scholarly journals Incorporating genomic information and predicting gene expression patterns in a simplified biogeochemical model

2013 ◽  
Vol 10 (1) ◽  
pp. 815-850
Author(s):  
P. Wang ◽  
A. B. Burd ◽  
M. A. Moran ◽  
R. R. Hood ◽  
V. J. Coles ◽  
...  
Keyword(s):  
Community Structure ◽  
Environmental Changes ◽  
Expression Patterns ◽  
Biological Response ◽  
Gene Clusters ◽  
Biogeochemical Model ◽  
Nitrogen And Phosphorus ◽  
Concentration Changes ◽  
Continuously Stirred Tank Reactor ◽  
And Function

Abstract. We present results from a new marine plankton model that combines selective biogeochemical processes with genetic information. The model allows for phytoplankton to adapt to a changing environment by invoking different utilization pathways for acquisition of nutrients (nitrogen and phosphorus) in response to concentration changes. The simulations use simplified environmental conditions represented by a continuously stirred tank reactor, which is populated by 96 different types of phytoplankton that differ in their physiological characteristics and nutrient uptake/metabolism genes. The results show that the simulated phytoplankton community structure is conceptually consistent with observed regional and global phytoplankton biogeography, the genome content from the dominant types of phytoplankton reflects the imposed environmental constraints, and the transcription of the gene clusters is qualitatively simulated according to the environmental changes. The model shows the feasibility of including genomic knowledge into a biogeochemical model and is suited to understanding and predicting changes in marine microbial community structure and function, and to simulating the biological response to rapid environmental changes.

scholarly journals Analysis of nifH DNA and RNA reveals a disproportionate contribution to nitrogenase activities by rare plankton-associated diazotrophs

2019 ◽  
Author(s):  
Qingsong Yang ◽  
Junde Dong ◽  
Manzoor Ahmad ◽  
Juan Ling ◽  
Weiguo Zhou ◽  
...  
Keyword(s):  
Community Structure ◽  
Environmental Changes ◽  
Northern South China Sea ◽  
Nifh Gene ◽  
Biological Response ◽  
Alpha Diversity ◽  
Equal Proportion ◽  
Dna And Rna ◽  
Abundant Otus ◽  
Nitrogenase Activities

Abstract Holobionts comprising nitrogen-fixing diazotrophs and phytoplankton or zooplankton are ubiquitous in the pelagic sea. However, neither the community structure of plankton-associated diazotrophs (PADs) nor their nitrogenase transcriptional activity are well-understood. In this study, we used nifH gene Illumina sequencing and quantitative PCR to characterize the total and active community structure of PADs in the euphotic zone of the northern South China Sea. The results of DNA- and RNA-derived nifH gene revealed a higher alpha-diversity in the active than in the total community. Moreover, the compositional resemblance among different sites was less for active than for total communities of PADs. Eight of the 20 abundant OTUs were phylogenetically affiliated with Trichodesmium and occurred in approximately equal proportion in both the DNA and RNA libraries. The analysis of nifH gene expression level showed uneven attribute of the abundance and nitrogenase activities by the remaining 12 OTUs. Taxa belonging to cluster III and Betaproteobacteria were present at moderate abundance but exhibited negligible nitrogenase transcription activity. Whereas, the abundances of Richelia, Deltaproteobacteria and Gammaproteobacteria were low but the contribution of these groups to nitrogenase transcription was disproportionately high. The substantial variation in community structure among active dizatrophic fractions compared to the total communities suggests that the former are better indicators of biological response to environmental changes. Altogether, our study highlights the importance of rare PADs groups in nitrogen fixation in plankton holobionts, evidenced by their high level of nitrogenase transcription.

scholarly journals Divergent Expression Patterns and Function of Two cxcr4 Paralogs in Hermaphroditic Epinephelus coioides

2018 ◽  
Vol 19 (10) ◽  
pp. 2943 ◽  
Author(s):  
Wei-Jia Lu ◽  
Li Zhou ◽  
Fan-Xiang Gao ◽  
Zhi-Hui Sun ◽  
Zhi Li ◽  
...  
Keyword(s):  
Gene Loss ◽  
Genome Duplication ◽  
Expression Patterns ◽  
Gene Clusters ◽  
Epinephelus Coioides ◽  
Adult Tissue ◽  
Receptor Recognition ◽  
And Function ◽  
Neurula Stage ◽  
Specific Ligand

Chemokine receptor Cxcr4 evolved two paralogs in the teleost lineage. However, cxcr4a and cxcr4b have been characterized only in a few species. In this study, we identified two cxcr4 paralogs from the orange-spotted grouper, Epinephelus coioides. The phylogenetic relationship and gene structure and synteny suggest that the duplicated cxcr4a/b should result from the teleost-specific genome duplication (Ts3R). The teleost cxcr4 gene clusters in two paralogous chromosomes exhibit a complementary gene loss/retention pattern. Ec_cxcr4a and Ec_cxcr4b show differential and biased expression patterns in grouper adult tissue, gonads, and embryos at different stages. During embryogenesis, Ec_cxcr4a/b are abundantly transcribed from the neurula stage and mainly expressed in the neural plate and sensory organs, indicating their roles in neurogenesis. Ec_Cxcr4a and Ec_Cxcr4b possess different chemotactic migratory abilities from the human SDF-1α, Ec_Cxcl12a, and Ec_Cxcl12b. Moreover, we uncovered the N-terminus and TM5 domain as the key elements for specific ligand–receptor recognition of Ec_Cxcr4a-Ec_Cxcl12b and Ec_Cxcr4b-Ec_Cxcl12a. Based on the biased and divergent expression patterns of Eccxcr4a/b, and specific ligand–receptor recognition of Ec_Cxcl12a/b–Ec_Cxcr4b/a, the current study provides a paradigm of sub-functionalization of two teleost paralogs after Ts3R.

scholarly journals Large shifts among eukaryotes, bacteria, and archaea define the vertical organization of a lake sediment

2016 ◽  
Author(s):  
Christian Wurzbacher ◽  
Andrea Fuchs ◽  
Katrin Attermeyer ◽  
Katharina Frindte ◽  
Hans-Peter Grossart ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Microbial Community Structure ◽  
Environmental Changes ◽  
Microbial Community Composition ◽  
Environmental Parameters ◽  
Global Trends ◽  
Water Columns ◽  
And Function ◽  
Microbial Hotspots

AbstractSediments are depositional areas where particles sink from water columns, but they are also microbial hotspots that play an important role in biogeochemical cycles. Unfortunately, the importance of both processes in structuring microbial community composition has not been assessed. We surveyed all organismic signals of the last ca. 170 years of sediment by metabarcoding, identifying global trends for eukaryotes, bacteria, archaea, and monitored 40 sediment parameters. We linked the microbial community structure to ongoing and historical environmental parameters and defined three distinct sediment horizons. This not only expands our knowledge of freshwater sediments, but also has profound implications for understanding the microbial community structure and function of sediment communities in relation to future, present, and past environmental changes.

Effects of Maternal Obesity and Gestational Diabetes Mellitus on the Placenta: Current Knowledge and Targets for Therapeutic Interventions

2020 ◽  
Vol 19 (2) ◽  
pp. 176-192
Author(s):  
Samantha Bedell ◽  
Janine Hutson ◽  
Barbra de Vrijer ◽  
Genevieve Eastabrook
Keyword(s):  
Diabetes Mellitus ◽  
Gestational Diabetes ◽  
Gestational Diabetes Mellitus ◽  
Maternal Obesity ◽  
Environmental Changes ◽  
Current Knowledge ◽  
Therapeutic Interventions ◽  
Placental Development ◽  
Exchange Site ◽  
And Function

: Obesity and gestational diabetes mellitus (GDM) are becoming more common among pregnant women worldwide and are individually associated with a number of placenta-mediated obstetric complications, including preeclampsia, macrosomia, intrauterine growth restriction and stillbirth. The placenta serves several functions throughout pregnancy and is the main exchange site for the transfer of nutrients and gas from mother to fetus. In pregnancies complicated by maternal obesity or GDM, the placenta is exposed to environmental changes, such as increased inflammation and oxidative stress, dyslipidemia, and altered hormone levels. These changes can affect placental development and function and lead to abnormal fetal growth and development as well as metabolic and cardiovascular abnormalities in the offspring. This review aims to summarize current knowledge on the effects of obesity and GDM on placental development and function. Understanding these processes is key in developing therapeutic interventions with the goal of mitigating these effects and preventing future cardiovascular and metabolic pathology in subsequent generations.

scholarly journals Microglial Function and Regulation during Development, Homeostasis and Alzheimer’s Disease

Cells ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 957
Author(s):  
Brad T. Casali ◽  
Erin G. Reed-Geaghan
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Immune Cells ◽  
Expression Patterns ◽  
Brain Parenchyma ◽  
Primary Role ◽  
And Function ◽  
Inflammatory Milieu ◽  
The Brain ◽  
Homeostatic State

Microglia are the resident immune cells of the brain, deriving from yolk sac progenitors that populate the brain parenchyma during development. During development and homeostasis, microglia play critical roles in synaptogenesis and synaptic plasticity, in addition to their primary role as immune sentinels. In aging and neurodegenerative diseases generally, and Alzheimer’s disease (AD) specifically, microglial function is altered in ways that significantly diverge from their homeostatic state, inducing a more detrimental inflammatory environment. In this review, we discuss the receptors, signaling, regulation and gene expression patterns of microglia that mediate their phenotype and function contributing to the inflammatory milieu of the AD brain, as well as strategies that target microglia to ameliorate the onset, progression and symptoms of AD.

scholarly journals Genome-wide identification and analysis of class III peroxidases in Betula pendula

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Kewei Cai ◽  
Huixin Liu ◽  
Song Chen ◽  
Yi Liu ◽  
Xiyang Zhao ◽  
...  
Keyword(s):  
Stress Responses ◽  
Betula Pendula ◽  
Expression Patterns ◽  
Class Iii ◽  
Physiological Processes ◽  
Plant Life ◽  
Genome Wide ◽  
Plant Life Cycle ◽  
Class Iii Peroxidases ◽  
And Function

Abstract Background Class III peroxidases (POD) proteins are widely present in the plant kingdom that are involved in a broad range of physiological processes including stress responses and lignin polymerization throughout the plant life cycle. At present, POD genes have been studied in Arabidopsis, rice, poplar, maize and Chinese pear, but there are no reports on the identification and function of POD gene family in Betula pendula. Results We identified 90 nonredundant POD genes in Betula pendula. (designated BpPODs). According to phylogenetic relationships, these POD genes were classified into 12 groups. The BpPODs are distributed in different numbers on the 14 chromosomes, and some BpPODs were located sequentially in tandem on chromosomes. In addition, we analyzed the conserved domains of BpPOD proteins and found that they contain highly conserved motifs. We also investigated their expression patterns in different tissues, the results showed that some BpPODs might play an important role in xylem, leaf, root and flower. Furthermore, under low temperature conditions, some BpPODs showed different expression patterns at different times. Conclusions The research on the structure and function of the POD genes in Betula pendula plays a very important role in understanding the growth and development process and the molecular mechanism of stress resistance. These results lay the theoretical foundation for the genetic improvement of Betula pendula.

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