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Big Data: Astronomical or Genomical?

Big Data: Astronomical or Genomical? | Biologie Intégrative | Scoop.it
Genomics is a Big Data science and is going to get much bigger, very soon, but it is not known whether the needs of genomics will exceed other Big Data domains. Projecting to the year 2025, we compared genomics with three other major generators of Big Data: astronomy, YouTube, and Twitter. Our estimates show that genomics is a “four-headed beast”—it is either on par with or the most demanding of the domains analyzed here in terms of data acquisition, storage, distribution, and analysis. We discuss aspects of new technologies that will need to be developed to rise up and meet the computational challenges that genomics poses for the near future. Now is the time for concerted, community-wide planning for the “genomical” challenges of the next decade.
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Read also: MARTIN NF & MARTIN F (2010) From Galactic archeology to soil metagenomics – surfing on massive data streams. New Phytologist 185: 343–347.

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Efficient CRISPR/Cas9-mediated Targeted Mutagenesis in Populus in the First Generation : Scientific Reports

Efficient CRISPR/Cas9-mediated Targeted Mutagenesis in Populus in the First Generation : Scientific Reports | Biologie Intégrative | Scoop.it
Recently, RNA-guided genome editing using the type II clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein (Cas) system has been applied to edit the plant genome in several herbaceous plant species. However, it remains unknown whether this system can be used for genome editing in woody plants. In this study, we describe the genome editing and targeted gene mutation in a woody species, Populus tomentosa Carr. via the CRISPR/Cas9 system. Four guide RNAs (gRNAs) were designed to target with distinct poplar genomic sites of the phytoene desaturase gene 8 (PtoPDS) which are followed by the protospacer-adjacent motif (PAM). After Agrobacterium-mediated transformation, obvious albino phenotype was observed in transgenic poplar plants. By analyzing the RNA-guided genome-editing events, 30 out of 59 PCR clones were homozygous mutants, 2 out of 59 were heterozygous mutants and the mutation efficiency at these target sites was estimated to be 51.7%. Our data demonstrate that the Cas9/sgRNA system can be exploited to precisely edit genomic sequence and effectively create knockout mutations in woody plants.
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PLOS Pathogens: Exploiting Fungal Virulence-Regulating Transcription Factors As Novel Antifungal Drug Targets

PLOS Pathogens: Exploiting Fungal Virulence-Regulating Transcription Factors As Novel Antifungal Drug Targets | Biologie Intégrative | Scoop.it

Systemic and invasive mycoses caused by primary and opportunistic fungal pathogens have been emerging as global problems because of the increase in the number of immunocompromised individuals, due to solid-organ transplants, anti-cancer chemotherapy, and extended human lifespan. A recent report estimated that fungal pathogens, such as Cryptococcus neoformans, Candida albicans, and Aspergillus fumigatus, are responsible for more than 1 million deaths annually [1]. Despite this, the availability of antifungal drugs or targets for antifungal drug development are very limited. This is unlike the situation of bacterial pathogens and, to an extent, the eukaryotic parasites (which is serious enough) because the animals share a more recent common ancestor with the fungi than other pathogens. Ergosterol and its biosynthetic enzymes are the most popular antifungal drug targets because of the structural distinguishability of ergosterol from cholesterol in mammalian cell membranes. Polyene macrolides directly bind to ergosterol and generate lethal transmembrane channels that leak essential cellular ions and perturb osmotic balances, which leads to cell death [2]. Azole and allylamine derivatives are inhibitors of the ergosterol biosynthetic pathway that inhibit 14α-demethylase and squalene epoxidase, respectively, eventually leading to the accumulation of toxic precursors of ergosterol in the cell membrane and subsequent impairment of membrane integrity [3]. Another promising antifungal drug target is the fungal cell wall. Echinocandin inhibits β-1,3-glucan synthase and impairs cell wall integrity [4]. Nucleotide biosynthesis is also, somewhat unexpectedly, an appropriate antifungal drug target. For example, flucytosine itself does not have antifungal activity; however, after its uptake into cells, it is rapidly converted to 5-fluorouracil, which inhibits DNA and protein synthesis by cytosine deaminase, absent in humans [5]. However, all these antifungal drugs have problems, such as toxicity (e.g., hepatotoxicity and nephrotoxicity), frequent emergence of resistance, and a limited spectrum [2–5]. To overcome these problems, novel antifungal drug targets and drugs need to be discovered and developed.

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Genome diversity in arbuscular mycorrhizal fungi

Genome diversity in arbuscular mycorrhizal fungi | Biologie Intégrative | Scoop.it

Highlights
• In arbuscular mycorrhizal fungi, multiple nuclei share a common cytoplasm.
• There can be genomic diversity among the nuclei in an isolate.
• Changes in relative abundance of genetic variants can be accompanied by changes in phenotype.
• However, whole genome sequencing found only modest levels of variation.
• Mitochondrial genomes show even less within-isolate variation.

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Snapshot of insect–fungus arms race

Snapshot of insect–fungus arms race | Biologie Intégrative | Scoop.it

The general populace associates the arms race with nations preparing for or attempting to avoid conflicts by developing and divulging their military superiority. 

In the insect world, something else drives the arms race: selection as exemplified by host-evolving defenses and pathogens’ coevolution of detoxifying mechanisms. Entomologists examine these host–pathogen interactions not only to obtain better insights on the forces driving natural selection, but also to devise novel environmentally safe alternatives to control insect population while reducing our nation’s dependence on conventional agricultural chemicals. In PNAS, the multidisciplinary and multinational team of Pedrini et al. unravel a mystery in the insect–fungus arms race (2)...


Via Christophe Jacquet
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PLOS Biology: A Field Guide to Genomics Research

PLOS Biology: A Field Guide to Genomics Research | Biologie Intégrative | Scoop.it

Drawing upon our own experiences in various roles on genomics projects—and at the risk of generalizing—we note the prevalence of no fewer than six different character traits that lead to problems in experimental design (“the farmer”), data interpretation (“the gold miner” and “the cowboy”), collaboration (“the hermit” and “the master and servant”), and civic virtue (“the jailer”). This list is not comprehensive, but we hope it will guide new adventurers in the approaches and attitudes needed to stake their claim in this novel terrain.

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Paul Stamets video collections on how mushrooms can save the world

Paul Stamets video collections on how mushrooms can save the world | Biologie Intégrative | Scoop.it

IIn the famous TED talk given by mycologist Paul Stamets, we explore 6 Ways That Mushrooms Save The World

Mushrooms may be the most overlooked product available to us. With the current problems that our species is facing a solution that can be made widely available in a short amount of time would be beneficial. And according to Paul Stamets there are six ways in which mushrooms can fulfill this role. Besides these benefits, mushrooms neither are difficult to spread nor have high costs.


First, mushrooms can be used for cleaning polluted soil. The health of the forest is dependent on the quantity of mushrooms in the area. They provide nutrients to trees, keep soil together, and provide a firm hold to the surrounding vegetation with their ability to hold large amounts of mass. Due to the rapid speed of their growth which reaches a large size by day twenty-five by converting hydrocarbons into carbohydrates, they can be introduced to the landscape with results arriving in a short time frame.
Second, insecticides can be produced using mushrooms. Mycelium not only is able to get rid of carpenter ants and termites, but it is also seen as attractive by the insect targeted which makes them come to the mushroom instead of needing to spread the mushroom around. This is quickly noticed when the insects deliver these mushrooms to the queen. After the insects have been eliminated, the mushroom serves as a permanent repellant to future invaders. An extract can be created to have insects move along a different direction. According to the pesticide industry this is the most effective solution against insects that they have encountered.
Third, we have more in common with mushrooms then to any other kingdom of animal or plant life. Since we are susceptible to the same pathogens, mushrooms can be used for developing antibiotics. The antibiotics derived can be used for bacterial infection, and a myriad of diseases. A natural extract can be developed for practical use. These would be inexpensive alternatives to conventional medicine. Not to mention that lab results have shown extremely high antiviral activity. The forest containing these mushrooms should be preserved due to these results.
Fourth, the bacteria that develop on mushrooms after they begin to rot develops a self-sustaining ecosystem. These bacteria are valuable to the trees which create the debris that end in nourishing the same mushrooms. The way to spread these mushrooms is as easy as using a cardboard box. A possible destination for these are refugee communities which need to be rebuilt. Plant corn then add water growing a garden. Then only a couple kernels of corn are needed for the mushrooms to start growing on.
Fifth, the benefits mushrooms provide to the surrounding plant life is extended to animals. The spores produced during a mushrooms growth attract insects. These insects lay eggs that hatch as larvae. Then the larvae attract birds which spread seeds. This allows the mushrooms to be transferred to areas that require habitat restoration. By putting them in burlock sacks along with storm debris and placing them near the source of the problem will clean the area. Possible places are placing them downstream from a farm which generates E.Coli and other garbage or a factory which deals with chemical toxins. Typical results can be expected within 48 hours with a 10,000x reduction in bacteria. Since storms are typical the debris needed to sustain these mushrooms will always be available.
Sixth, mushrooms can generate ethanol by feeding off cellulose and making fungal sugars in the process. This is a solution to the energy crisis by providing a renewable source of fuel. Mushrooms do not generate any pollution and would lower production costs by feeding off debris. These lower production costs are in addition to the costs that will be saved due to transportation. Relying on Mycelium would reduce dependency on fuels that require damaging the environment to collect.
Mushrooms provide multiple benefits with little investment and no risks. The benefits are wide-ranging; sustaining the forest, producing insecticides, creating antibiotics, improving the environment for plants and animals, and providing an environmentally-friendly source of fuel. Due to their fast growth and easy handling, mushrooms should not be taken for granted. With their ability to derive energy from radiation future prospects might even extend to other planets. 

 


Via palkarlsen
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Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples

Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples | Biologie Intégrative | Scoop.it

The relation between ecological and genetic divergence of Helvella species (saddle fungi) has been perplexing. While a few species have been clearly demonstrated to be ectomycorrhizal fungi, ecological roles of many other species have been controversial, alternately considered as either saprotrophic or mycorrhizal. We applied SATé to build an inclusive deoxyribonucleic acid sequence alignment for the internal transcribed spacers (ITS) of annotated Helvella species and related environmental sequences. Phylogenetic informativeness of ITS and its regions were assessed using PhyDesign. Mycorrhizal lineages present a diversity of ecology, host type and geographic distribution. In two Helvella clades, no Helvella ITS sequences were recovered from root tips. Inclusion of environmental sequences in the ITS phylogeny from these sequences has the potential to link these data and reveal Helvella ecology. This study can serve as a model for revealing the diversity of relationships between unculturable fungi and their potential plant hosts. How non-mycorrhizal life styles within Helvella evolved will require expanded metagenomic investigation of soil and other environmental samples along with study of Helvella genomes.

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The role of the microbiome of truffles in aroma formation: a meta-analysis approach

Truffles (Tuber spp.) are ascomycete subterraneous fungi that form ectomycorrhizas in a symbiotic relationship with plant roots. Their fruiting bodies are appreciated for their distinctive aromas which might be partially derived from microbes. Indeed truffle fruiting bodies are colonized by a diverse microbial community made of bacteria, yeasts, guest filamentous fungi and viruses. The aim of this mini-review is double. First the current knowledge on the microbial community composition of truffles has been synthesized to highlight similarities and differences among four truffle species (T. magnatum, T. melanosporum, T. aestivum and T. borchii) at various stages of their life cycle. Second the potential role of the microbiome in truffle aroma formation has been addressed for the same four species. Our results suggest that on one side odorants which are common to many truffle species might be of mixed truffle and microbial origin while on the other side less common odorants might be derived from microbes only. They also highlight that bacteria, the dominant group in the truffle's microbiome, might also be the most important contributors to truffle aromas not only in T. borchii as already demonstrated but also in T. magnatum, T. aestivum and T. melanosporum.

Via Jean-Michel Ané, Stéphane Hacquard
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Aboveground-belowground biodiversity linkages differ in early and late successional temperate forests : Scientific Reports

Aboveground-belowground biodiversity linkages differ in early and late successional temperate forests : Scientific Reports | Biologie Intégrative | Scoop.it

Understanding ecological linkages between above- and below-ground biota is critical for deepening our knowledge on the maintenance and stability of ecosystem processes. Nevertheless, direct comparisons of plant-microbe diversity at the community level remain scarce due to the knowledge gap between microbial ecology and plant ecology. We compared the α- and β- diversities of plant and soil bacterial communities in two temperate forests that represented early and late successional stages. We documented different patterns of aboveground-belowground diversity relationships in these forests. We observed no linkage between plant and bacterial α-diversity in the early successional forest, and even a negative correlation in the late successional forest, indicating that high bacterial α-diversity is not always linked to high plant α-diversity. Beta-diversity coupling was only found at the late successional stage, while in the early successional forest, the bacterial β-diversity was closely correlated with soil property distances. Additionally, we showed that the dominant competitive tree species in the late successional forest may play key roles in driving forest succession by shaping the soil bacterial community in the early successional stage. This study sheds new light on the potential aboveground-belowground linkage in natural ecosystems, which may help us understand the mechanisms that drive ecosystem succession.


Via Stéphane Hacquard
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RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements

RNA-seq-Based Gene Annotation and Comparative Genomics of Four Fungal Grass Pathogens in the Genus Zymoseptoria Identify Novel Orphan Genes and Species-Specific Invasions of Transposable Elements | Biologie Intégrative | Scoop.it
The fungal pathogen Zymoseptoria tritici (synonym Mycosphaerella graminicola) is a prominent pathogen of wheat. The reference genome of the isolate IPO323 is one of the best-assembled eukaryotic genomes and encodes more than 10,000 predicted genes. However, a large proportion of the previously annotated gene models are incomplete, with either no start or no stop codons. The availability of RNA-seq data allows better predictions of gene structure. We here used two different RNA-seq datasets, de novo transcriptome assemblies, homology-based comparisons, and trained ab initio gene callers to generate a new gene annotation of Z. tritici IPO323. The annotation pipeline was also applied to re-sequenced genomes of three closely related species of Z. tritici: Z. pseudotritici, Z. ardabiliae, and Z. brevis. Comparative analyses of the predicted gene models using the four Zymoseptoria species revealed sets of species-specific orphan genes enriched with putative pathogenicity-related genes encoding small secreted proteins that may play essential roles in virulence and host specificity. De novo repeat identification allowed us to show that few families of transposable elements are shared between Zymoseptoria species while we observe many species-specific invasions and expansions. The annotation data presented here provide a high-quality resource for future studies of Z. tritici and its sister species and provide detailed insight into gene and genome evolution of fungal plant pathogens.
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Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of 13C-labeled Plant Metabolites and Lignocellulose

Multidimensional High-Resolution Magic Angle Spinning and Solution-State NMR Characterization of 13C-labeled Plant Metabolites and Lignocellulose | Biologie Intégrative | Scoop.it

Lignocellulose, which includes mainly cellulose, hemicellulose, and lignin, is a potential resource for the production of chemicals and for other applications. For effective production of materials derived from biomass, it is important to characterize the metabolites and polymeric components of the biomass. Nuclear magnetic resonance (NMR) spectroscopy has been used to identify biomass components; however, the NMR spectra of metabolites and lignocellulose components are ambiguously assigned in many cases due to overlapping chemical shift peaks. Using our 13C-labeling technique in higher plants such as poplar samples, we demonstrated that overlapping peaks could be resolved by three-dimensional NMR experiments to more accurately assign chemical shifts compared with two-dimensional NMR measurements. Metabolites of the 13C-poplar were measured by high-resolution magic angle spinning NMR spectroscopy, which allows sample analysis without solvent extraction, while lignocellulose components of the 13C-poplar dissolved in dimethylsulfoxide/pyridine solvent were analyzed by solution-state NMR techniques. Using these methods, we were able to unambiguously assign chemical shifts of small and macromolecular components in 13C-poplar samples. Furthermore, using samples of less than 5 mg, we could differentiate between two kinds of genes that were overexpressed in poplar samples, which produced clearly modified plant cell wall components.

 

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AGRICULTURE: Climate change creates mystery-shrouded future for prized cash crop - Thursday, April 25, 2013 www.eenews.net

AGRICULTURE: Climate change creates mystery-shrouded future for prized cash crop - Thursday, April 25, 2013 www.eenews.net | Biologie Intégrative | Scoop.it
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Biologist treks across southwestern China to answer the "killer mushroom" question

Biologist treks across southwestern China to answer the "killer mushroom" question | Biologie Intégrative | Scoop.it

McMaster University biologist Jianping Xu trekked over 30 kilometers a day through mountainous terrain and inclement weather in southwestern China to discover that a wild mushroom wasn't at the root of 400 unexplained deaths.

 

http://phys.org/news/2012-12-biologist-treks-southwestern-china-killer.html


Via Jared Berent
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