Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

AbstractThe genomes of non-bilaterian metazoans are key to understanding the molecular basis of early animal evolution. However, a full comprehension of how animal-specific traits such as nervous systems arose is hindered by the scarcity and fragmented nature of genomes from key taxa, such as Porifera. Ephydatia muelleri is a freshwater sponge found across the northern hemisphere. Here we present its 326 Mb genome, assembled to high contiguity (N50: 9.88 Mb) with 23 chromosomes on 24 scaffolds. Our analyses reveal a metazoan-typical genome architecture, with highly shared synteny across Metazoa, and suggest that adaptation to the extreme temperatures and conditions found in freshwater often involves gene duplication. The pancontinental distribution and ready laboratory culture of E. muelleri make this a highly practical model system, which with RNAseq, DNA methylation and bacterial amplicon data spanning its development and range allows exploration of genomic changes both within sponges and in early animal evolution.

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Tracing animal genomic evolution with the chromosomal-level assembly of the freshwater sponge Ephydatia muelleri

Nature Communications ◽

10.1038/s41467-020-17397-w ◽

2020 ◽

Vol 11 (1) ◽

Cited By ~ 3

Author(s):

Nathan J. Kenny ◽

Warren R. Francis ◽

Ramón E. Rivera-Vicéns ◽

Ksenia Juravel ◽

Alex de Mendoza ◽

...

Keyword(s):

Genomic Evolution ◽

Freshwater Sponge ◽

Ephydatia Muelleri

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Expanding the nematode model system: The molecular basis of inflammation and infection recovery in C. elegans

Virulence ◽

10.1080/21505594.2016.1239011 ◽

2016 ◽

Vol 8 (3) ◽

pp. 244-245 ◽

Cited By ~ 1

Author(s):

Gabriel Hendricks ◽

Eleftherios Mylonakis

Keyword(s):

Molecular Basis ◽

Model System ◽

C Elegans

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Public-good driven release of heterogeneous resources leads to genotypic diversification of an isogenic yeast population in melibiose.

10.1101/2021.04.12.439421 ◽

2021 ◽

Author(s):

Anjali Mahilkar ◽

Phaniendra Alugoju ◽

Vijendra Kavatalkar ◽

Rajeshkannan E. ◽

Jayadeva Bhat ◽

...

Keyword(s):

Carbon Source ◽

Public Good ◽

Molecular Basis ◽

Model System ◽

Microbial Populations ◽

Adaptive Diversification ◽

E Coli ◽

Hydrolysis Of ◽

Convenient Model ◽

Heterogeneous Resources

Adaptive diversification of an isogenic population, and its molecular basis has been a subject of a number of studies in the last few years. Microbial populations offer a relatively convenient model system to study this question. In this context, an isogenic population of bacteria (E. coli, B. subtilis, and Pseudomonas) has been shown to lead to genetic diversification in the population, when propagated for a number of generations. This diversification is known to occur when the individuals in the population have access to two or more resources/environments, which are separated either temporally or spatially. Here, we report adaptive diversification in an isogenic population of yeast, S. cerevisiae, when propagated in an environment containing melibiose as the carbon source. The diversification is driven due to a public good, enzyme α-galactosidase, leading to hydrolysis of melibiose into two distinct resources, glucose and galactose. The diversification is driven by a mutations at a single locus, in the GAL3 gene in the GAL/MEL regulon in the yeast.

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Retinoic acid down-regulates the expression of EmH-3 homeobox-containing gene in the freshwater sponge Ephydatia muelleri

Mechanisms of Ageing and Development ◽

10.1016/s0047-6374(01)00235-4 ◽

2001 ◽

Vol 122 (8) ◽

pp. 779-794 ◽

Cited By ~ 11

Author(s):

Elina Nikko ◽

Gisèle Van de Vyver ◽

Evelyn Richelle-Maurer

Keyword(s):

Retinoic Acid ◽

Freshwater Sponge ◽

Ephydatia Muelleri

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Treading the Path towards Genetic Control of Snail Resistance to Schistosome Infection

Tropical Medicine and Infectious Disease ◽

10.3390/tropicalmed3030086 ◽

2018 ◽

Vol 3 (3) ◽

pp. 86 ◽

Cited By ~ 8

Author(s):

Damilare Famakinde

Keyword(s):

Genetic Control ◽

Molecular Basis ◽

Model System ◽

Effective Control ◽

Schistosome Infection ◽

Snail Control ◽

Promising Tool ◽

Natural Vector ◽

Future Challenges ◽

Genetic Techniques

Schistosomiasis remains the most important tropical snail-borne trematodiasis that threatens many millions of human lives. In achieving schistosomiasis elimination targets, sustainable control of the snail vectors represents a logical approach. Nonetheless, the ineffectiveness of the present snail control interventions emphasizes the need to develop new complementary strategies to ensure more effective control outcomes. Accordingly, the use of genetic techniques aimed at driving resistance traits into natural vector populations has been put forward as a promising tool for integrated snail control. Leveraging the Biomphalaria-Schistosoma model system, studies unraveling the complexities of the vector biology and those exploring the molecular basis of snail resistance to schistosome infection have been expanding in various breadths, generating many significant discoveries, and raising the hope for future breakthroughs. This review provides a compendium of relevant findings, and without neglecting the current existing gaps and potential future challenges, discusses how a transgenic snail approach may be adapted and harnessed to control human schistosomiasis.

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All in the Family: Primary Megakaryocytes for Studies of Platelet αIIbβ3 Signaling

Thrombosis and Haemostasis ◽

10.1055/s-0037-1616223 ◽

2001 ◽

Vol 86 (07) ◽

pp. 259-265 ◽

Cited By ~ 11

Author(s):

Andrew Leavitt ◽

Sanford Shattil

Keyword(s):

Molecular Basis ◽

Intrinsic Value ◽

Model System ◽

Integrin Signaling ◽

Gene Products ◽

Hematopoietic Stem ◽

The Family ◽

Viral Transduction ◽

Inside Out ◽

Platelet Formation

SummaryIntegrin αIIbβ3 mediates key platelet adhesive responses during hemostasis and thrombosis. Adhesive ligand binding to αIIbβ3 is regulated by “inside-out” signals, while adhesion-dependent cytoskeletal events are regulated by “outside-in” signals from αIIbβ3. Currently, the molecular basis of bidirectional αIIbβ3 signaling is incompletely understood. The functional assessment of integrin signaling pathways in nucleated cells has been facilitated by techniques such as viral transduction which enable expression of dominant-active and dominant-inhibitory gene products. This approach cannot be used with anucleate platelets. However, recent advances in the ability to expand human and murine megakaryocytes from hematopoietic stem cells provide a tractable and genetically manipulatable system for studies of αIIbβ3 signaling. This overview will discuss some of the advantages and limitations of this approach and provide examples of its utility. Thus, in addition to their intrinsic value for understanding hematopoiesis and platelet formation, primary megakaryocytes represent a model system complementary to platelets for unraveling the remaining mysteries of αIIbβ3 signaling.

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Molecular Basis of Bacterial Longevity

mBio ◽

10.1128/mbio.01726-17 ◽

2017 ◽

Vol 8 (6) ◽

Cited By ~ 12

Author(s):

Kieran B. Pechter ◽

Liang Yin ◽

Yasuhiro Oda ◽

Larry Gallagher ◽

Jianming Yang ◽

...

Keyword(s):

Molecular Basis ◽

Large Scale ◽

Molecular Mechanisms ◽

Rhodopseudomonas Palustris ◽

Model System ◽

Molecular Characteristics ◽

Quiescent State ◽

Bacteria Growth ◽

Longevity Genes ◽

Longevity Gene

ABSTRACT It is well known that many bacteria can survive in a growth-arrested state for long periods of time, on the order of months or even years, without forming dormant structures like spores or cysts. How is such longevity possible? What is the molecular basis of such longevity? Here we used the Gram-negative phototrophic alphaproteobacterium Rhodopseudomonas palustris to identify molecular determinants of bacterial longevity. R. palustris maintained viability for over a month after growth arrest due to nutrient depletion when it was provided with light as a source of energy. In transposon sequencing (Tn-seq) experiments, we identified 117 genes that were required for long-term viability of nongrowing R. palustris cells. Genes in this longevity gene set are annotated to play roles in a number of cellular processes, including DNA repair, tRNA modification, and the fidelity of protein synthesis. These genes are critically important only when cells are not growing. Three genes annotated to affect translation or posttranslational modifications were validated as bona fide longevity genes by mutagenesis and complementation experiments. These genes and others in the longevity gene set are broadly conserved in bacteria. This raises the possibility that it will be possible to define a core set of longevity genes common to many bacterial species. IMPORTANCE Bacteria in nature and during infections often exist in a nongrowing quiescent state. However, it has been difficult to define experimentally the molecular characteristics of this crucial element of the bacterial life cycle because bacteria that are not growing tend to die under laboratory conditions. Here we present and validate the phototrophic bacterium Rhodopseudomonas palustris as a model system for identification of genes required for the longevity of nongrowing bacteria. Growth-arrested R. palustris maintained almost full viability for weeks using light as an energy source. Such cells were subjected to large-scale mutagenesis to identify genes required for this striking longevity trait. The results define conserved determinants of survival under nongrowing conditions and create a foundation for more extensive studies to elucidate general molecular mechanisms of bacterial longevity. IMPORTANCE Bacteria in nature and during infections often exist in a nongrowing quiescent state. However, it has been difficult to define experimentally the molecular characteristics of this crucial element of the bacterial life cycle because bacteria that are not growing tend to die under laboratory conditions. Here we present and validate the phototrophic bacterium Rhodopseudomonas palustris as a model system for identification of genes required for the longevity of nongrowing bacteria. Growth-arrested R. palustris maintained almost full viability for weeks using light as an energy source. Such cells were subjected to large-scale mutagenesis to identify genes required for this striking longevity trait. The results define conserved determinants of survival under nongrowing conditions and create a foundation for more extensive studies to elucidate general molecular mechanisms of bacterial longevity.

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THE USE OF KNOWLEDGE MAP MODEL IN CONSTRUCTION INDUSTRY

Journal of Civil Engineering and Management ◽

10.3846/jcem.2010.38 ◽

2010 ◽

Vol 16 (3) ◽

pp. 332-344 ◽

Cited By ~ 18

Author(s):

H. Ping Tserng ◽

Samuel Yen-Liang Yin ◽

Meng-Hsueh Lee

Keyword(s):

Tacit Knowledge ◽

Construction Industry ◽

Explicit Knowledge ◽

Model System ◽

Knowledge Map ◽

Specific Domain ◽

Bridge Maintenance ◽

Practical Model ◽

Use Of Knowledge ◽

Classification Structure

The construction industry consists of many unstructured documents, which accumulate a large volume of tacit knowledge. In the general domain, a Knowledge Map can illustrate connections of knowledge and transfer tacit knowledge to explicit knowledge, but this is unsuitable on specific domain such as construction industry. This research generalized existing mapping rules to be applied to general and specific domain; and presented a novel and practical model for building knowledge map, named Knowledge Map Model (KMM). This model comprised of five procedures, including identifying problems, discussing with experts and users, establishing the classification structure, establishing the document base, and deciding the display model. Furthermore, this research establishes Knowledge Map Model System (KMMS) as a major tool to improve the knowledge map reused and shared among the practical process. Finally, this re‐search validated the KMM in a real project of bridge maintenance. Santrauka Statybos pramoneje taikoma daug nestruktūrizuotu dokumentu, kuriuose sukaupti tiksliai neišreikšti, numanomi duome‐nys. Bendruoju atveju žiniu žemelapis gali parodyti žiniu tarpusavio ryšius ir transformuoti numanomas žinias i tikslias žinias, tačiau tai netinka specifinems sritims, tokioms kaip statyba. Šis mokslinis tyrimas apibendrino esamas žiniu žeme‐lapiu sudarymo taisykles, kurios galetu būti taikomos bendrosioms ir specifinems sritims, ir pristate nauja, praktini žiniu žemelapio sudarymo modeli, pavadinta KMM (Knowledge Map Model). Modeli sudaro penkios procedūros: problemu identifikavimo, aptarimo su ekspertais ir vartotojais, klasifikavimo struktūros nustatymo, dokumento formos nustatymo ir sprendimo del vaizdinio parinkimo. Be to, šiais moksliniais tyrimais nustatyta, kad žiniu žemelapio modelio sistema (KMMS) yra svarbi priemone, padedanti pritaikyti žiniu žemelapio naudojima praktiniams tikslams. Galiausiai šis tyrimas pagrinde KMM taikyma vykdant realu tilto eksploatacijos projekta.

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