syntrophicum sp. nov. strain Cad16T is a photoautotrophic purple sulfur bacterium belonging to the family of Chromatiaceae in the class of Gammaproteobacteria. The type strain Cad16T was isolated from the chemocline of the alpine meromictic Lake Cadagno in Switzerland. Strain Cad16T represents a key species within this sulfur-driven bacterial ecosystem with respect to carbon fixation. The 7.74-Mbp genome of strain Cad16T has been sequenced and annotated. It encodes 6237 predicted protein sequences and 59 RNA sequences. Phylogenetic comparison based on 16S rRNA revealed that Thiodictyon elegans strain DSM 232T the most closely related species. Genes involved in sulfur oxidation, central carbon metabolism and transmembrane transport were found. Noteworthy, clusters of genes encoding the photosynthetic machinery and pigment biosynthesis are found on the 0.48 Mb plasmid pTs485. We provide a detailed insight into the Cad16T genome and analyze it in the context of the microbial ecosystem of Lake Cadagno.

Read more
July 7, 2019  |  

RIFRAF: a frame-resolving consensus algorithm.

Protein coding genes can be studied using long-read next generation sequencing. However, high rates of indel sequencing errors are problematic, corrupting the reading frame. Even the consensus of multiple independent sequence reads retains indel errors. To solve this problem, we introduce Reference-Informed Frame-Resolving multiple-Alignment Free template inference algorithm (RIFRAF), a sequence consensus algorithm that takes a set of error-prone reads and a reference sequence and infers an accurate in-frame consensus. RIFRAF uses a novel structure, analogous to a two-layer hidden Markov model: the consensus is optimized to maximize alignment scores with both the set of noisy reads and with a reference. The template-to-reads component of the model encodes the preponderance of indels, and is sensitive to the per-base quality scores, giving greater weight to more accurate bases. The reference-to-template component of the model penalizes frame-destroying indels. A local search algorithm proceeds in stages to find the best consensus sequence for both objectives.Using Pacific Biosciences SMRT sequences from an HIV-1 env clone, NL4-3, we compare our approach to other consensus and frame correction methods. RIFRAF consistently finds a consensus sequence that is more accurate and in-frame, especially with small numbers of reads. It was able to perfectly reconstruct over 80% of consensus sequences from as few as three reads, whereas the best alternative required twice as many. RIFRAF is able to achieve these results and keep the consensus in-frame even with a distantly related reference sequence. Moreover, unlike other frame correction methods, RIFRAF can detect and keep true indels while removing erroneous ones.RIFRAF is implemented in Julia, and source code is publicly available at https://github.com/MurrellGroup/Rifraf.jl.Supplementary data are available at Bioinformatics online.

Read more
July 7, 2019  |  

HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning.

Second-generation DNA sequencing techniques generate short reads that can result in fragmented genome assemblies. Third-generation sequencing platforms mitigate this limitation by producing longer reads that span across complex and repetitive regions. However, the usefulness of such long reads is limited because of high sequencing error rates. To exploit the full potential of these longer reads, it is imperative to correct the underlying errors. We propose HECIL-Hybrid Error Correction with Iterative Learning-a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read alignments. We demonstrate that HECIL outperforms state-of-the-art error correction algorithms for an overwhelming majority of evaluation metrics on diverse, real-world data sets including E. coli, S. cerevisiae, and the malaria vector mosquito A. funestus. Additionally, we provide an optional avenue of improving the performance of HECIL’s core algorithm by introducing an iterative learning paradigm that enhances the correction policy at each iteration by incorporating knowledge gathered from previous iterations via data-driven confidence metrics assigned to prior corrections.

Read more
July 7, 2019  |  

Immunoglobulin gene analysis as a tool for investigating human immune responses.

The human immunoglobulin repertoire is a hugely diverse set of sequences that are formed by processes of gene rearrangement, heavy and light chain gene assortment, class switching and somatic hypermutation. Early B cell development produces diverse IgM and IgD B cell receptors on the B cell surface, resulting in a repertoire that can bind many foreign antigens but which has had self-reactive B cells removed. Later antigen-dependent development processes adjust the antigen affinity of the receptor by somatic hypermutation. The effector mechanism of the antibody is also adjusted, by switching the class of the antibody from IgM to one of seven other classes depending on the required function. There are many instances in human biology where positive and negative selection forces can act to shape the immunoglobulin repertoire and therefore repertoire analysis can provide useful information on infection control, vaccination efficacy, autoimmune diseases, and cancer. It can also be used to identify antigen-specific sequences that may be of use in therapeutics. The juxtaposition of lymphocyte development and numerical evaluation of immune repertoires has resulted in the growth of a new sub-speciality in immunology where immunologists and computer scientists/physicists collaborate to assess immune repertoires and develop models of immune action.© 2018 The Authors. Immunological Reviews Published by John Wiley & Sons Ltd.

Read more
July 7, 2019  |  

Identification and genome analysis of Deinococcus actinosclerus SJTR1, a novel 17ß-estradiol degradation bacterium.

Biodegradation with microorganisms is considered as an efficient strategy to remove the environmental pollutants. In this work, Deinococcus actinosclerus SJTR1 isolated from the wastewater was confirmed with great degradation capability to 17ß-estradiol, one typical estrogen chemical. It could degrade nearly 90% of 17ß-estradiol (10 mg/L) in 5 days and transform it into estrone; its degradation kinetics fitted for the first-order kinetic equation. The whole genome sequence of D. actinosclerus SJTR1 was obtained and annotated, containing one chromosome (3,315,586 bp) and four plasmids (ranging from 17,267 bp to 460,244 bp). A total of 3913 CDSs and 73 RNA genes (including 12 rRNA genes, 50 tRNA genes, and 11 ncRNA genes) were identified in its whole genome sequence. On this basis, a series of potential genes involved in steroid metabolism and stress responses of D. actinosclerus SJTR1 were predicted. It is the first report of Deinococcus strain with the degradation capability to estrogens. This work could enrich the genome sources of the estrogen-degrading strains and promote the degradation mechanism study of 17ß-estradiol in bacteria.

Read more

Subscribe for blog updates:

Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.