scholarly journals LARGE-SCALE GENOME SAMPLING REVEALS UNIQUE IMMUNITY AND METABOLIC ADAPTATIONS IN BATS

2021 ◽  
Author(s):  
Diana Moreno Santillan ◽  
Tanya Lama ◽  
Yocelyn Gutiérrez Guerrero ◽  
Alexis Brown ◽  
Paul Donat ◽  
...  
Keyword(s):  
Immune System ◽  
Gene Family ◽  
Molecular Mechanisms ◽  
Small Body ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Metabolic Genes ◽  
Pathway Gene ◽  
Genomic Study ◽  
Molecular Patterns

Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune system and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.

scholarly journals LARGE-SCALE GENOME SAMPLING REVEALS UNIQUE IMMUNITY AND METABOLIC ADAPTATIONS IN BATS

2021 ◽  
Author(s):  
Diana Moreno Santillan ◽  
Tanya Lama ◽  
Yocelyn Gutiérrez Guerrero ◽  
Alexis Brown ◽  
Paul Donat ◽  
...  
Keyword(s):  
Immune System ◽  
Gene Family ◽  
Molecular Mechanisms ◽  
Small Body ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Metabolic Genes ◽  
Pathway Gene ◽  
Genomic Study ◽  
Molecular Patterns

Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune system and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.

scholarly journals LARGE-SCALE GENOME SAMPLING REVEALS UNIQUE IMMUNITY AND METABOLIC ADAPTATIONS IN BATS

2021 ◽  
Author(s):  
Diana Moreno Santillan ◽  
Tanya Lama ◽  
Yocelyn Gutiérrez Guerrero ◽  
Alexis Brown ◽  
Paul Donat ◽  
...  
Keyword(s):  
Immune System ◽  
Gene Family ◽  
Molecular Mechanisms ◽  
Small Body ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Metabolic Genes ◽  
Pathway Gene ◽  
Genomic Study ◽  
Molecular Patterns

Comprising more than 1400 species, bats possess adaptations unique among mammals including powered flight, unexpected longevity given small body size, and extraordinary immunity. Some of the molecular mechanisms underlying these unique adaptations includes DNA repair, metabolism and immunity. However, analyses have been limited to a few divergent lineages, reducing the scope of inferences on gene family evolution across the Order Chiroptera. We conducted an exhaustive comparative genomic study of 37 bat species encompassing a large number of lineages, with a particular emphasis on multi-gene family evolution across immune system and metabolic genes. In agreement with previous analyses, we found lineage-specific expansions of the APOBEC3 and MHC-I gene families, and loss of the proinflammatory PYHIN gene family. We inferred more than 1,000 gene losses unique to bats, including genes involved in the regulation of inflammasome pathways such as epithelial defense receptors, the natural killer gene complex and the interferon-gamma induced pathway. Gene set enrichment analyses revealed genes lost in bats are involved in defense response against pathogen-associated molecular patterns and damage-associated molecular patterns. Gene family evolution and selection analyses indicate bats have evolved fundamental functional differences compared to other mammals in both innate and adaptive immune system, with the potential to enhance anti-viral immune response while dampening inflammatory signaling. In addition, metabolic genes have experienced repeated expansions related to convergent shifts to plant-based diets. Our analyses support the hypothesis that, in tandem with flight, ancestral bats had evolved a unique set of immune adaptations whose functional implications remain to be explored.

scholarly journals Large-scale genomic study reveals robust activation of the immune system following advanced Inner Engineering meditation retreat

2021 ◽  
Vol 118 (51) ◽  
pp. e2110455118
Author(s):  
Vijayendran Chandran ◽  
Mei-Ling Bermúdez ◽  
Mert Koka ◽  
Brindha Chandran ◽  
Dhanashri Pawale ◽  
...  
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Positive Impact ◽  
Well Being ◽  
Core Network ◽  
Protein Protein Interaction ◽  
Genomic Study ◽  
Meditation Retreat

The positive impact of meditation on human well-being is well documented, yet its molecular mechanisms are incompletely understood. We applied a comprehensive systems biology approach starting with whole-blood gene expression profiling combined with multilevel bioinformatic analyses to characterize the coexpression, transcriptional, and protein–protein interaction networks to identify a meditation-specific core network after an advanced 8-d Inner Engineering retreat program. We found the response to oxidative stress, detoxification, and cell cycle regulation pathways were down-regulated after meditation. Strikingly, 220 genes directly associated with immune response, including 68 genes related to interferon signaling, were up-regulated, with no significant expression changes in the inflammatory genes. This robust meditation-specific immune response network is significantly dysregulated in multiple sclerosis and severe COVID-19 patients. The work provides a foundation for understanding the effect of meditation and suggests that meditation as a behavioral intervention can voluntarily and nonpharmacologically improve the immune response for treating various conditions associated with excessive or persistent inflammation with a dampened immune system profile.

scholarly journals Comparative Genomic Insights into the Longhorned Tick, Haemaphysalis Longicornis

2020 ◽  
Author(s):  
Rui-Ling Zhang ◽  
Qian Zhang ◽  
Zhong Zhang
Keyword(s):  
Gene Family ◽  
Genome Assembly ◽  
Animal Health ◽  
Gene Families ◽  
High Ratio ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Haemaphysalis Longicornis ◽  
Gene Set ◽  
Terrestrial Vertebrates

Abstract Background: The longhorned tick, Haemaphysalis longicornis Neumann, is widely distributed across temperate regions. It can parasitize terrestrial vertebrates, including birds and a large number of mammals. They are a concern in human and animal health notably for their potential to transmit infectious agents. Methods: Genome survey was investigated using GenomeScope v1.0.0 with a maximum k-mer coverage cutoff of 1,000. Non-redundant assembly was polished with Illumina short reads using two rounds of NextPolish v1.1.0. Genome completeness was assessed using BUSCO v3.0.2 pipeline analyses against arthropod gene set (n = 1, 066). Ab initio predictions were generated using BRAKER v2.1.5. Transcriptomic reads were mapped to the genome with HISAT2 v2.2.0 and assembled with StringTie v2.1.2. Gene functions were assigned against UniProtKB database using Diamond v0.9.24. Orthogroups of 16 Chelicerata species were inferred using OrthoFinder v2.3.8 and gene family evolution was estimated using CAFÉ v4.2.1. Gene families related to digestion and detoxification, i.e. cytochrome P450 (CYP), carboxyl/cholinesterase (CCE), glutathione-S-transferase (GST), ATP-binding cassette (ABC) transporter were annotated by searching in the genome assembly. Results: The final genome assembly has a size of 3.12 Gb, a scaffold N50 of 1.09 Mb, and captured 92.4% of the BUSCO gene set (n=1,066). Genome architecture pattern of the longhorned tick resembles another tick, Ixodes scapularis (Say), particularly in large size, highly repetitive DNA (~65%) and protein-coding genes (21,550). We also identified 5,601 non-coding RNAs with a high ratio of tRNAs (4,271). Gene family evolution revealed 350 rapidly evolving gene families. Combining function enrichment analyses of gene ontology (GO) and KEGG pathway, 255 families experiencing significant expansions mainly involves in cuticle synthesis, digestion and detoxification. Conclusions: The new genome assembly, annotation and comparative genomic analyses provide a valuable resource for insights into parasitic life mode of the longhorned tick.

scholarly journals A two-type branching process model of gene family evolution

2021 ◽  
Author(s):  
Arthur Zwaenepoel ◽  
Yves Van de Peer
Keyword(s):  
Gene Family ◽  
Process Model ◽  
Branching Process ◽  
Gene Loss ◽  
Simulated Data ◽  
Gene Families ◽  
Gene Family Evolution ◽  
Comparative Genomic ◽  
Model Parameters ◽  
Data Sets

AbstractPhylogenetic models of gene family evolution based on birth-death processes (BDPs) vide an awkward fit to comparative genomic data sets. A central assumption of these models is the constant per-gene loss rate in any particular family. Because of the possibility of partial functional redundancy among gene family members, gene loss dynamics are however likely to be dependent on the number of genes in a family, and different variations of commonly employed BDP models indeed suggest this is the case. We propose a simple two-type branching process model to better approximate the stochastic evolution of gene families by gene duplication and loss and perform Bayesian statistical inference of model parameters in a phylogenetic context. We evaluate the statistical methods using simulated data sets and apply the model to gene family data for Drosophila, yeasts and primates, providing new quantitative insights in the long-term maintenance of duplicated genes.

scholarly journals Brain Immune Interactions—Novel Emerging Options to Treat Acute Ischemic Brain Injury

Cells ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 2429
Author(s):  
Sajjad Muhammad ◽  
Shafqat Rasul Chaudhry ◽  
Ulf Dietrich Kahlert ◽  
Mika Niemelä ◽  
Daniel Hänggi
Keyword(s):  
Ischemic Stroke ◽  
Immune System ◽  
Molecular Mechanisms ◽  
Time Window ◽  
Critical Role ◽  
Current Evidence ◽  
Future Research ◽  
Mortality And Morbidity ◽  
Molecular Patterns ◽  
The Brain

Ischemic stroke is still among the leading causes of mortality and morbidity worldwide. Despite intensive advancements in medical sciences, the clinical options to treat ischemic stroke are limited to thrombectomy and thrombolysis using tissue plasminogen activator within a narrow time window after stroke. Current state of the art knowledge reveals the critical role of local and systemic inflammation after stroke that can be triggered by interactions taking place at the brain and immune system interface. Here, we discuss different cellular and molecular mechanisms through which brain–immune interactions can take place. Moreover, we discuss the evidence how the brain influence immune system through the release of brain derived antigens, damage-associated molecular patterns (DAMPs), cytokines, chemokines, upregulated adhesion molecules, through infiltration, activation and polarization of immune cells in the CNS. Furthermore, the emerging concept of stemness-induced cellular immunity in the context of neurodevelopment and brain disease, focusing on ischemic implications, is discussed. Finally, we discuss current evidence on brain–immune system interaction through the autonomic nervous system after ischemic stroke. All of these mechanisms represent potential pharmacological targets and promising future research directions for clinically relevant discoveries.

scholarly journals A new gene family diagnostic for intracellular biomineralization of amorphous Ca-carbonates by cyanobacteria

2021 ◽  
Author(s):  
Karim Benzerara ◽  
Elodie Duprat ◽  
Tristan Bitard-Feildel ◽  
Géraldine Caumes ◽  
Corinne Cassier-Chauvat ◽  
...  
Keyword(s):  
Gene Family ◽  
Molecular Mechanisms ◽  
Phylogenetic Analyses ◽  
Marine Species ◽  
Comparative Genomic ◽  
Environmental Distribution ◽  
Calcium Carbonates ◽  
Terminal Domain ◽  
Biomineralization Process ◽  
New Gene

Cyanobacteria have massively contributed to carbonate deposit formation over the geological history. They are traditionally thought to biomineralize CaCO3 extracellularly as an indirect byproduct of photosynthesis. However, the recent discovery of freshwater cyanobacteria forming intracellular amorphous calcium carbonates (iACC) challenges this view. Despite the geochemical interest of such a biomineralization process, its molecular mechanisms and evolutionary history remain elusive. Here, using comparative genomics, we identify a new gene (ccyA) and protein (calcyanin) family specifically associated with cyanobacterial iACC biomineralization. Calcyanin is composed of a conserved C-terminal domain, which likely adopts an original fold, and a variable N- terminal domain whose structure allows differentiating 4 major types among the 35 known calcyanin homologues. Calcyanin lacks detectable full-length homologs with known function. Yet, genetic and comparative genomic analyses suggest a possible involvement in Ca homeostasis, making this gene family a particularly interesting target for future functional studies. Whatever its function, this new gene family appears as a gene diagnostic of intracellular calcification in cyanobacteria. By searching for ccyA in publicly available genomes, we identified 13 additional cyanobacterial strains forming iACC. This significantly extends our knowledge about the phylogenetic and environmental distribution of cyanobacterial iACC biomineralization, especially with the detection of multicellular genera as well as a marine species. Phylogenetic analyses indicate that iACC biomineralization is ancient, with independent losses in various lineages and some HGT cases that resulted in the broad but patchy distribution of calcyanin across modern cyanobacteria. Overall, iACC biomineralization emerges as a new case of genetically controlled biomineralization in bacteria.

scholarly journals Sugar Transporter Proteins (STPs) in Gramineae Crops: Comparative Analysis, Phylogeny, Evolution, and Expression Profiling

Cells ◽  
2019 ◽  
Vol 8 (6) ◽  
pp. 560 ◽  
Author(s):  
Weilong Kong ◽  
Baoguang An ◽  
Yue Zhang ◽  
Jing Yang ◽  
Shuangmiao Li ◽  
...  
Keyword(s):  
Gene Family ◽  
Evolutionary Dynamics ◽  
Brachypodium Distachyon ◽  
Oryza Rufipogon ◽  
Comparative Genomic ◽  
Sugar Transporter ◽  
Transporter Proteins ◽  
Genomic Study ◽  
Duplication Events ◽  
Selective Forces

Sugar transporter proteins (STPs), such as H+/sugar symporters, play essential roles in plants’ sugar transport, growth, and development, and possess an important potential to enhance plants’ performance of multiple agronomic traits, especially crop yield and stress tolerance. However, the evolutionary dynamics of this important gene family in Gramineae crops are still not well-documented and functional differentiation of rice STP genes remain unclear. To address this gap, we conducted a comparative genomic study of STP genes in seven representative Gramineae crops, which are Brachypodium distachyon (Bd), Hordeum vulgare (Hv), Setaria italica (Si), Sorghum bicolor (Sb), Zea mays (Zm), Oryza rufipogon (Or), and Oryza sativa ssp. japonica (Os). In this case, a total of 177 STP genes were identified and grouped into four clades. Of four clades, the Clade I, Clade III, and Clade IV showed an observable number expansion compared to Clade II. Our results of identified duplication events and divergence time of duplicate gene pairs indicated that tandem, Whole genome duplication (WGD)/segmental duplication events play crucial roles in the STP gene family expansion of some Gramineae crops (expect for Hv) during a long-term evolutionary process. However, expansion mechanisms of the STP gene family among the tested species were different. Further selective force studies revealed that the STP gene family in Gramineae crops was under purifying selective forces and different clades and orthologous groups with different selective forces. Furthermore, expression analysis showed that rice STP genes play important roles not only in flower organs development but also under various abiotic stresses (cold, high-temperature, and submergence stresses), blast infection, and wounding. The current study highlighted the expansion and evolutionary patterns of the STP gene family in Gramineae genomes and provided some important messages for the future functional analysis of Gramineae crop STP genes.

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