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This completely revised edition explores novel discoveries in
bacterial genomic research, with a focus on technical and
computational improvements as well as methods used for bacterial
pangenome analysis, which relies on microbiome studies and
metagenomic data. Beginning with up-to-date sequencing methods, the
book continues with sections covering methods for deep phylogenetic
analysis, the role of metagenomic data in understanding the
genomics of the many yet uncultured bacteria, progress in
genome-to-phenome inference, as well as computational genomic
tools. Written for the highly successful Methods in Molecular
Biology series, chapters include the type of practical detail
necessary for reproducible results in the lab. Authoritative and
up-to-date, Bacterial Pangenomics: Methods and Protocols, Second
Edition serves as an ideal guide for both highly qualified
investigators in bacterial genomics and for less experienced
researchers, including students and teachers, who could use a
reference for approaching genomic analysis and genome data.
This volume looks at the latest methodologies used to study
cellular metabolism with in silico approaches. The chapters in this
book are divided into 3 parts: part I discusses tools and methods
used for metabolic reconstructions and basic constraint-based
metabolic modeling (CBMM); Part II explores protocols for the
generation of experimental data for metabolic reconstruction and
modeling, including transcriptomics, proteomics, and mutant
generations; and Part III cover advanced techniques for
quantitative modeling of cellular metabolism, including dynamic
Flux Balance Analysis and multi-objective optimization. Written in
the highly successful Methods in Molecular Biology series format,
chapters include introductions to their respective topics, lists of
the necessary materials and reagents, step-by-step, readily
reproducible laboratory protocols, and tips on troubleshooting and
avoiding known pitfalls. Cutting-edge and thorough, Metabolic
Network Reconstruction and Modeling: Methods and Protocols is a
valuable resource for qualified investigators studying cellular
metabolism, and novice researchers who want to start working with
CBMM.
Bacterial genomics is a mature research interdisciplinary field,
which is approached by ecologists, geneticists, bacteriologists,
molecular biologists and evolutionary biologists working in
medical, industrial and basic science. Thanks to the large
diffusion of bacterial genome analysis, Bacterial Pangenomics:
Methods and Protocols is able to provide the most recent
methodologies about the study of bacterial pangenomes by covering
the three major areas: the experimental methods for approaching
bacterial pangenomics, the bio informatic pipelines for analysis
and annotation of sequence data and finally the methods for
inferring functional and evolutionary features from the pangenome.
Written in the successful Methods in Molecular Biology series
format, chapters include introductions to their respective topics,
lists of the necessary materials and reagents, step-by-step,
readily reproducible protocols and notes on troubleshooting and
avoiding known pitfalls. Authoritative and easily accessible,
Bacterial Pangenomics: Methods and Protocols will serve as a field
guide for both qualified bacterial genomics investigators who want
to update their technical knowledge, for less experienced
researchers who want to start working with bacterial genomics and
pangenomics, as well as serving as a manual and supplemental
textbook for graduate students of genomics and bioinformatics.
Bacterial genomics is a mature research interdisciplinary field,
which is approached by ecologists, geneticists, bacteriologists,
molecular biologists and evolutionary biologists working in
medical, industrial and basic science. Thanks to the large
diffusion of bacterial genome analysis, Bacterial Pangenomics:
Methods and Protocols is able to provide the most recent
methodologies about the study of bacterial pangenomes by covering
the three major areas: the experimental methods for approaching
bacterial pangenomics, the bio informatic pipelines for analysis
and annotation of sequence data and finally the methods for
inferring functional and evolutionary features from the pangenome.
Written in the successful Methods in Molecular Biology series
format, chapters include introductions to their respective topics,
lists of the necessary materials and reagents, step-by-step,
readily reproducible protocols and notes on troubleshooting and
avoiding known pitfalls. Authoritative and easily accessible,
Bacterial Pangenomics: Methods and Protocols will serve as a field
guide for both qualified bacterial genomics investigators who want
to update their technical knowledge, for less experienced
researchers who want to start working with bacterial genomics and
pangenomics, as well as serving as a manual and supplemental
textbook for graduate students of genomics and bioinformatics.
This completely revised edition explores novel discoveries in
bacterial genomic research, with a focus on technical and
computational improvements as well as methods used for bacterial
pangenome analysis, which relies on microbiome studies and
metagenomic data. Beginning with up-to-date sequencing methods, the
book continues with sections covering methods for deep phylogenetic
analysis, the role of metagenomic data in understanding the
genomics of the many yet uncultured bacteria, progress in
genome-to-phenome inference, as well as computational genomic
tools. Written for the highly successful Methods in Molecular
Biology series, chapters include the type of practical detail
necessary for reproducible results in the lab. Authoritative and
up-to-date, Bacterial Pangenomics: Methods and Protocols, Second
Edition serves as an ideal guide for both highly qualified
investigators in bacterial genomics and for less experienced
researchers, including students and teachers, who could use a
reference for approaching genomic analysis and genome data.
In this brief, the authors explore and review the current knowledge
regarding the role of molybdenum in the evolution of biological
systems and their interaction with biogeochemical cycles. Special
emphasis is placed on biological nitrogen fixation and the nitrogen
element cycle. The origin and evolution of molybdenum cofactor
biosynthetic pathways as well as the evolutionary significance of
molybdenum containing enzymes appearance is analyzed. Original data
regarding nitrogen fixation pathways and related enzymes molecular
evolution processes is presented. The trace element molybdenum is
essential for nearly all organisms and forms the catalytic center
of a large variety of enzymes such as nitrogenase, nitrate
reductases, sulphite oxidase and xanthine oxidoreductases.
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