scholarly journals The Eco-Evo Mandala: Simplifying Bacterioplankton Complexity into Ecohealth Signatures

Entropy ◽  
2021 ◽  
Vol 23 (11) ◽  
pp. 1471
Author(s):  
Elroy Galbraith ◽  
Matteo Convertino

The microbiome emits informative signals of biological organization and environmental pressure that aid ecosystem monitoring and prediction. Are the many signals reducible to a habitat-specific portfolio that characterizes ecosystem health? Does an optimally structured microbiome imply a resilient microbiome? To answer these questions, we applied our novel Eco-Evo Mandala to bacterioplankton data from four habitats within the Great Barrier Reef, to explore how patterns in community structure, function and genetics signal habitat-specific organization and departures from theoretical optimality. The Mandala revealed communities departing from optimality in habitat-specific ways, mostly along structural and functional traits related to bacterioplankton abundance and interaction distributions (reflected by ϵ and λ as power law and exponential distribution parameters), which are not linearly associated with each other. River and reef communities were similar in their relatively low abundance and interaction disorganization (low ϵ and λ) due to their protective structured habitats. On the contrary, lagoon and estuarine inshore reefs appeared the most disorganized due to the ocean temperature and biogeochemical stress. Phylogenetic distances (D) were minimally informative in characterizing bacterioplankton organization. However, dominant populations, such as Proteobacteria, Bacteroidetes, and Cyanobacteria, were largely responsible for community patterns, being generalists with a large functional gene repertoire (high D) that increases resilience. The relative balance of these populations was found to be habitat-specific and likely related to systemic environmental stress. The position on the Mandala along the three fundamental traits, as well as fluctuations in this ecological state, conveys information about the microbiome’s health (and likely ecosystem health considering bacteria-based multitrophic dependencies) as divergence from the expected relative optimality. The Eco-Evo Mandala emphasizes how habitat and the microbiome’s interaction network topology are first- and second-order factors for ecosystem health evaluation over taxonomic species richness. Unhealthy microbiome communities and unbalanced microbes are identified not by macroecological indicators but by mapping their impact on the collective proportion and distribution of interactions, which regulates the microbiome’s ecosystem function.

2020 ◽  
Vol 60 (2) ◽  
pp. 261-266 ◽  
Author(s):  
Karen G Burnett ◽  
David S Durica ◽  
Donald L Mykles ◽  
Jonathon H Stillman

Synopsis How stable genotypes interact with their environment to generate phenotypic variation that can be acted upon by evolutionary and ecological forces is a central focus of research across many scientific disciplines represented within SICB. The Building Bridges Symposium brought together scientists using a variety of organisms, methods, and levels of biological organization to study the emergent properties of genomes. Workshops associated with the Symposium aimed to identify the leading edges and major barriers to research in this field, and to recommend future directions that might accelerate the pace of progress. The papers included in this Symposium volume draw attention to the strength of using comparative approaches in non-model organisms to study the many aspects of genotype–environment interaction that drive phenotype variation. These contributions and the concluding white paper also illustrate the need for novel conceptual frameworks that can bridge and accommodate data and conclusions from the broad range of study systems employed by comparative and integrative biologists to address genome-to-phenome questions.


2020 ◽  
Author(s):  
Aimei Fei ◽  
Wanqing Wu ◽  
Longzhi Tan ◽  
Cheng Tang ◽  
Zhengrong Xu ◽  
...  

SummaryOlfactory sensory neurons (OSNs) are functionally defined by their expression of a unique odorant receptor (OR). Mechanisms underlying singular OR expression are well studied, and involve a massive cross-chromosomal enhancer interaction network. Trace amine-associated receptors (TAARs) form a distinct family of olfactory receptors, and here we find that mechanisms regulating Taar gene choice display many unique features. The epigenetic signature of Taar genes in TAAR OSNs is different from that in OR OSNs. We further identify that two TAAR enhancers conserved across placental mammals are absolutely required for expression of the entire Taar gene repertoire. Deletion of either enhancer dramatically decreases the expression probabilities of different Taar genes, while deletion of both enhancers completely eliminates the TAAR OSN populations. In addition, both of the enhancers are sufficient to drive transgene expression in the partially overlapped TAAR OSNs. We also show that the TAAR enhancers operate in cis to regulate Taar gene expression. Our findings reveal a coordinated control of Taar gene choice in OSNs by two remote enhancers, and provide an excellent model to study molecular mechanisms underlying formation of an olfactory subsystem.


2019 ◽  
Author(s):  
Mark K. Adams ◽  
Charles A.S. Banks ◽  
Janet L. Thornton ◽  
Mihaela E. Sardiu ◽  
Maxime Killer ◽  
...  

ABSTRACTDespite the continued analysis of HDAC inhibitor efficacy in clinical trials, the heterogeneous nature of the protein complexes they target limits our understanding of the beneficial and off-target effects associated with their application. Among the many HDAC protein complexes found within the cell, Sin3 complexes are conserved from yeast to humans and likely play important roles as regulators of transcriptional activity. The functional attributes of these protein complexes remain poorly characterized in humans. Contributing to the poor definition of Sin3 complex attributes in higher eukaryotes is the presence of two Sin3 scaffolding proteins, SIN3A and SIN3B. Here we show that paralog switching influences the interaction networks of the Sin3 complexes. While SIN3A and SIN3B do have unique interaction network components, we find that SIN3A and SIN3B interact with a common set of proteins. Additionally, our results suggest that SIN3A and SIN3B may possess the capacity to form hetero-oligomeric complexes. While one principal form of SIN3B exists in humans, the analysis of rare SIN3B proteoforms provides insight into the domain organization of SIN3B. Together, these findings shed light on the shared and divergent properties of human Sin3 proteins and highlight the heterogeneous nature of the complexes they organize.


2020 ◽  
Author(s):  
Ziyuan Hu ◽  
Murray Logan ◽  
XiaoXia Sun ◽  
Richard Brinkman ◽  
Song Sun

<p>Coastal areas are under compounding pressures from urbanization, industrialization, infrastructure growth, and aquaculture.  There is hence an urgent need for developing solutions for coastal pollution and ecosystem safety. In this work, based on our long-term and multidisciplinary ecosystem monitoring data, we develop tools to translate the observing data into management information to sustainable coastal use and development. From the existing data and experimental studies, we develop approaches to understand key processes and factors controlling coastal ecosystems and to define thresholds and guidelines values of ecological parameters to determine. With focus on marine ecosystem health assessment, we use the integrating data to describe ecosystem condition, its potential trend and the impact of existing pressures. This present study initially focused on the coastal area of the Yellow Sea, in the JIAOZHOU Bay. The technique of the structured research can be applied to other coastal regions as well to understand how these ecosystems respond to local and global pressures.</p>


2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Aimei Fei ◽  
Wanqing Wu ◽  
Longzhi Tan ◽  
Cheng Tang ◽  
Zhengrong Xu ◽  
...  

AbstractOlfactory sensory neurons (OSNs) are functionally defined by their expression of a unique odorant receptor (OR). Mechanisms underlying singular OR expression are well studied, and involve a massive cross-chromosomal enhancer interaction network. Trace amine-associated receptors (TAARs) form a distinct family of olfactory receptors, and here we find that mechanisms regulating Taar gene choice display many unique features. The epigenetic signature of Taar genes in TAAR OSNs is different from that in OR OSNs. We further identify that two TAAR enhancers conserved across placental mammals are absolutely required for expression of the entire Taar gene repertoire. Deletion of either enhancer dramatically decreases the expression probabilities of different Taar genes, while deletion of both enhancers completely eliminates the TAAR OSN populations. In addition, both of the enhancers are sufficient to drive transgene expression in the partially overlapped TAAR OSNs. We also show that the TAAR enhancers operate in cis to regulate Taar gene expression. Our findings reveal a coordinated control of Taar gene choice in OSNs by two remote enhancers, and provide an excellent model to study molecular mechanisms underlying formation of an olfactory subsystem.


2020 ◽  
Vol 11 ◽  
Author(s):  
Klaus Lehnertz ◽  
Timo Bröhl ◽  
Thorsten Rings

The field of Network Physiology aims to advance our understanding of how physiological systems and sub-systems interact to generate a variety of behaviors and distinct physiological states, to optimize the organism's functioning, and to maintain health. Within this framework, which considers the human organism as an integrated network, vertices are associated with organs while edges represent time-varying interactions between vertices. Likewise, vertices may represent networks on smaller spatial scales leading to a complex mixture of interacting homogeneous and inhomogeneous networks of networks. Lacking adequate analytic tools and a theoretical framework to probe interactions within and among diverse physiological systems, current approaches focus on inferring properties of time-varying interactions—namely strength, direction, and functional form—from time-locked recordings of physiological observables. To this end, a variety of bivariate or, in general, multivariate time-series-analysis techniques, which are derived from diverse mathematical and physical concepts, are employed and the resulting time-dependent networks can then be further characterized with methods from network theory. Despite the many promising new developments, there are still problems that evade from a satisfactory solution. Here we address several important challenges that could aid in finding new perspectives and inspire the development of theoretic and analytical concepts to deal with these challenges and in studying the complex interactions between physiological systems.


2020 ◽  
Vol 160 (9) ◽  
pp. 506-522
Author(s):  
Thomas Greither ◽  
Julia Schumacher ◽  
Mario Dejung ◽  
Hermann M. Behre ◽  
Hans Zischler ◽  
...  

Impairment of male fertility is one of the major public health issues worldwide. Nevertheless, genetic causes of male sub- and infertility can often only be suspected due to the lack of reliable and easy-to-use routine tests. Yet, the development of a marker panel is complicated by the large quantity of potentially predictive markers. Actually, hundreds or even thousands of genes could have fertility relevance. Thus, a systematic method enabling a selection of the most predictive markers out of the many candidates is required. As a criterion for marker selection, we derived a gene-specific score, which we refer to as fertility relevance probability (FRP). For this purpose, we first categorized 2,753 testis-expressed genes as either candidate markers or non-candidates, according to phenotypes in male knockout mice. In a parallel approach, 2,502 genes were classified as candidate markers or non-candidates based on phenotypes in men. Subsequently, we conducted logistic regression analyses with evolutionary rates of genes (<i>dN</i>/<i>dS</i>), transcription levels in testis relative to other organs, and connectivity of the encoded proteins in a protein-protein interaction network as covariates. In confirmation of the procedure, FRP values showed the expected pattern, thus being overall higher in genes with known relevance for fertility than in their counterparts without corresponding evidence. In addition, higher FRP values corresponded with an increased dysregulation of protein abundance in spermatozoa of 37 men with normal and 38 men with impaired fertility. Present analyses resulted in a ranking of genes according to their probable predictive power as candidate markers for male fertility impairment. Thus, <i>AKAP4</i>, <i>TNP1</i>, <i>DAZL</i>, <i>BRDT</i>, <i>DMRT1</i>, <i>SPO11</i>, <i>ZPBP</i>, <i>HORMAD1</i>, and <i>SMC1B</i> are prime candidates toward a marker panel for male fertility impairment. Additional candidate markers are <i>DDX4</i>, <i>SHCBP1L</i>, <i>CCDC155</i>, <i>ODF1</i>, <i>DMRTB1</i>, <i>ASZ1</i>, <i>BOLL</i>, <i>FKBP6</i>, <i>SLC25A31</i>, <i>PRSS21</i>, and <i>RNF17</i>. FRP inference additionally provides clues for potential new markers, thereunder <i>TEX37</i> and <i>POU4F2</i>. The results of our logistic regression analyses are freely available at the PreFer Genes website (https://prefer-genes.uni-mainz.de/).


2021 ◽  
pp. 119-130
Author(s):  
Franklin M. Harold

Why are there so many kinds of organisms, and why do they cluster into discrete groups associated with particular locales? These and other ecological questions find answers in the expansive version of evolution that is presently emerging. Heredity, variation, natural selection, and adaptation are rooted in the level of genes, but incorporate features that grow out of the many tiers of biological organization. The communitarian view of life complements the one focused on the individual organism, and requires us to reexamine the meaning of both organism and individual. It embraces broad-gauge phenomena such as nutrient cycles, and gave birth to Gaia: the vision of Earth as a self-regulating system that has kept our planet hospitable to life for nearly 4 billion years.


Author(s):  

A new approach to the Kritskiy-Menkel joint data analysis has been proposed to obtain the runoff summarized hydrological characteristics. The approach not only enables to increase the accuracy of the runoff distribution parameters in the conditions of the initial information lack but to take into account the hydrological regime stationary state disruptions due to climate changes. On the basis of the analysis of the many-year runoff series for the whole basin the runoff water content phase occurred due to the climate change is to be revealed and consequently the runoff data file is to be conventionally divided into two time periods corresponding to the water content phases. Zone-average parameters are to be calculated with Kritskiy-Menkel method. These parameters enable to obtain the calculated distribution curves in the conditions of the initial hydrological information lack. The calculated runoff values of the pre-set probability for the whole period of observations can be resulted from plotting of the joint distribution for the two periods according to the parameters obtained at the previous stage. The proposed algorithm is recommended to be used in case of the observed non-stationary state being an effect of the climatic change on a considerable territory.


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