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A History Timeline About Immunology. Immunology, the study of the immune system and its responses to invading pathogens, has a rich an
Via Gilbert C FAURE
Visual summaries, data visualizations, and illustrated explorations to enhance and complement work published across journals.
Via Dr. Stefan Gruenwald
The new variant may undermine some vaccine-derived defenses. But the immune system’s best assassins are likely to hold the line.
Via Gilbert C FAURE
The viral receptor on human cells plays a critical role in disease progression
Via Gilbert C FAURE
A team of biologists from the Wellcome Sanger Institute, the European Bioinformatics Institute and the Universidad de los Andes has identified 142,809 species of bacteriophages -- viruses that infect and replicate in bacteria -- living in the human gut. Using a DNA-sequencing method called metagenomics, Wellcome Sanger Institute’s Dr. Luis Camarillo-Guerrero and colleagues explored and catalogued the biodiversity of the viral species found in 28,060 public human gut metagenomes and 2,898 bacterial isolate genomes cultured from the human gut. “It’s important to remember that not all viruses are harmful, but represent an integral component of the gut ecosystem,” said co-author Dr. Alexandre Almeida, a postdoctoral researcher at the European Bioinformatics Institute and the Wellcome Sanger Institute. “For one thing, most of the viruses we found have DNA as their genetic material, which is different from the pathogens most people know, such as SARS-CoV-2 or Zika, which are RNA viruses.” “Secondly, these samples came mainly from healthy individuals who didn’t share any specific diseases.” “It’s fascinating to see how many unknown species live in our gut, and to try and unravel the link between them and human health.” The researchers also identified a previously unknown clade of bacteriophages, named Gubaphage. This was found to be the second most prevalent virus clade in the human gut, after crAssphage, which was discovered in 2014. “An important aspect of our work was to ensure that the reconstructed viral genomes were of the highest quality,” Dr. Camarillo-Guerrero said. “A stringent quality control pipeline coupled with a machine learning approach enabled us to mitigate contamination and obtain highly complete viral genomes.” “High-quality viral genomes pave the way to better understand what role viruses play in our gut microbiome, including the discovery of new treatments such as antimicrobials from bacteriophage origin.” The team’s results form the basis of the Gut Phage Database, a highly curated database of phage genomes that will be an invaluable resource for those studying bacteriophages and the role they play on regulating the health of both our gut bacteria and ourselves. “Bacteriophage research is currently experiencing a renaissance,” said Dr. Trevor Lawley, a researcher at the Wellcome Sanger Institute. “This high-quality, large-scale catalogue of human gut viruses comes at the right time to serve as a blueprint to guide ecological and evolutionary analysis in future virome studies.” Findings published in Cell (Feb. 18, 2021): https://doi.org/10.1016/j.cell.2021.01.029
Via Juan Lama
The Index is composed of three ‘pillars’ – composite indicators developed to capture the different dimensions and challenges of digital learning: 1) Individual’s learning outcomes; 2) Availability of digital learning; and 3) Institutions and policies for digital learning. The report details the Index’s construction as well as results, alongside current trends in digitalisation of learning in Europe, providing timely policy pointers to European- and national-level policy makers.
Via Nik Peachey
The British Society for Immunology has partnered with the Centre for Inflammation Research at the University of Edinburgh to present a three-part animated series for public audiences on the human immune system and how immune memories form in response to infections like coronavirus.
Via Gilbert C FAURE
In addition to potential wildlife reservoirs of coronavirus infection (eg bats, civet cats, pangolins, mice, rats, etc), there are a number of animal coronaviruses which infect livestock (cattle, swine, poultry, camels) and companion animals (dogs, cats). These viruses cause a range of diseases which predominately result in respiratory symptoms or gastroenteritis. Successful commercial vaccines have been developed for the majority of these veterinary coronavirus diseases. There are lessons to be learned from these successes and also from diseases that have proved to be more problematic.
Via Ed Rybicki
Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots of Brassicaceae, poplar, and maize. We then compared 3,837 bacterial genomes to identify thousands of plant-associated gene clusters. Genomes of plant-associated bacteria encode more carbohydrate metabolism functions and fewer mobile elements than related non-plant-associated genomes do. We experimentally validated candidates from two sets of plant-associated genes: one involved in plant colonization, and the other serving in microbe–microbe competition between plant-associated bacteria. We also identified 64 plant-associated protein domains that potentially mimic plant domains; some are shared with plant-associated fungi and oomycetes. This work expands the genome-based understanding of plant–microbe interactions and provides potential leads for efficient and sustainable agriculture through microbiome engineering.
Via Francis Martin
Although the complex interactions between hosts and microbial associates are increasingly well documented, we still know little about how and why hosts shape microbial communities in nature. We characterized the leaf microbiota within 200 clonal accessions in eight field experiments and detected effects of both local environment and host genotype on community structure. Within environments, hosts′ genetics preferentially associate with a core of ubiquitous microbial hubs that, in turn, structure the community. These microbial hubs correlate with host performance, and a GWAS revealed strong candidate genes for the host factors impacting heritable hubs. Our results reveal how selection may act to enhance fitness through microbial associations and bolster the possibility of enhancing crop performance through these host factors.
Via Kamoun Lab @ TSL
Recent evidences suggest that human gut microbiota with major component as bacteria can induce immunity. It is also known that gut lining depletes with ageing and that there is increased risk of autoimmune and inflammatory disorders with ageing. It is therefore likely that both may be correlated as depletion of gut lining exposes the gut bacterial antigens to host immune mechanisms, which may induce immunity to certain bacterial proteins, but at the same time such immunity may also be auto-immunogenic to host. This autoimmunity may make a protein molecule nonfunctional and thereby may be involved in late onset metabolic, autoimmune and inflammatory disorders such as, Diabetes, Rheumatoid Arthritis, Hyperlipidemias and Cancer. In this in-silico study we found a large number of peptides identical between human and gut bacteria which were binding to HLA-II alleles, and hence, likely to be auto-immunogenic. Further we observed that such autoimmune candidates were enriched in bacterial species belonging to Firmicutes and Proteobacteria phyla, which lead us to conclude that these phyla may have higher disease impact in genetically predisposed individuals. Functional annotation of human proteins homologous to candidate gut-bacterial peptides showed significant enrichment in metabolic processes and pathways. Cognitive trait, Ageing, Alzheimer, Type 2 diabetes, Chronic Kidney Failure (CKF), Chronic Obstructive Pulmonary Disease (COPD) and various Cancers were the major diseases represented in the dataset. This dataset provides us with gut bacterial autoimmune candidates which can be studied for their clinical significance in late onset diseases.
Via Krishan Maggon
The classification of complex organisms is in chaos. Stephen T. Garnett and Les Christidis propose a solution.
And that solution in part is that leg- and leaf-ologists (aka animal and plant taxonomists) take the example of the International Committee on Taxonomy of Viruses. Excellent!
Via Ed Rybicki
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Two recent papers have demonstrated that during a critical early period of brain development, the gut’s microbiome — the assortment of bacteria that grow within in it — helps to mold a brain system that’s important for social skills later in life. Scientists found this influence in fish, but molecular and neurological evidence plausibly suggests that some form of it could also occur in mammals, including humans. In a recent paper published in PLOS Biology, researchers found that zebra fish who grew up lacking a gut microbiome were far less social than their peers with colonized colons, and the structure of their brains reflected the difference. In a related article in BMC Genomics in late September, they described molecular characteristics of the neurons affected by the gut bacteria. Equivalents of those neurons appear in rodents, and scientists can now look for them in other species, including humans.
Via Dr. Stefan Gruenwald
COVID-19 deteriorates type II pneumocytes and damages the alveolar immunologic balancing process through the inadvertent activation of a sequence of localized and general inflammatory responses.Due to an aggregation of uncleaved angiotensin II, the stimulated inflammatory cells cause cytokines synt...
Via Gilbert C FAURE
Powerful advances in genome sequencing technology, informatics, automation, and artificial intelligence, have propelled humankind to the threshold of a new beginning in understanding, utilizing, and conserving biodiversity. For the first time in history, it is possible to efficiently sequence the genomes of all known species, and to use genomics to help discover the remaining 80 to 90 percent of species that are currently hidden from science. A GRAND CHALLENGE The Earth BioGenome Project (EBP), a moonshot for biology, aims to sequence, catalog and characterize the genomes of all of Earth’s eukaryotic biodiversity over a period of ten years. A GRAND VISION Create a new foundation for biology to drive
solutions for preserving biodiversity and sustaining human societies.
Via Dr. Stefan Gruenwald
Among the many activities attributed to the type I interferon (IFN) multigene family, their roles as mediators of the antiviral immune response have emerged as important components of the host response to Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection.
Via Gilbert C FAURE
The present crisis has brought rapid and dramatic changes to the world of work, and the world of teaching has been no exception. Teachers have suddenly been forced, by circumstances, to adapt their skills to working online in live virtual classrooms with little or no preparation or training.
Most schools and teachers have faced the challenge and, ready or not, teachers have launched their students into online classrooms using commonly used tools like Zoom or Skype. But now the initial panic is over, we can take a closer look at the kinds of technology available for the delivery of live online learning and the kinds of training teachers need to be able to use that technology effectively.
Via Dr. Stefan Gruenwald, Franc Viktor Nekrep
The transmission and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are of paramount importance in controlling and combating the coronavirus disease 2019 (COVID-19) pandemic.
Via Gilbert C FAURE
Permafrost covers 24 percent of the Earth’s land surface, and the soil constituents vary with local geology. Arctic lands offer unexplored microbial biodiversity and microbial feedbacks, including the release of carbon to the atmosphere. In some locations, hundreds of millions of years’ worth of carbon is buried. The layers may still contain ancient frozen microbes, Pleistocene megafauna and even buried smallpox victims. As the permafrost thaws with increasing rapidity, scientists’ emerging challenge is to discover and identify the microbes, bacteria and viruses that may be stirring. Some of these microbes are known to scientists. Methanogenic Archaea, for example metabolize soil carbon to release methane, a potent greenhouse gas. Other permafrost microbes (methanotrophs) consume methane. The balance between these microbes plays a critical role in determining future climate warming. Others are known but have unpredictable behavior after release. New evidence of genes moving between thawing ecosystems indicates a restructuring at multiple levels. In the Arctic Ocean, planktonic Chloroflexi bacteria recently acquired genes used for degrading carbon from land-based Actinobacteria species. As melt-swollen Arctic rivers carried sediments from thawing permafrost to the sea, the genes for processing permafrost carbon were also transported. Permafrost thaw in Siberia led to a 2016 anthrax outbreak and the death of 200,000 reindeer and a child.* But the hardy spores of Bacillus anthracis may represent an exception to the brutal freeze-thaw cycle that degrades more delicate bacterial and viral pathogens. Their adaptable characteristics have allowed them to remain frozen and viable over centuries of inactivity. Organisms that co-evolved within now-extinct ecosystems from the Cenozoic to the Pleistocene may also emerge and interact with our modern environment in entirely novel ways. A potential example, the emerging Orthopoxvirus species Alaskapox causing skin lesions, has appeared and disappeared in Alaska twice in the last five years. It is possible that the virus was transmitted through animal-human contact, but this novel virus’s origin remains unknown.
Via Dr. Stefan Gruenwald
Extracellular vesicles (EVs) are lipid compartments capable of trafficking proteins, lipids, RNA and metabolites between cells. Plant cells have been shown to secrete EVs during immune responses, but virtually nothing is known about their formation, contents or ultimate function. Recently developed methods for isolating plant EVs have revealed that these EVs are enriched in stress response proteins and signaling lipids, and appear to display antifungal activity. Comparison to work on animal EVs, and the observation that host-derived small interfering RNAs and microRNAs can silence fungal genes, suggests that plant EVs may also mediate trans-kingdom RNA interference. Many fundamental questions remain, however, regarding how plant EVs are produced, how they move, and if and how they are taken up by target cells.
Tritrophic interactions involving a biocontrol agent, a pathogen and a plant have been analyzed predominantly from the perspective of the biocontrol agent. We have conducted the first comprehensive transcriptomic analysis of all three organisms in an effort to understand the elusive properties of Pseudozyma flocculosa in the context of its biocontrol activity against Blumeria graminis f.sp. hordei as it parasitizes Hordeum vulgare.After inoculation of P. flocculosa, the tripartite interaction was monitored over time and samples collected for scanning electron microscopy and RNA sequencing.Based on our observations, P. flocculosa indirectly parasitizes barley, albeit transiently, by diverting nutrients extracted by B. graminis from barley leaves through a process involving unique effectors. This brings novel evidence that such molecules can also influence fungal–fungal interactions. Their release is synchronized with a higher expression of powdery mildew haustorial effectors, a sharp decline in the photosynthetic machinery of barley and a developmental peak in P. flocculosa. The interaction culminates with a collapse of B. graminis haustoria, thereby stopping P. flocculosa growth, as barley plants show higher metabolic activity.To conclude, our study has uncovered a complex and intricate phenomenon, described here as hyperbiotrophy, only achievable through the conjugated action of the three protagonists.
Via Kamoun Lab @ TSL
Credit: IAVI LA JOLLA - Cows are leaving the pasture and entering the field...of HIV vaccine research. As outlined in a study published today in Nature, lead author Devin Sok, Director, Antibody Di..
Via Ed Rybicki
Plants engineer the rhizosphere to their advantage by secreting various nutrients and secondary metabolites. Coupling transcriptomic and metabolomic analyses of the pea (Pisum sativum) rhizosphere, a suite of bioreporters has been developed in Rhizobium leguminosarum bv viciae strain 3841, and these detect metabolites secreted by roots in space and time. Fourteen bacterial lux fusion bioreporters, specific for sugars, polyols, amino acids, organic acids, or flavonoids, have been validated in vitro and in vivo. Using different bacterial mutants (nodC and nifH), the process of colonization and symbiosis has been analyzed, revealing compounds important in the different steps of the rhizobium-legume association. Dicarboxylates and sucrose are the main carbon sources within the nodules; in ineffective (nifH) nodules, particularly low levels of sucrose were observed, suggesting that plant sanctions affect carbon supply to nodules. In contrast, high myo-inositol levels were observed prior to nodule formation and also in nifH senescent nodules. Amino acid biosensors showed different patterns: a γ-aminobutyrate biosensor was active only inside nodules, whereas the phenylalanine bioreporter showed a high signal also in the rhizosphere. The bioreporters were further validated in vetch (Vicia hirsuta), producing similar results. In addition, vetch exhibited a local increase of nod gene-inducing flavonoids at sites where nodules developed subsequently. These bioreporters will be particularly helpful in understanding the dynamics of root exudation and the role of different molecules secreted into the rhizosphere.
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