Bioinformatics, Comparative Genomics and Molecular Evolution
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PLOS Computational Biology: An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis

PLOS Computational Biology: An Evolution-Based Approach to De Novo Protein Design and Case Study on Mycobacterium tuberculosis | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
This is promising research. It makes sense ti use this approach and it seems to be effective. I envisage this will have impact on both synthetic biology and modeling.
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Bioinformatics, Comparative Genomics and Molecular Evolution
A page dedicated at the dispersal of papers and facts related to these fascinating Scientific Endeavours
Curated by Arjen ten Have
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The Diversification of Plant NBS-LRR Defense Genes Directs the Evolution of MicroRNAs That Target Them

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KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins

KMAD: knowledge-based multiple sequence alignment for intrinsically disordered proteins | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea : Nature : Nature Research

The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea : Nature : Nature Research | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Seagrasses colonized the sea on at least three independent occasions to form the basis of one of the most productive and widespread coastal ecosystems on the planet. Here we report the genome of Zostera marina (L.), the first, to our knowledge, marine angiosperm to be fully sequenced. This reveals unique insights into the genomic losses and gains involved in achieving the structural and physiological adaptations required for its marine lifestyle, arguably the most severe habitat shift ever accomplished by flowering plants. Key angiosperm innovations that were lost include the entire repertoire of stomatal genes, genes involved in the synthesis of terpenoids and ethylene signalling, and genes for ultraviolet protection and phytochromes for far-red sensing. Seagrasses have also regained functions enabling them to adjust to full salinity. Their cell walls contain all of the polysaccharides typical of land plants, but also contain polyanionic, low-methylated pectins and sulfated galactans, a feature shared with the cell walls of all macroalgae and that is important for ion homoeostasis, nutrient uptake and O2/CO2 exchange through leaf epidermal cells. The Z. marina genome resource will markedly advance a wide range of functional ecological studies from adaptation of marine ecosystems under climate warming, to unravelling the mechanisms of osmoregulation under high salinities that may further inform our understanding of the evolution of salt tolerance in crop plants.
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What a nice system to study evolution!
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Combining dependent P-values with an empirical adaptation of Brown’s method

Combining dependent P-values with an empirical adaptation of Brown’s method | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Great resource for those not strong in statistics.
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Computing Biology

Computing Biology | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Is Computational Biology increasingly—and steadily—progressing toward addressing the mammoth challenge of actually computing biology? That is, have we reached the stage where we do not support biological research but drive it? This question is vitally important for all—young and established computational biologists. Even though forecasting future research can be risky, we still venture to predict that the future will see considerably more research projects drifting toward this ambitious aspiration. Computational Biology is powerful for abstracting signatures of disease, for predicting it, and for proposing medications. It is effective in figuring out disease mechanisms and forceful in bridging experimental disciplines to obtain testable predictions. However, perhaps its biggest challenges lie in putting together the available broad and disparate information, devising tools to efficiently and effectively carry out these tasks while sifting through noise and recognizing cell specificity, and most importantly coming up with sound, coherent, and testable schemes.

 

Nussinov R, Papin JA (2016) Computing Biology. PLoS Comput Biol 12(7): e1005050. doi:10.1371/journal.pcbi.1005050


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Interesting read on the driving source of biological research: Computing Biology?
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Uncalculating cooperation is used to signal trustworthiness

Uncalculating cooperation is used to signal trustworthiness | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
uncal
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Things in game theory are starting to fall together.
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Structure-based discovery of opioid analgesics with reduced side effects : Nature : Nature Research

Structure-based discovery of opioid analgesics with reduced side effects : Nature : Nature Research | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Structure-based discovery of opioid analgesics with reduced side effects
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What Bioinformatics can do for you! There goes the pain!
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Rescooped by Arjen ten Have from Plants and Microbes
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PLOS ONE: Directed Evolution of FLS2 towards Novel Flagellin Peptide Recognition (2016)

PLOS ONE: Directed Evolution of FLS2 towards Novel Flagellin Peptide Recognition (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Microbe-associated molecular patterns (MAMPs) are molecules, or domains within molecules, that are conserved across microbial taxa and can be recognized by a plant or animal immune system. Although MAMP receptors have evolved to recognize conserved epitopes, the MAMPs in some microbial species or strains have diverged sufficiently to render them unrecognizable by some host immune systems. In this study, we carried out in vitro evolution of the Arabidopsis thaliana flagellin receptor FLAGELLIN-SENSING 2 (FLS2) to isolate derivatives that recognize one or more flagellin peptides from bacteria for which the wild-type Arabidopsis FLS2 confers little or no response. A targeted approach generated amino acid variation at FLS2 residues in a region previously implicated in flagellin recognition. The primary screen tested for elevated response to the canonical flagellin peptide from Pseudomonas aeruginosa, flg22. From this pool, we then identified five alleles of FLS2 that confer modest (quantitatively partial) recognition of an Erwinia amylovora flagellin peptide. Use of this Erwinia-based flagellin peptide to stimulate Arabidopsis plants expressing the resulting FLS2 alleles did not lead to a detectable reduction of virulent P. syringae pv. tomato growth. However, combination of two identified mutations into a single allele further increased FLS2-mediated responses to the E. amylovora flagellin peptide. These studies demonstrate the potential to raise the sensitivity of MAMP receptors toward particular targets.


Via Kamoun Lab @ TSL
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Metagenomics: Pathogen diagnostics for the masses : Nature Reviews Genetics : Nature Publishing Group

Metagenomics: Pathogen diagnostics for the masses : Nature Reviews Genetics : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Universality of human microbial dynamics : Nature : Nature Publishing Group

Universality of human microbial dynamics : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Human-associated microbial communities have a crucial role in determining our health and well-being, and this has led to the continuing development of microbiome-based therapies such as faecal microbiota transplantation. These microbial communities are very complex, dynamic and highly personalized ecosystems, exhibiting a high degree of inter-individual variability in both species assemblages and abundance profiles. It is not known whether the underlying ecological dynamics of these communities, which can be parameterized by growth rates, and intra- and inter-species interactions in population dynamics models, are largely host-independent (that is, universal) or host-specific. If the inter-individual variability reflects host-specific dynamics due to differences in host lifestyle, physiology or genetics, then generic microbiome manipulations may have unintended consequences, rendering them ineffective or even detrimental. Alternatively, microbial ecosystems of different subjects may exhibit universal dynamics, with the inter-individual variability mainly originating from differences in the sets of colonizing species. Here we develop a new computational method to characterize human microbial dynamics. By applying this method to cross-sectional data from two large-scale metagenomic studies—the Human Microbiome Project and the Student Microbiome Project—we show that gut and mouth microbiomes display pronounced universal dynamics, whereas communities associated with certain skin sites are probably shaped by differences in the host environment. Notably, the universality of gut microbial dynamics is not observed in subjects with recurrent Clostridium difficile infection but is observed in the same set of subjects after faecal microbiota transplantation. These results fundamentally improve our understanding of the processes that shape human microbial ecosystems, and pave the way to designing general microbiome-based therapies.
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Beyond prebiotic chemistry

How can matter transition from the nonliving to the living state? The answer is essential for understanding the origin of life on Earth and for identifying promising targets in the search for life on other planets. Most studies have focused on the likely chemistry of RNA, protein, lipid, or metabolic “worlds” and autocatalytic sets, including attempts to make life in the lab. But these efforts may be too narrowly focused on the biochemistry of life as we know it today. A radical rethink is necessary, one that explores not just plausible chemical scenarios but also new physical processes and driving forces. Such investigations could lead to a physical understanding not only of the origin of life but also of life itself, as well as to new tools for designing artificial biology.

 

Beyond prebiotic chemistry
Leroy Cronin, Sara Imari Walker

Science  03 Jun 2016:
Vol. 352, Issue 6290, pp. 1174-1175
http://dx.doi.org/10.1126/science.aaf6310

 


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The early history and emergence of molecular functions and modular scale-free network behavior

The early history and emergence of molecular functions and modular scale-free network behavior | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
The formation of protein structural domains requires that biochemical functions, defined by conserved amino acid sequence motifs, be embedded into a structural scaffold.
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Interesting view on early domain evolution. 
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Scientific Reports: Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species (2016)

Scientific Reports: Directional Selection from Host Plants Is a Major Force Driving Host Specificity in Magnaporthe Species (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

One major threat to global food security that requires immediate attention, is the increasing incidence of host shift and host expansion in growing number of pathogenic fungi and emergence of new pathogens. The threat is more alarming because, yield quality and quantity improvement efforts are encouraging the cultivation of uniform plants with low genetic diversity that are increasingly susceptible to emerging pathogens. However, the influence of host genome differentiation on pathogen genome differentiation and its contribution to emergence and adaptability is still obscure. Here, we compared genome sequence of 6 isolates of Magnaporthe species obtained from three different host plants. We demonstrated the evolutionary relationship between Magnaporthe species and the influence of host differentiation on pathogens. Phylogenetic analysis showed that evolution of pathogen directly corresponds with host divergence, suggesting that host-pathogen interaction has led to co-evolution. Furthermore, we identified an asymmetric selection pressure on Magnaporthe species. Oryza sativa-infecting isolates showed higher directional selection from host and subsequently tends to lower the genetic diversity in its genome. We concluded that, frequent gene loss or gain, new transposon acquisition and sequence divergence are host adaptability mechanisms for Magnaporthe species, and this coevolution processes is greatly driven by directional selection from host plants.


Via Steve Marek, Kamoun Lab @ TSL
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Optimal design of gene knockout experiments for gene regulatory network inference

Optimal design of gene knockout experiments for gene regulatory network inference | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Seems to me this is applicable to metabolic studies as well!
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Ewan's Blog: Bioinformatician at large: Sharing clinical data: everyone wins

Ewan's Blog: Bioinformatician at large: Sharing clinical data: everyone wins | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Most of it is kind of obvious and certainly this is in no way exclusive to clinical data but still this is a nice, simple essay.
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Genome Research: Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen (2016)

Genome Research: Transposons passively and actively contribute to evolution of the two-speed genome of a fungal pathogen (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

Genomic plasticity enables adaptation to changing environments, which is especially relevant for pathogens that engage in 'arms races' with their hosts. In many pathogens, genes mediating virulence cluster in highly variable, transposon-rich, physically distinct genomic compartments. However, understanding of the evolution of these compartments, and the role of transposons therein, remains limited. Here, we show that transposons are the major driving force for adaptive genome evolution in the fungal plant pathogen Verticillium dahliae. We show that highly variable lineage-specific (LS) regions evolved by genomic rearrangements that are mediated by erroneous double-strand repair, often utilizing transposons. We furthermore show that recent genetic duplications are enhanced in LS regions, against an older episode of duplication events. Finally, LS regions are enriched in active transposons, which contribute to local genome plasticity. Thus, we provide evidence for genome shaping by transposons, both in an active and passive manner, which impacts the evolution of pathogen virulence.


Via Kamoun Lab @ TSL
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Computational biology, Evolution and plant pathology in one!
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Science: Basidiomycete yeasts in the cortex of ascomycete macro lichens (2016)

Science: Basidiomycete yeasts in the cortex of ascomycete macro lichens (2016) | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it

For over 140 years, lichens have been regarded as a symbiosis between a single fungus, usually an ascomycete, and a photosynthesizing partner. Other fungi have long been known to occur as occasional parasites or endophytes, but the one lichen–one fungus paradigm has seldom been questioned. Here we show that many common lichens are composed of the known ascomycete, the photosynthesizing partner, and, unexpectedly, specific basidiomycete yeasts. These yeasts are embedded in the cortex, and their abundance correlates with previously unexplained variations in phenotype. Basidiomycete lineages maintain close associations with specific lichen species over large geographical distances and have been found on six continents. The structurally important lichen cortex, long treated as a zone of differentiated ascomycete cells, appears to consistently contain two unrelated fungi.


Via Kamoun Lab @ TSL
Arjen ten Have's insight:
Postgenome research will definitely change the face of biological research. Yet another example here. Why should an interaction hold two partners?
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Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions

Ecological consequences of human niche construction: Examining long-term anthropogenic shaping of global species distributions | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
National Academy of Sciences
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PLOS Collections: Article collections published by the Public Library of Science

PLOS Collections: Article collections published by the Public Library of Science | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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As if I do not have enough stuff to read!
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Proteomics/Introduction to Proteomics - Wikibooks, open books for an open world

Proteomics/Introduction to Proteomics - Wikibooks, open books for an open world | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Excellent resource for bioinformaticians!!
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Evolution: Duplicate gene co-regulation slows evolution : Nature Reviews Genetics : Nature Publishing Group

Evolution: Duplicate gene co-regulation slows evolution : Nature Reviews Genetics : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Determinants of genetic diversity : Nature Reviews Genetics : Nature Publishing Group

Determinants of genetic diversity : Nature Reviews Genetics : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach

Multiplexing Genetic and Nucleosome Positioning Codes: A Computational Approach | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
Eukaryotic DNA is strongly bent inside fundamental packaging units: the nucleosomes. It is known that their positions are strongly influenced by the mechanical properties of the underlying DNA sequence. Here we discuss the possibility that these mechanical properties and the concomitant nucleosome positions are not just a side product of the given DNA sequence, e.g. that of the genes, but that a mechanical evolution of DNA molecules might have taken place. We first demonstrate the possibility of multiplexing classical and mechanical genetic information using a computational nucleosome model. In a second step we give evidence for genome-wide multiplexing in Saccharomyces cerevisiae and Schizosacharomyces pombe . This suggests that the exact positions of nucleosomes play crucial roles in chromatin function.
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And here comes another functional constraint at DNA level.
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Cooperation, competition and the emergence of criticality in communities of adaptive systems - IOPscience

Cooperation, competition and the emergence of criticality in communities of adaptive systems - IOPscience | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Share your insight
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Proteogenomics connects somatic mutations to signalling in breast cancer : Nature : Nature Publishing Group

Proteogenomics connects somatic mutations to signalling in breast cancer : Nature : Nature Publishing Group | Bioinformatics, Comparative Genomics and Molecular Evolution | Scoop.it
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Proteomics comes of age: Proteogenomics connects somatic mutations to breast cancer
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