scholarly journals Life out of water: Genomic and physiological mechanisms underlying skin phenotypic plasticity

2019 ◽  
Author(s):  
Yun-wei Dong ◽  
Tessa S. Blanchard ◽  
Angela Noll ◽  
Picasso Vasquez ◽  
Juergen Schmitz ◽  
...  
Keyword(s):  
Morphological Data ◽  
Evolutionary Analysis ◽  
Ion Regulation ◽  
Mechanical Reinforcement ◽  
Air Exposure ◽  
Cell Structures ◽  
Freshwater Habitats ◽  
Terrestrial Habitats ◽  
Skin Morphogenesis ◽  
And Function

AbstractThe Devonian radiation of vertebrates from aquatic into terrestrial habitats required behavioral, physiological, and morphological adaptations. Changes to skin structure and function were likely crucial, but adaptations were needed to resolve contrasting demands of maintaining a mechanical and physiological barrier while also facilitating ion and gas transport. Little is known of the mechanisms that underlie skin plasticity and adaptation between water and air. We performed experiments using two isogenic lineages of an amphibious killifish (Kryptolebias marmoratus from brackish and freshwater habitats) and used transcriptional and morphological data to reveal mechanisms recruited to resolve the dual challenges of skin providing both a barrier and an exchange interface during terrestrial acclimation. Transcriptional regulators of skin morphogenesis were quickly activated upon emersion. Regulation of cell-cell adhesion complexes, coupled with pathways homologous with those that regulate stratum corneum formation, was consistent with barrier function and mechanical reinforcement. Cutaneous respiration was associated with regulation of angiogenesis pathways and with blood vessel architecture that facilitated extremely short diffusion distances and direct delivery to ionocyotes. Evolutionary analyses revealed directional selection operating on proteins involved in barrier and respiratory functions, reinforcing the importance of these mechanisms for enabling the amphibious lifestyle of K. marmoratus. Fish from brackish niches were more resilient to emersion and also differed from freshwater fish in ionoregulatory responses to emersion. We conclude that plasticity of barrier, respiratory, and ionoregulatory functions in skin evolved to support the amphibious lifestyle of K. marmoratus; similar processes may have facilitated the terrestrial radiation of ancient fishes.Significance statementThe transition of vertebrate life from water to land coincided with solving multiple physiological challenges including avoiding drying out while also exchanging gases and ions with the environment. Though changes in the skin were likely important, little is known of the mechanisms that underlie skin flexibility and adaptation between water and air. We performed air exposure experiments with an amphibious killifish; gene expression profiling, microscopy, and evolutionary analysis of proteins revealed cell structures, proteins, and molecular pathways that support skin flexibility and adaptations during air exposure, and ion regulation contributed to differences in killifish abilities to adjust to air. Amphibious killifish are useful models to help us understand changes that enable water to air transitions in contemporary and ancient fishes.

scholarly journals Genomic and physiological mechanisms underlying skin plasticity during water to air transition in an amphibious fish

2020 ◽  
pp. jeb.235515
Author(s):  
Yun-wei Dong ◽  
Tessa S. Blanchard ◽  
Angela Noll ◽  
Picasso Vasquez ◽  
Juergen Schmitz ◽  
...  
Keyword(s):  
Transcriptional Regulation ◽  
Cell Adhesion ◽  
Blood Vessel ◽  
Physiological Mechanisms ◽  
Mechanical Reinforcement ◽  
Salinity Acclimation ◽  
Air Exposure ◽  
Kryptolebias Marmoratus ◽  
Skin Morphogenesis ◽  
Cutaneous Respiration

The terrestrial radiation of vertebrates required changes in skin that resolved the dual demands of maintaining a mechanical and physiological barrier while also facilitating ion and gas transport. Using the amphibious killifish Kryptolebias marmoratus, we found that transcriptional regulation of skin morphogenesis was quickly activated upon air exposure (1h). Rapid regulation of cell-cell adhesion complexes and pathways that regulate stratum corneum formation was consistent with barrier function and mechanical reinforcement. Unique blood vessel architecture and regulation of angiogenesis likely supported cutaneous respiration. Differences in ionoregulatory transcripts and ionocyte morphology were correlated with differences in salinity acclimation and resilience to air exposure. Evolutionary analyses reinforced the adaptive importance of these mechanisms. We conclude that rapid plasticity of barrier, respiratory, and ionoregulatory functions in skin evolved to support K. marmoratus’ amphibious lifestyle; similar processes may have facilitated the terrestrial radiation of other contemporary and ancient fishes.

scholarly journals Ancestry of the AUTS2 family–A novel group of polycomb-complex proteins involved in human neurological disease

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0232101
Author(s):  
Robert A. Sellers ◽  
David L. Robertson ◽  
May Tassabehji
Keyword(s):  
Autosomal Dominant ◽  
Large Population ◽  
Evolutionary Analysis ◽  
Genome Data ◽  
High Prevalence ◽  
And Function ◽  
Polycomb Complex ◽  
Putative Domain ◽  
Human Specific

Autism susceptibility candidate 2 (AUTS2) is a neurodevelopmental regulator associated with an autosomal dominant intellectual disability syndrome, AUTS2 syndrome, and is implicated as an important gene in human-specific evolution. AUTS2 exists as part of a tripartite gene family, the AUTS2 family, which includes two relatively undefined proteins, Fibrosin (FBRS) and Fibrosin-like protein 1 (FBRSL1). Evolutionary ancestors of AUTS2 have not been formally identified outside of the Animalia clade. A Drosophila melanogaster protein, Tay bridge, with a role in neurodevelopment, has been shown to display limited similarity to the C-terminal of AUTS2, suggesting that evolutionary ancestors of the AUTS2 family may exist within other Protostome lineages. Here we present an evolutionary analysis of the AUTS2 family, which highlights ancestral homologs of AUTS2 in multiple Protostome species, implicates AUTS2 as the closest human relative to the progenitor of the AUTS2 family, and demonstrates that Tay bridge is a divergent ortholog of the ancestral AUTS2 progenitor gene. We also define regions of high relative sequence identity, with potential functional significance, shared by the extended AUTS2 protein family. Using structural predictions coupled with sequence conservation and human variant data from 15,708 individuals, a putative domain structure for AUTS2 was produced that can be used to aid interpretation of the consequences of nucleotide variation on protein structure and function in human disease. To assess the role of AUTS2 in human-specific evolution, we recalculated allele frequencies at previously identified human derived sites using large population genome data, and show a high prevalence of ancestral alleles, suggesting that AUTS2 may not be a rapidly evolving gene, as previously thought.

Water Quantity and Hydrology

2018 ◽  
pp. 67-88 ◽  
Author(s):  
Matthew McCartney
Keyword(s):  
Water Discharge ◽  
Freshwater Ecosystems ◽  
Freshwater Ecosystem ◽  
Ecosystem Structure ◽  
Freshwater Biodiversity ◽  
Freshwater Habitats ◽  
And Function ◽  
Induced Changes ◽  
Ecosystem Structure And Function ◽  
Hydrological Monitoring

Freshwater ecosystems are naturally dynamic. The source of water, discharge, turnover, and residence times all affect which organisms can live in different freshwater habitats and are key determinants of freshwater ecosystem structure and function. Human-induced changes to the volume and timing of both surface and ground water flows are a leading driver of global declines in freshwater biodiversity and are likely to be exacerbated by climate change. The conservation of many wetlands around the world, including in some cases the preservation of unique flora and fauna, is now entirely dependent on continued human intervention and water management. Such management can only be successful if based on sound understanding of water budgets and hydrological processes informed by accurate hydrological monitoring. This chapter provides a brief introduction to hydrological monitoring—what needs to be measured and how—for freshwater ecology and conservation.

scholarly journals Revealing hidden insect–fungus interactions; moderately specialized, modular and anti-nested detritivore networks

2018 ◽  
Vol 285 (1876) ◽  
pp. 20172833 ◽  
Author(s):  
Rannveig M. Jacobsen ◽  
Anne Sverdrup-Thygeson ◽  
Håvard Kauserud ◽  
Tone Birkemoe
Keyword(s):  
Dead Wood ◽  
Wood Decay ◽  
Pathogenic Fungi ◽  
Ecosystem Structure ◽  
Decay Fungi ◽  
Wood Decay Fungi ◽  
Terrestrial Habitats ◽  
And Function ◽  
Randomized Networks ◽  
Ecosystem Structure And Function

Ecological networks are composed of interacting communities that influence ecosystem structure and function. Fungi are the driving force for ecosystem processes such as decomposition and carbon sequestration in terrestrial habitats, and are strongly influenced by interactions with invertebrates. Yet, interactions in detritivore communities have rarely been considered from a network perspective. In the present study, we analyse the interaction networks between three functional guilds of fungi and insects sampled from dead wood. Using DNA metabarcoding to identify fungi, we reveal a diversity of interactions differing in specificity in the detritivore networks, involving three guilds of fungi. Plant pathogenic fungi were relatively unspecialized in their interactions with insects inhabiting dead wood, while interactions between the insects and wood-decay fungi exhibited the highest degree of specialization, which was similar to estimates for animal-mediated seed dispersal networks in previous studies. The low degree of specialization for insect symbiont fungi was unexpected. In general, the pooled insect–fungus networks were significantly more specialized, more modular and less nested than randomized networks. Thus, the detritivore networks had an unusual anti-nested structure. Future studies might corroborate whether this is a common aspect of networks based on interactions with fungi, possibly owing to their often intense competition for substrate.

scholarly journals Hair Follicle Stem Cells Are Specified and Function in Early Skin Morphogenesis

2008 ◽  
Vol 3 (1) ◽  
pp. 33-43 ◽  
Author(s):  
Jonathan A. Nowak ◽  
Lisa Polak ◽  
H. Amalia Pasolli ◽  
Elaine Fuchs
Keyword(s):  
Stem Cells ◽  
Hair Follicle ◽  
Hair Follicle Stem Cells ◽  
Skin Morphogenesis ◽  
And Function ◽  
Follicle Stem Cells

scholarly journals Viral macrodomains: a structural and evolutionary assessment of the pharmacological potential

Open Biology ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 200237 ◽  
Author(s):  
Johannes Gregor Matthias Rack ◽  
Valentina Zorzini ◽  
Zihan Zhu ◽  
Marion Schuller ◽  
Dragana Ahel ◽  
...  
Keyword(s):  
Virus Disease ◽  
Cross Reactivity ◽  
Structural Basis ◽  
Evolutionary Analysis ◽  
Structural Studies ◽  
Post Translational Modification ◽  
Necrosis Virus ◽  
Adp Ribosylation ◽  
Pharmacological Potential ◽  
And Function

Viral macrodomains possess the ability to counteract host ADP-ribosylation, a post-translational modification implicated in the creation of an antiviral environment via immune response regulation. This brought them into focus as promising therapeutic targets, albeit the close homology to some of the human macrodomains raised concerns regarding potential cross-reactivity and adverse effects for the host. Here, we evaluate the structure and function of the macrodomain of SARS-CoV-2, the causative agent of COVID-19. We show that it can antagonize ADP-ribosylation by PARP14, a cellular (ADP-ribosyl)transferase necessary for the restriction of coronaviral infections. Furthermore, our structural studies together with ligand modelling revealed the structural basis for poly(ADP-ribose) binding and hydrolysis, an emerging new aspect of viral macrodomain biology. These new insights were used in an extensive evolutionary analysis aimed at evaluating the druggability of viral macrodomains not only from the Coronaviridae but also Togaviridae and Iridoviridae genera (causing diseases such as Chikungunya and infectious spleen and kidney necrosis virus disease, respectively). We found that they contain conserved features, distinct from their human counterparts, which may be exploited during drug design.

scholarly journals Loop 1 of APOBEC3C regulates its antiviral activity against HIV-1

2020 ◽  
Author(s):  
Ananda Ayyappan Jaguva Vasudevan ◽  
Kannan Balakrishnan ◽  
Christoph G. W. Gertzen ◽  
Fanni Borvető ◽  
Zeli Zhang ◽  
...  
Keyword(s):  
Antiviral Activity ◽  
Consensus Sequence ◽  
Antiviral Effect ◽  
Last Common Ancestor ◽  
Evolutionary Analysis ◽  
Gene Duplications ◽  
Ancestral Gene ◽  
Catalytic Function ◽  
And Function ◽  
Hiv 1

ABSTRACTAPOBEC3 deaminases (A3s) provide mammals with an anti-retroviral barrier by catalyzing dC-to-dU deamination on viral ssDNA. Within primates, A3s have evolved diversely via gene duplications and fusions. Human APOBEC3C (hA3C) efficiently restricts the replication of viral infectivity factor (vif)-deficient Simian immunodeficiency virus (SIVΔvif), but for unknown reasons, it inhibits HIV-1Δvif weakly. In catarrhines (Old World monkeys and apes), the A3C loop 1 displays the conserved amino acid pair WE, while the corresponding consensus sequence in A3F and A3D is the largely divergent pair RK, which is also the inferred ancestral sequence for the last common ancestor of A3C|D|F in primates. Here, we report that modifying the WE residues in hA3C loop 1 to RK leads to stronger interactions with ssDNA substrate, facilitating catalytic function, which resulted in a drastic increase in both deamination activity and the ability to restrict HIV-1 and LINE-1 replication. Conversely, the modification hA3F_WE resulted only in a marginal decrease in HIV-1Δvif inhibition. The two series of ancestral gene duplications that generated A3C, A3D-CTD and A3F-CTD allowed neo/subfunctionalization: A3F-CTD maintained the ancestral RK residues in loop 1, while strong evolutionary pressure selected for the RK→WE modification in catarrhines A3C, possibly allowing for novel substrate specificity and function.AUTHOR SUMMARYThe restriction factors of the APOBEC3 (A3) family of cytidine deaminases inhibit the replication of Vif-deficient retroviruses mainly by mutating their viral genomes. While there are seven A3 proteins (A3A-A3H) found in humans only A3G and A3F potently inhibit HIV-1 replication. A3C in general and its retroviral restriction capacity have not been widely studied probably due to its weak anti-HIV-1 activity, however, it displays a strong antiviral effect against SIV. Understanding the role of A3C is important because it is highly expressed in CD4+ T cells, is upregulated upon HIV-1 infection, and is distributed cell-wide. In this study, we report that replacing two residues in loop 1 of A3C protein with conserved positively-charged amino acids enhance the substrate DNA binding, which markedly facilitates its deamination-dependent antiviral activity against HIV-1 as well as increasing the restriction of LINE-1 retroelements. Furthermore, our evolutionary analysis demonstrates that the pressure that caused the loss of potential loop 1 residues occurred only in A3C but not in primate homologues. Overall, our study highlights the possibility of A3C acting as a super restriction factor, however, this was likely evolutionarily selected against to achieve a balance between anti-viral/anti-LINE-1 activity and genotoxicity.

scholarly journals Impact of Diverse Ion Channels on Regulatory T Cell Functions

2021 ◽  
Vol 55 (S3) ◽  
pp. 145-156
Keyword(s):  
Ion Channels ◽  
Transient Receptor Potential ◽  
Receptor Potential ◽  
Future Research ◽  
Ion Regulation ◽  
Cell Functions ◽  
Treg Number ◽  
Promising Therapeutic Approach ◽  
Transient Receptor ◽  
And Function

The population of regulatory T cells (Tregs) is critical for immunological self-tolerance and homeostasis. Proper ion regulation contributes to Treg lineage identity, regulation, and effector function. Identified ion channels include Ca2+ release-activated Ca2+, transient receptor potential, P2X, volume-regulated anion and K+ channels Kv1.3 and KCa3.1. Ion channel modulation represents a promising therapeutic approach for the treatment of autoimmune diseases such as rheumatoid arthritis and multiple sclerosis. This review summarizes studies with gene-targeted mice and pharmacological modulators affecting Treg number and function. Furthermore, participation of ion channels is illustrated and the power of future research possibilities is discussed.

scholarly journals Seasonal dynamics in taxonomy and function within bacterial and viral metagenomic assemblages recovered from a freshwater agricultural pond

2020 ◽  
Vol 15 (1) ◽  
Author(s):  
Jessica Chopyk ◽  
Daniel J. Nasko ◽  
Sarah Allard ◽  
Anthony Bui ◽  
Mihai Pop ◽  
...  
Keyword(s):  
High Throughput Sequencing ◽  
Antibiotic Resistance Genes ◽  
Pond Water ◽  
Taxonomic Composition ◽  
Storm Event ◽  
Rrna Gene ◽  
Illumina Hiseq ◽  
Culture Independent ◽  
Freshwater Habitats ◽  
And Function

Abstract Background Ponds are important freshwater habitats that support both human and environmental activities. However, relative to their larger counterparts (e.g. rivers, lakes), ponds are understudied, especially with regard to their microbial communities. Our study aimed to fill this knowledge gap by using culture-independent, high-throughput sequencing to assess the dynamics, taxonomy, and functionality of bacterial and viral communities in a freshwater agricultural pond. Results Water samples (n = 14) were collected from a Mid-Atlantic agricultural pond between June 2017 and May 2018 and filtered sequentially through 1 and 0.2 μm filter membranes. Total DNA was then extracted from each filter, pooled, and subjected to 16S rRNA gene and shotgun sequencing on the Illumina HiSeq 2500 platform. Additionally, on eight occasions water filtrates were processed for viral metagenomes (viromes) using chemical concentration and then shotgun sequenced. A ubiquitous freshwater phylum, Proteobacteria was abundant at all sampling dates throughout the year. However, environmental characteristics appeared to drive the structure of the community. For instance, the abundance of Cyanobacteria (e.g. Nostoc) increased with rising water temperatures, while a storm event appeared to trigger an increase in overall bacterial diversity, as well as the relative abundance of Bacteroidetes. This event was also associated with an increase in the number of antibiotic resistance genes. The viral fractions were dominated by dsDNA of the order Caudovirales, namely Siphoviridae and Myovirdae. Conclusions Overall, this study provides one of the largest datasets on pond water microbial ecology to date, revealing seasonal trends in the microbial taxonomic composition and functional potential.

Design complexity and fracture control in the equine hoof wall.

1997 ◽  
Vol 200 (11) ◽  
pp. 1639-1659 ◽  
Author(s):  
M A Kasapi ◽  
J M Gosline
Keyword(s):  
Crack Propagation ◽  
Wall Thickness ◽  
Outer Wall ◽  
Compact Tension ◽  
Morphological Data ◽  
Form And Function ◽  
Morphological Findings ◽  
Equine Hoof ◽  
Living Tissues ◽  
And Function

Morphological and mechanical studies were conducted on samples of equine hoof wall to help elucidate the relationship between form and function of this complex, hierarchically organized structure. Morphological findings indicated a dependence of tubule size, shape and helical alignment of intermediate filaments (IFs) within the lamellae on the position through the wall thickness. The plane of the intertubular IFs changed from perpendicular to the tubule axis in the inner wall to almost parallel to the tubule axis in the outer wall. Morphological data predicted the existence of three crack diversion mechanisms which might prevent cracks from reaching the sensitive, living tissues of the hoof: a mid-wall diversion mechanism of intertubular material to inhibit inward and upward crack propagation, and inner- and outer-wall diversion mechanisms that prevent inward crack propagation. Tensile and compact tension fracture tests were conducted on samples of fully hydrated equine hoof wall. Longitudinal stiffness decreased from 0.56 to 0.30 GPa proceeding inwardly, whereas ultimate (maximum) properties were constant. Fracture toughness parameters indicated that no compromise results from the declining stiffness, with J-integral values ranging from 5.5 to 7.8 kJ m-2 through the wall thickness; however, highest toughness was found in specimens with cracks initiated tangential to the wall surface (10.7 kJ m-2). Fracture paths agreed with morphological predictions and further suggested that the wall has evolved into a structure capable of both resisting and redirecting cracks initiated in numerous orientations.

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