scholarly journals Comparative genomics analyses indicate differential methylated amine utilisation trait within members of the genusGemmobacter

2018 ◽  
Author(s):  
E. Kröber ◽  
J Peixoto ◽  
MR Cunningham ◽  
L. Spurgin ◽  
D Wischer ◽  
...  
Keyword(s):  
Comparative Genomics ◽  
Carbon Source ◽  
Microbial Degradation ◽  
The Public ◽  
Genetic Potential ◽  
Cave Waters ◽  
Public Repositories ◽  
Earth’S Climate ◽  
Movile Cave ◽  
Methylated Amines

AbstractMethylated amines are ubiquitous in the environment and play a role in regulating the earth’s climate via a set of complex biological and chemical reactions. Microbial degradation of these compounds is thought to be a major sink. Recently we isolated a facultative methylotroph,Gemmobactersp. LW-1, an isolate from the unique environment Movile Cave, Romania, which is capable of methylated amine utilisation as a carbon source. Here, using a comparative genomics approach, we investigate how widespread methylated amine utilisation trait is within the member of the bacterial genusGemmobacter. Five genomes of differentGemmobacterspecies isolated from diverse environments, such as activated sludge, fresh water, sulphuric cave waters (Movile Cave) and the marine environment were available from the public repositories and used for the analysis. Our results indicate that some members of the genusGemmobacter, namelyG. aquatilis, G. caeniandG. sp. LW-1 have the genetic potential of methylated amine utilisation while others (G. megateriumandG. nectariphilus) have not.

Popularising Croll: an opportunity for expression and creativity

2021 ◽  
pp. 1-4
Author(s):  
Jo WOOLF
Keyword(s):  
Public Awareness ◽  
Public Domain ◽  
Scientific Theories ◽  
Ice Ages ◽  
Profound Impact ◽  
The Public ◽  
Different Ages ◽  
Points Of View ◽  
Earth’S Climate

ABSTRACT James Croll (1821–1890) was a gifted scientist whose revolutionary theories had a profound impact on our understanding of the Earth's climate, ice ages and glaciation. While his contributions are recognised by an increasing number of modern-day scientists, in the public domain his legacy has been all but forgotten. Popularising Croll's story brings its own challenges: we know more about the science than we do about the man, and his theories do not lend themselves to quick and easy explanation. While Croll's scientific theories, presented alone, risk being viewed as complex and difficult to digest, his lifelong struggle against adversity is a compelling story with the potential for widespread public appeal. In recent years, interested individuals and institutions have begun to increase public awareness of Croll through talks and lectures, exhibitions, theatrical events and articles in print and online. There are many more possibilities that are worth investigating, in order to inspire and engage people locally, nationally and even internationally. Croll's story is fascinating from many points of view, and is open to interpretation by people of different ages and backgrounds. Perhaps even the gaps in our knowledge can be turned to advantage, allowing for imagination, creativity and expression.

scholarly journals Improving tuberculosis surveillance by detecting international transmission using publicly available whole-genome sequencing data

2019 ◽  
Author(s):  
Andrea Sanchini ◽  
Christine Jandrasits ◽  
Julius Tembrockhaus ◽  
Thomas Andreas Kohl ◽  
Christian Utpatel ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Large Scale ◽  
Added Value ◽  
Whole Genome Sequencing Data ◽  
Whole Genome ◽  
International Transmission ◽  
The Public ◽  
Public Dataset ◽  
Public Repositories

AbstractIntroductionImproving the surveillance of tuberculosis (TB) is especially important for multidrug-resistant (MDR) and extensively drug-resistant (XDR)-TB. The large amount of publicly available whole-genome sequencing (WGS) data for TB gives us the chance to re-use data and to perform additional analysis at a large scale.AimWe assessed the usefulness of raw WGS data of global MDR/XDR-TB isolates available from public repositories to improve TB surveillance.MethodsWe extracted raw WGS data and the related metadata of Mycobacterium tuberculosis isolates available from the Sequence Read Archive. We compared this public dataset with WGS data and metadata of 131 MDR- and XDR-TB isolates from Germany in 2012-2013.ResultsWe aggregated a dataset that includes 1,081 MDR and 250 XDR isolates among which we identified 133 molecular clusters. In 16 clusters, the isolates were from at least two different countries. For example, cluster2 included 56 MDR/XDR isolates from Moldova, Georgia, and Germany. By comparing the WGS data from Germany and the public dataset, we found that 11 clusters contained at least one isolate from Germany and at least one isolate from another country. We could, therefore, connect TB cases despite missing epidemiological information.ConclusionWe demonstrated the added value of using WGS raw data from public repositories to contribute to TB surveillance. By comparing the German and the public dataset, we identified potential international transmission events. Thus, using this approach might support the interpretation of national surveillance results in an international context.

scholarly journals Navigating Public Microarray Databases

2004 ◽  
Vol 5 (6-7) ◽  
pp. 471-479 ◽  
Author(s):  
Christopher J. Penkett ◽  
Jürg Bähler
Keyword(s):  
Data Sources ◽  
European Bioinformatics Institute ◽  
Published Data ◽  
Expression Data ◽  
The Public ◽  
Genome Wide ◽  
Public Repositories ◽  
Set Up ◽  
Downstream Analysis ◽  
Microarray Studies

With the ever-escalating amount of data being produced by genome-wide microarray studies, it is of increasing importance that these data are captured in public databases so that researchers can use this information to complement and enhance their own studies. Many groups have set up databases of expression data, ranging from large repositories, which are designed to comprehensively capture all published data, through to more specialized databases. The public repositories, such as ArrayExpress at the European Bioinformatics Institute contain complete datasets in raw format in addition to processed data, whilst the specialist databases tend to provide downstream analysis of normalized data from more focused studies and data sources. Here we provide a guide to the use of these public microarray resources.

scholarly journals Climate predictions: the influence of nonlinearity and randomness

2012 ◽  
Vol 370 (1962) ◽  
pp. 1007-1011 ◽  
Author(s):  
J. Michael T. Thompson ◽  
Jan Sieber
Keyword(s):  
Climate Change ◽  
Global Warming ◽  
Large Scale ◽  
Statistical Properties ◽  
Gradual Change ◽  
Theme Issue ◽  
The Public ◽  
Systematic Biases ◽  
Earth’S Climate ◽  
Public Demand

The current threat of global warming and the public demand for confident projections of climate change pose the ultimate challenge to science: predicting the future behaviour of a system of such overwhelming complexity as the Earth's climate. This Theme Issue addresses two practical problems that make even prediction of the statistical properties of the climate, when treated as the attractor of a chaotic system (the weather), so challenging. The first is that even for the most detailed models, these statistical properties of the attractor show systematic biases. The second is that the attractor may undergo sudden large-scale changes on a time scale that is fast compared with the gradual change of the forcing (the so-called climate tipping).

Development of Information Management System Used in Laboratory

2012 ◽  
Vol 605-607 ◽  
pp. 2518-2521 ◽  
Author(s):  
Yu Hu
Keyword(s):  
Information Management ◽  
Management System ◽  
Laboratory Information Management System ◽  
Information Management System ◽  
Public Domain ◽  
Public Repository ◽  
The Public ◽  
Public Repositories ◽  
Laboratory Information Management

The aim of this paper is to develop a Laboratory Information Management System (LIMS). The system will act as a secure repository for both public and proprietary data. The public repository will contain all the data from other public repositories as well as the data released by the researchers into the public domain. The secure repository will manage the data and maintain its privacy until the researcher who owns it shares it with the public. This secure repository needs login credentials that should be validated to access the system. It is this type of system that would be used to design the experiments that would be submitted to the LIMS system.

scholarly journals Bacterial metabolism of methylated amines and identification of novel methylotrophs in Movile Cave

2014 ◽  
Vol 9 (1) ◽  
pp. 195-206 ◽  
Author(s):  
Daniela Wischer ◽  
Deepak Kumaresan ◽  
Antonia Johnston ◽  
Myriam El Khawand ◽  
Jason Stephenson ◽  
...  
Keyword(s):  
Bacterial Metabolism ◽  
Movile Cave ◽  
Methylated Amines

scholarly journals Draft Genome Sequences of Facultative Methylotrophs, Gemmobacter sp. Strain LW1 and Mesorhizobium sp. Strain 1M-11, Isolated from Movile Cave, Romania

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Deepak Kumaresan ◽  
Daniela Wischer ◽  
Alexandra M. Hillebrand-Voiculescu ◽  
J. Colin Murrell
Keyword(s):  
Nitrogen Source ◽  
Water Samples ◽  
Draft Genome ◽  
Microbial Mat ◽  
Genome Sequences ◽  
Carbon And Nitrogen ◽  
Movile Cave ◽  
Methylated Amines

Facultative methylotrophs belonging to the genera Gemmobacter and Mesorhizobium were isolated from microbial mat and cave water samples obtained from the Movile Cave ecosystem. Both bacteria can utilize methylated amines as their sole carbon and nitrogen source. Here, we report the draft genome sequences of Gemmobacter sp. strain LW1 and Mesorhizobium sp. strain IM1.

scholarly journals GenoVault: a cloud based genomics repository

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Sankalp Jain ◽  
Amit Saxena ◽  
Suprit Hesarur ◽  
Kirti Bhadhadhara ◽  
Neeraj Bharti ◽  
...  
Keyword(s):  
Private Cloud ◽  
File Transfer ◽  
Web Based ◽  
The Public ◽  
Private Data ◽  
Object Based ◽  
Block Storage ◽  
Public Repositories ◽  
Next Generation Sequencing Ngs ◽  
Ngs Data

AbstractGenoVault is a cloud-based repository for handling Next Generation Sequencing (NGS) data. It is developed using OpenStack-based private cloud with various services like keystone for authentication, cinder for block storage, neutron for networking and nova for managing compute instances for the Cloud. GenoVault uses object-based storage, which enables data to be stored as objects instead of files or blocks for faster retrieval from different distributed object nodes. Along with a web-based interface, a JavaFX-based desktop client has also been developed to meet the requirements of large file uploads that are usually seen in NGS datasets. Users can store files in their respective object-based storage areas and the metadata provided by the user during file uploads is used for querying the database. GenoVault repository is designed taking into account future needs and hence can scale both vertically and horizontally using OpenStack-based cloud features. Users have an option to make the data shareable to the public or restrict the access as private. Data security is ensured as every container is a separate entity in object-based storage architecture which is also supported by Secure File Transfer Protocol (SFTP) for data upload and download. The data is uploaded by the user in individual containers that include raw read files (fastq), processed alignment files (bam, sam, bed) and the output of variation detection (vcf). GenoVault architecture allows verification of the data in terms of integrity and authentication before making it available to collaborators as per the user’s permissions. GenoVault is useful for maintaining the organization-wide NGS data generated in various labs which is not yet published and submitted to public repositories like NCBI. GenoVault also provides support to share NGS data among the collaborating institutions. GenoVault can thus manage vast volumes of NGS data on any OpenStack-based private cloud.

scholarly journals Geographical Landscape and Transmission Dynamics of SARS-CoV-2 Variants Across India: A Longitudinal Perspective

2021 ◽  
Vol 12 ◽  
Author(s):  
Neha Jha ◽  
Dwight Hall ◽  
Akshay Kanakan ◽  
Priyanka Mehta ◽  
Ranjeet Maurya ◽  
...  
Keyword(s):  
Public Health ◽  
Regional Analysis ◽  
Sequencing Data ◽  
Differential Distribution ◽  
Public Health Perspective ◽  
The Public ◽  
Detection And Tracking ◽  
Prevalent Strain ◽  
Public Repositories ◽  
Aid Decision

Globally, SARS-CoV-2 has moved from one tide to another with ebbs in between. Genomic surveillance has greatly aided the detection and tracking of the virus and the identification of the variants of concern (VOC). The knowledge and understanding from genomic surveillance is important for a populous country like India for public health and healthcare officials for advance planning. An integrative analysis of the publicly available datasets in GISAID from India reveals the differential distribution of clades, lineages, gender, and age over a year (Apr 2020–Mar 2021). The significant insights include the early evidence towards B.1.617 and B.1.1.7 lineages in the specific states of India. Pan-India longitudinal data highlighted that B.1.36* was the predominant clade in India until January–February 2021 after which it has gradually been replaced by the B.1.617.1 lineage, from December 2020 onward. Regional analysis of the spread of SARS-CoV-2 indicated that B.1.617.3 was first seen in India in the month of October in the state of Maharashtra, while the now most prevalent strain B.1.617.2 was first seen in Bihar and subsequently spread to the states of Maharashtra, Gujarat, and West Bengal. To enable a real time understanding of the transmission and evolution of the SARS-CoV-2 genomes, we built a transmission map available on https://covid19-indiana.soic.iupui.edu/India/EmergingLineages/April2020/to/March2021. Based on our analysis, the rate estimate for divergence in our dataset was 9.48 e-4 substitutions per site/year for SARS-CoV-2. This would enable pandemic preparedness with the addition of future sequencing data from India available in the public repositories for tracking and monitoring the VOCs and variants of interest (VOI). This would help aid decision making from the public health perspective.

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