A novel lytic Salmonella bacteriophage was isolated by using Klebsiella pneumoniae as host cells. The phage's genome was determined to be 47,564 bp and has the highest similarity to Salmonella phage ...E1 and Salmonella phage 64795_sal3, with coverages of 61% and 56%, respectively. Here, we announce the phage's complete genome.
We report here the whole-genome sequence of a new Enterococcus faecalis phage, vB_EfaS_IME197, which has a linear double-stranded DNA genome of 41,307 bp with 34% G+C content. We describe the main ...features of the genome of vB_EfaS_IME197.
Genome sequencing technologies reveal a huge amount of genomic sequences. Neural network-based methods can be prime candidates for retrieving insights from these sequences because of their ...applicability to large and diverse datasets. However, the highly variable lengths of genome sequences severely impair the presentation of sequences as input to the neural network. Genetic variations further complicate tasks that involve sequence comparison or alignment.
Inspired by the theory and applications of "spaced seeds," we propose a graph representation of genome sequences called "gapped pattern graph." These graphs can be transformed through a Graph Convolutional Network to form lower-dimensional embeddings for downstream tasks. On the basis of the gapped pattern graphs, we implemented a neural network model and demonstrated its performance on diverse tasks involving microbe and mammalian genome data. Our method consistently outperformed all the other state-of-the-art methods across various metrics on all tasks, especially for the sequences with limited homology to the training data. In addition, our model was able to identify distinct gapped pattern signatures from the sequences.
The framework is available at https://github.com/deepomicslab/GCNFrame.
High-throughput sequencing (HTS) is an effective tool for bacteriophage genome and its termini analysis. HTS technology parallelizes the sequencing process, producing thousands to millions of reads ...concurrently. Terminal information of a bacteriophage genome is important and basic knowledge for understanding the biology of the bacteriophage. We have created a high-occurrence reads as termini theory and developed practical methods to determine the bacteriophage genome termini, which is based on the large data of HTS. With this method, the termini of the bacteriophage genome can be efficiently and reliably identified as a by-product of bacteriophage genome sequencing, by solely analyzing the sequence statistics of the raw sequencing data (reads), without any further lab experiments.
Language-independent embedded speech recognition is a necessary and important application. Considering personal privacy, collection difficulty of all the reference words, and limited storage space of ...mobile devices, language-independent (LI) embedded speech recognition should be classified into lightweight speaker-dependent (SD) cases. Dynamic time warping (DTW) is the state-of-the-art algorithm for small foot-print SD automatic speech recognition. To decrease the high computational complexity of DTW, and to avoid constraints-induced coarse approximation and inaccuracy problems, we introduce a novel confidence index dynamic time warping (CIDTW) approach. CIDTW defines a new cost function, called the confidence index cost function (CICF), to measure the similarity between merged speech training and testing data, while follows the same DTW process. With extensive experiments on three representative SD datasets, CIDTW achieves better accuracy and overall six times faster speeds compared with DTW.
Methicillin-resistant Staphylococcus aureus(MRSA) is an increasing cause of serious infection,both in the community and hospital settings. Despite sophisticated strategies and efforts, the antibiotic ...options for treating MRSA infection are narrowing because of the limited number of newly developed antimicrobials. Here, four newly-isolated MRSA-virulent phages, IME-SA1, IMESA2, IME-SA118 and IME-SA119, were sequenced and analyzed. Their genome termini were identified using our previously proposed "termini analysis theory". We provide evidence that remarkable conserved terminus sequences are found in IME-SA1/2/118/119, and, moreover, are widespread throughout Twortlikevirus Staphylococcus phage G1 and K species. Results also suggested that each phage of the two species has conserved 5′ terminus while the 3′ terminus is variable. More importantly, a variable region with a specific pattern was found to be present near the conserved terminus of Twortlikevirus S. phage G1 species. The clone with the longest variable region had variable terminus lengths in successive generations, while the clones with the shortest variable region and with the average length variable region maintained the same terminal length as themselves during successive generations. IME-SA1 bacterial infection experiments showed that the variation is not derived from adaptation of the phage to different host strains. This is the first study of the conserved terminus and variable region of Twortlikevirus S. phages.
Citrobacter freundii is an opportunistic pathogen that can cause diarrhea, septicemia, meningitis, and urinary tract infections. We report here the complete genome sequence of C. freundii strain ...P10159, isolated from urine samples from a patient in China with esophageal carcinoma. The genome has 5,080,321 bp and 4,768 coding sequences, with a G+C content of 51.7%.
Vibrio parahaemolyticus is the leading bacterial cause of seafood-associated gastroenteritis worldwide. Moreover, infections and outbreaks caused by V. parahaemolyticus has kept increasing over the ...last two decades. In this study, we investigated the genetic diversity, virulence factors and farm-to-table spread pattern of V. parahaemolyticus by analyzing 383 genomes of food-associated isolates. These strains were isolated from diverse sample types from six provinces of China in 2014, being classified into three tiers of the farm-to-table spread process: food production, circulation and consumption. The genetic diversity of V. parahaemolyticus in different classifications, including geographical location, sample type, source and spread tier, was similar, as the median number of pairwise SNPs within each classification was between 33,013 and 33,659. Specifically, there was no clear boundaries in genetic diversity of the isolates from inland vs. coastal provinces, as well as of those from freshwater vs. seawater products. Moreover, the virulence genes and genomic islands were only found in a small number of isolates, indicating a low disease risk of the food-associated isolates in this study. By further exploring 28 recently emerged clonal groups, we identified seven farm-to-table spread events, showing a common pattern of single-source radial spread accompanied with occasional gene gain/loss events. Generally speaking, our work highlighted the colonization of V. parahaemolyticus in inland provinces and freshwater environment, and provided a snapshot of the farm-to-table spread pattern of V. parahaemolyticus food-associated isolates. Our results showed the feasibility of tracking the farm-to-table spread of foodborne pathogen, which would help construct the whole genome sequencing-based molecular tracking network in the future.
•High genetic diversity and low disease risk of V. parahaemolyticus food-associated isolates.•Colonization of V. parahaemolyticus in inland provinces and freshwater environment.•Single-source radial farm-to-table spread pattern of the food-associated isolates.
Front Cover: Deep Omics Tran, Ngoc Hieu; Zhang, Xianglilan; Li, Ming
Proteomics (Weinheim),
January 2018, 2018-01-00, Volume:
18, Issue:
2
Journal Article
Peer reviewed
Open access
DOI: 10.1002/pmic.201700319
The cover art is an representation of the DeepNovo system which does de novo peptide sequencing from tandem mass spec data, by a deep learning neural network. The deep ...learning's data‐centric approach significantly improves the previous algorithmic‐centric approaches. More deep learning examples in proteomics can be found in the viewpoint article by Ngoc Hieu Tran et al., in article number pmic.201700319.
<正>Dear Editor,Bacteriophages predominate in the biosphere and outnumber their hosts by at least one order of magnitude(Srinivasiah et al.,2008).They have been used for over90 years as an ...alternative to antibiotics in Eastern Europe(Deresinski,2009).With the increasing emergence of antibiotic resistance,the therapeutic potential of bacteriophages is being reevaluated(Kutter et al.,2010).Until recently,phages possessing ds DNA genomes have been
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