Bridging Microbial Functional Traits With Localized Process Rates at Soil Interfaces

In this review, we introduce microbially-mediated soil processes, players, their functional traits, and their links to processes at biogeochemical interfaces [e.g., rhizosphere, detritusphere, (bio)-pores, and aggregate surfaces]. A conceptual view emphasizes the central role of the rhizosphere in interactions with other biogeochemical interfaces, considering biotic and abiotic dynamic drivers. We discuss the applicability of three groups of traits based on microbial physiology, activity state, and genomic functional traits to reflect microbial growth in soil. The sensitivity and credibility of modern molecular approaches to estimate microbial-specific growth rates require further development. A link between functional traits determined by physiological (e.g., respiration, biomarkers) and genomic (e.g., genome size, number of ribosomal gene copies per genome, expression of catabolic versus biosynthetic genes) approaches is strongly affected by environmental conditions such as carbon, nutrient availability, and ecosystem type. Therefore, we address the role of soil physico-chemical conditions and trophic interactions as drivers of microbially-mediated soil processes at relevant scales for process localization. The strengths and weaknesses of current approaches (destructive, non-destructive, and predictive) for assessing process localization and the corresponding estimates of process rates are linked to the challenges for modeling microbially-mediated processes in heterogeneous soil microhabitats. Finally, we introduce a conceptual self-regulatory mechanism based on the flexible structure of active microbial communities. Microbial taxa best suited to each successional stage of substrate decomposition become dominant and alter the community structure. The rates of decomposition of organic compounds, therefore, are dependent on the functional traits of dominant taxa and microbial strategies, which are selected and driven by the local environment.

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Faculty Opinions recommendation of The role of functional traits and trade-offs in structuring phytoplankton communities: scaling from cellular to ecosystem level.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1093896.548833 ◽

2007 ◽

Author(s):

Jonathan Shurin

Keyword(s):

Functional Traits ◽

Trade Offs ◽

Phytoplankton Communities ◽

Ecosystem Level

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Neuronal nitric oxide synthase and systemic vasodilation in rats with cirrhosis

AJP Renal Physiology ◽

10.1152/ajprenal.2000.279.6.f1110 ◽

2000 ◽

Vol 279 (6) ◽

pp. F1110-F1115 ◽

Cited By ~ 50

Author(s):

Lieming Xu ◽

Ethan P. Carter ◽

Mamiko Ohara ◽

Pierre-Yves Martin ◽

Boris Rogachev ◽

...

Keyword(s):

Nitric Oxide ◽

Liver Cirrhosis ◽

Nitric Oxide Synthase ◽

Control Treatment ◽

Sodium Balance ◽

Hyperdynamic Circulation ◽

Molecular Approaches ◽

Advanced Liver Cirrhosis ◽

Oxide Synthase

Cirrhosis is typically associated with a hyperdynamic circulation consisting of low blood pressure, low systemic vascular resistance (SVR), and high cardiac output. We have recently reported that nonspecific inhibition of nitric oxide synthase (NOS) with nitro-l-arginine methyl ester reverses the hyperdynamic circulation in rats with advanced liver cirrhosis induced by carbon tetrachloride (CCl4). Although an important role for endothelial NOS (eNOS) is documented in cirrhosis, the role of neuronal NOS (nNOS) has not been investigated. The present study was carried out to specifically investigate the role of nNOS during liver cirrhosis. Specifically, physiological, biochemical, and molecular approaches were employed to evaluate the contribution of nNOS to the cirrhosis-related hyperdynamic circulation in CCl4-induced cirrhotic rats with ascites. Cirrhotic animals had a significant increase in water and sodium retention. In the aorta from cirrhotic animals, both nNOS protein expression and cGMP concentration were significantly elevated compared with control. Treatment of cirrhotic rats for 7 days with the specific nNOS inhibitor 7-nitroindazole (7-NI) normalized the low SVR and mean arterial pressure, elevated cardiac index, and reversed the positive sodium balance. Increased plasma arginine vasopressin concentrations in the cirrhotic animals were also repressed with 7-NI in association with diminished water retention. The circulatory changes were associated with a reduction in aortic nNOS expression and cGMP. However, 7-NI treatment did not restore renal function in cirrhotic rats (creatinine clearance: 0.76 ± 0.03 ml · min−1· 100 g body wt−1in cirrhotic rats vs. 0.79 ± 0.05 ml · min−1· 100 g body wt−1in cirrhotic rats+7-NI; P NS.). Taken together, these results indicate that nNOS-derived NO contributes to the development of the hyperdynamic circulation and fluid retention in cirrhosis.

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Cancer, Retrogenes, and Evolution

Life ◽

10.3390/life11010072 ◽

2021 ◽

Vol 11 (1) ◽

pp. 72

Author(s):

Klaudia Staszak ◽

Izabela Makałowska

Keyword(s):

Specific Resistance ◽

Neoplastic Transformation ◽

Resistance Mechanisms ◽

Response To Therapy ◽

Additional Gene ◽

Cancer Subtypes ◽

Gene Copies ◽

Specific Cancer ◽

Evolution Of Genomes

This review summarizes the knowledge about retrogenes in the context of cancer and evolution. The retroposition, in which the processed mRNA from parental genes undergoes reverse transcription and the resulting cDNA is integrated back into the genome, results in additional copies of existing genes. Despite the initial misconception, retroposition-derived copies can become functional, and due to their role in the molecular evolution of genomes, they have been named the “seeds of evolution”. It is convincing that retrogenes, as important elements involved in the evolution of species, also take part in the evolution of neoplastic tumors at the cell and species levels. The occurrence of specific “resistance mechanisms” to neoplastic transformation in some species has been noted. This phenomenon has been related to additional gene copies, including retrogenes. In addition, the role of retrogenes in the evolution of tumors has been described. Retrogene expression correlates with the occurrence of specific cancer subtypes, their stages, and their response to therapy. Phylogenetic insights into retrogenes show that most cancer-related retrocopies arose in the lineage of primates, and the number of identified cancer-related retrogenes demonstrates that these duplicates are quite important players in human carcinogenesis.

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Characterization of symbiotic and associated bacteria from entomopathogenic nematode Heterorhabditis sp. (nematode: Heterorhabditidae) isolated from India

Egyptian Journal of Biological Pest Control ◽

10.1186/s41938-020-00343-9 ◽

2020 ◽

Vol 30 (1) ◽

Author(s):

Rashid Pervez ◽

Showkat Ahmad Lone ◽

Sasmita Pattnaik

Keyword(s):

Insect Pests ◽

Entomopathogenic Nematode ◽

Alcaligenes Faecalis ◽

Symbiotic Bacteria ◽

Rrna Gene ◽

Main Body ◽

Associated Bacteria ◽

Molecular Approaches

Abstract Background Entomopathogenic nematodes (EPNs) harboring symbiotic bacteria are one of the safest alternatives to the chemical insecticides for the control of various insect pests. Infective juveniles of EPNs locate a target insect, enter through the openings, and reach the hemocoel, where they release the symbiotic bacteria and the target gets killed by the virulence factors of the bacteria. Photorhabdus with Heterorhabditis spp. are well documented; little is known about the associated bacteria. Main body In this study, we explored the presence of symbiotic and associated bacteria from Heterorhabditis sp. (IISR-EPN 09) and characterized by phenotypic, biochemical, and molecular approaches. Six bacterial isolates, belonging to four different genera, were recovered and identified as follows: Photorhabdus luminescens, one each strain of Providencia vermicola, Pseudomonas entomophila, Alcaligenes aquatilis, and two strains of Alcaligenes faecalis based on the phenotypic, biochemical criteria and the sequencing of 16S rRNA gene. Conclusion P. luminescens is symbiotically associated with Heterorhabditis sp. (IISR-EPN 09), whereas P. vermicola, P. entomophila, A. aquatilis, and A. faecalis are the associated bacteria. Further studies are needed to determine the exact role of the bacterial associates with the Heterorhabditis sp.

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Disentangling the role of competition, light interception, and functional traits in tree growth rate variation in South Asian tropical moist forests

Forest Ecology and Management ◽

10.1016/j.foreco.2020.118908 ◽

2021 ◽

Vol 483 ◽

pp. 118908

Author(s):

Mizanur Rahman ◽

Masum Billah ◽

Md Obydur Rahman ◽

Debit Datta ◽

Muhammad Ahsanuzzaman ◽

...

Keyword(s):

Growth Rate ◽

Functional Traits ◽

South Asian ◽

Tree Growth ◽

Light Interception ◽

Rate Variation ◽

Tree Growth Rate

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Molecular Approaches to the Role of the Microbiota in Inflammatory Bowel Disease

Annals of the New York Academy of Sciences ◽

10.1196/annals.1326.010 ◽

2006 ◽

Vol 1072 (1) ◽

pp. 39-51 ◽

Cited By ~ 14

Author(s):

C. O ELSON ◽

Y. CONG ◽

F. QI ◽

R. M HERSHBERG ◽

S. R TARGAN

Keyword(s):

Inflammatory Bowel Disease ◽

Bowel Disease ◽

Molecular Approaches ◽

Inflammatory Bowel

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Molecular Approaches to Strain Improvement and Determination of the Role of Specific Gene Products in Biocontrol by Trichoderma Spp.

10.32747/1993.7604308.bard ◽

1993 ◽

Author(s):

Gary Harman ◽

Ilan Chet

Keyword(s):

Strain Improvement ◽

Specific Gene ◽

Gene Products ◽

Trichoderma Spp ◽

Molecular Approaches

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Investigating the role of EGF-CFC gene family in recurrent pregnancy loss through bioinformatics and molecular approaches

Systems Biology in Reproductive Medicine ◽

10.1080/19396368.2021.1965673 ◽

2021 ◽

pp. 1-13

Author(s):

João Matheus Bremm ◽

Juliano André Boquett ◽

Marcus Silva Michels ◽

Thayne Woycinck Kowalski ◽

Flávia Gobetti Gomes ◽

...

Keyword(s):

Gene Family ◽

Pregnancy Loss ◽

Recurrent Pregnancy Loss ◽

Molecular Approaches

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Lipid Metabolic Reprogramming in Hepatocellular Carcinoma

Cancers ◽

10.3390/cancers10110447 ◽

2018 ◽

Vol 10 (11) ◽

pp. 447 ◽

Cited By ~ 35

Author(s):

Hayato Nakagawa ◽

Yuki Hayata ◽

Satoshi Kawamura ◽

Tomoharu Yamada ◽

Naoto Fujiwara ◽

...

Keyword(s):

Risk Factors ◽

Hepatocellular Carcinoma ◽

Local Environment ◽

Metabolic Reprogramming ◽

Glutamine Metabolism ◽

Metabolic Alterations ◽

Rich Condition ◽

Visceral Adipose ◽

Hcc Cells

Metabolic reprogramming for adaptation to the local environment has been recognized as a hallmark of cancer. Although alterations in fatty acid (FA) metabolism in cancer cells have received less attention compared to other metabolic alterations such as glucose or glutamine metabolism, recent studies have uncovered the importance of lipid metabolic reprogramming in carcinogenesis. Obesity and nonalcoholic steatohepatitis (NASH) are well-known risk factors of hepatocellular carcinoma (HCC), and individuals with these conditions exhibit an increased intake of dietary FAs accompanied by enhanced lipolysis of visceral adipose tissue due to insulin resistance, resulting in enormous exogenous FA supplies to hepatocytes via the portal vein and lymph vessels. This “lipid-rich condition” is highly characteristic of obesity- and NASH-driven HCC. Although the way in which HCC cells adapt to such a condition and exploit it to aid their progression is not understood, we recently obtained new insights into this mechanism through lipid metabolic reprogramming. In addition, accumulating evidence supports the importance of lipid metabolic reprogramming in various situations of hepatocarcinogenesis. Thus, in this review, we discuss the latest findings regarding the role of FA metabolism pathways in hepatocarcinogenesis, focusing on obesity- and NASH-driven lipid metabolic reprogramming.

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