scholarly journals Isoprene-degrading bacteria associated with the phyllosphere of Salix fragilis, a high isoprene-emitting willow of the Northern Hemisphere

2021 ◽  
Vol 16 (1) ◽  
Author(s):  
Lisa Gibson ◽  
Andrew T. Crombie ◽  
Niall P. McNamara ◽  
J. Colin Murrell
Keyword(s):  
Northern Hemisphere ◽  
Atmospheric Chemistry ◽  
Gene Clusters ◽  
Metagenomic Analysis ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Salix Fragilis ◽  
Degrading Bacteria ◽  
Key Species ◽  
Insight Into

Abstract Background Isoprene accounts for about half of total biogenic volatile organic compound emissions globally, and as a climate active gas it plays a significant and varied role in atmospheric chemistry. Terrestrial plants are the largest source of isoprene, with willow (Salix) making up one of the most active groups of isoprene producing trees. Bacteria act as a biological sink for isoprene and those bacteria associated with high isoprene-emitting trees may provide further insight into its biodegradation. Results A DNA-SIP experiment incubating willow (Salix fragilis) leaves with 13C-labelled isoprene revealed an abundance of Comamonadaceae, Methylobacterium, Mycobacterium and Polaromonas in the isoprene degrading community when analysed by 16S rRNA gene amplicon sequencing. Metagenomic analysis of 13C-enriched samples confirmed the abundance of Comamonadaceae, Acidovorax, Polaromonas, Variovorax and Ramlibacter. Mycobacterium and Methylobacterium were also identified after metagenomic analysis and a Mycobacterium metagenome-assembled genome (MAG) was recovered. This contained two complete isoprene degradation metabolic gene clusters, along with a propane monooxygenase gene cluster. Analysis of the abundance of the alpha subunit of the isoprene monooxygenase, isoA, in unenriched DNA samples revealed that isoprene degraders associated with willow leaves are abundant, making up nearly 0.2% of the natural bacterial community. Conclusions Analysis of the isoprene degrading community associated with willow leaves using DNA-SIP and focused metagenomics techniques enabled recovery of the genome of an active isoprene-degrading Mycobacterium species and provided valuable insight into bacteria involved in degradation of isoprene on the leaves of a key species of isoprene-emitting tree in the northern hemisphere.

scholarly journals Bayesian mixture regression analysis for regulation of Pluripotency in ES cells

2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Mehran Aflakparast ◽  
Geert Geeven ◽  
Mathisca C.M. de Gunst
Keyword(s):  
Gene Expression ◽  
Additional Data ◽  
Gene Clusters ◽  
Chromatin State ◽  
Valuable Insight ◽  
Mrna Levels ◽  
Regulatory Interactions ◽  
Mixture Modelling ◽  
Gene Similarity ◽  
Insight Into

Abstract Background Observed levels of gene expression strongly depend on both activity of DNA binding transcription factors (TFs) and chromatin state through different histone modifications (HMs). In order to recover the functional relationship between local chromatin state, TF binding and observed levels of gene expression, regression methods have proven to be useful tools. They have been successfully applied to predict mRNA levels from genome-wide experimental data and they provide insight into context-dependent gene regulatory mechanisms. However, heterogeneity arising from gene-set specific regulatory interactions is often overlooked. Results We show that regression models that predict gene expression by using experimentally derived ChIP-seq profiles of TFs can be significantly improved by mixture modelling. In order to find biologically relevant gene clusters, we employ a Bayesian allocation procedure which allows us to integrate additional biological information such as three-dimensional nuclear organization of chromosomes and gene function. The data integration procedure involves transforming the additional data into gene similarity values. We propose a generic similarity measure that is especially suitable for situations where the additional data are of both continuous and discrete type, and compare its performance with similar measures in the context of mixture modelling. Conclusions We applied the proposed method on a data from mouse embryonic stem cells (ESC). We find that including additional data results in mixture components that exhibit biologically meaningful gene clusters, and provides valuable insight into the heterogeneity of the regulatory interactions.

scholarly journals A comparative and functional genomics analysis of the genus Romboutsia provides insight into adaptation to an intestinal lifestyle

2019 ◽  
Author(s):  
Jacoline Gerritsen ◽  
Bastian Hornung ◽  
Jarmo Ritari ◽  
Lars Paulin ◽  
Ger T. Rijkers ◽  
...  
Keyword(s):  
Anaerobic Respiration ◽  
Gene Clusters ◽  
Rrna Gene ◽  
16S Rrna Gene Sequences ◽  
Carbohydrate Utilization ◽  
Soil Isolate ◽  
The Family ◽  
Intestinal Origin ◽  
The Common ◽  
Insight Into

AbstractCultivation-independent surveys have shown that the recently described genus Romboutsia within the family Peptostreptococcaceae is more diverse than previously acknowledged. The majority of Romboutsia-associated 16S rRNA gene sequences have an intestinal origin, but the specific roles that Romboutsia species play in the digestive tract are largely unknown. The complete genomes of the human intestinal isolate Romboutsia hominis FRIFIT (DSM 28814) and the soil isolate Romboutsia lituseburensis A25KT (DSM 797) were sequenced. An evaluation of the common traits of this recently defined genus was done based on comparative genome analysis of the two strains together with the previously elucidated genome of the type species Romboutsia ilealis CRIBT. These analyses showed that the genus Romboutsia covers a broad range of metabolic capabilities with respect to carbohydrate utilization, fermentation of single amino acids, anaerobic respiration and metabolic end products. Main differences between strains were found in their abilities to utilize specific carbohydrates, to synthesize vitamins and other cofactors, and their nitrogen assimilation capabilities. In addition, differences were found with respect to bile metabolism and motility-related gene clusters.

scholarly journals Influence of Human Activities on Broad-Scale Estuarine-Marine Habitats Using Omics-Based Approaches Applied to Marine Sediments

2019 ◽  
Vol 7 (10) ◽  
pp. 419 ◽  
Author(s):  
Shah ◽  
Crosswell ◽  
Metcalfe ◽  
Carlin ◽  
Morrison ◽  
...  
Keyword(s):  
Marine Sediments ◽  
Human Activities ◽  
Large Scale ◽  
Urban Expansion ◽  
Nitrite Reduction ◽  
Future Research ◽  
Rrna Gene ◽  
Marine Habitats ◽  
Degrading Bacteria ◽  
Insight Into

Rapid urban expansion and increased human activities have led to the progressive deterioration of many marine ecosystems. The diverse microbial communities that inhabit these ecosystems are believed to influence large-scale geochemical processes and, as such, analyzing their composition and functional metabolism can be a means to assessing an ecosystem’s resilience to physical and chemical perturbations, or at the very least provide baseline information and insight into future research needs. Here we show the utilization of organic and inorganic contaminant screening coupled with metabolomics and bacterial 16S rRNA gene sequencing to assess the microbial community structure of marine sediments and their functional metabolic output. The sediments collected from Moreton Bay (Queensland, Australia) contained low levels of organic and inorganic contaminants, typically below guideline levels. The sequencing dataset suggest that sulfur and nitrite reduction, dehalogenation, ammonia oxidation, and xylan degradation were the major metabolic functions. The community metabolites suggest a level of functional homogeneity down the 40-cm core depth sampled, with sediment habitat identified as a significant driver for metabolic differences. The communities present in river and sandy channel samples were found to be the most active, with the river habitats likely to be dominated by photoheterotrophs that utilized carbohydrates, fatty acids and alcohols as well as reduce nitrates to release atmospheric nitrogen and oxidize sulfur. Bioturbated mud habitats showed overlapping faunal activity between riverine and sandy ecosystems. Nitrogen-fixing bacteria and lignin-degrading bacteria were most abundant in the sandy channel and bioturbated mud, respectively. The use of omics-based approaches provide greater insight into the functional metabolism of these impacted habitats, extending beyond discrete monitoring to encompassing whole community profiling that represents true phenotypical outputs. Ongoing omics-based monitoring that focuses on more targeted pathway analyses is recommended in order to quantify the flux changes within these systems and establish variations from these baseline measurements.

scholarly journals Identification of isoprene-degrading bacteria in phyllosphere and soil communities from high isoprene-emitting oil palm trees by DNA-stable isotope probing

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Ornella Carrión ◽  
Lisa Gibson ◽  
Dafydd M.O. Elias ◽  
Niall P. McNamara ◽  
Theo A. van Alen ◽  
...  
Keyword(s):  
Stable Isotope ◽  
Atmospheric Chemistry ◽  
Oil Palm ◽  
Agricultural Land ◽  
Gene Clusters ◽  
Stable Isotope Probing ◽  
Sequencing Data ◽  
Terrestrial Plants ◽  
Palm Trees ◽  
Degrading Bacteria

Isoprene is the most abundant biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those from methane. Due to its volatile nature and high reactivity, isoprene plays a complex role in atmospheric chemistry and hence, climate. However, very little is known about its biological degradation in the environment. The vast majority of isoprene (500 Tg ·y-1) is produced by terrestrial plants and oil palm is considered one of the highest isoprene-producing trees, with estimated emissions of 175 μg·g-1 dry leaves ·h-1. Oil palm is also a heavily cultivated crop since it is the source of 30% of the vegetable oil in the world and in countries such as Malaysia represents >85% of total agricultural land. The vast expansion of a single crop that emits such high amounts of isoprene have raised serious concerns about its impact on air quality and climate change. We performed DNA Stable Isotope Probing (DNA-SIP) to study the isoprene-degrading community of oil palm trees in a Malaysian plantation and identified novel genera of isoprene-utilising bacteria in both oil palm soils and leaves. isoA amplicon sequencing data also confirmed that oil palm trees harbour a novel diversity of isoA genes, which encode the alpha subunit of the isoprene monooxygenase, a key enzyme in isoprene metabolism. In addition, metagenome assembled genomes (MAGs) were reconstructed from metagenomes from oil palm soil and leaf incubations and analysed to identify isoprene degradation gene clusters in these microorganisms. Finally, analysis of unenriched metagenomes showed that isoA-containing bacteria are more abundant in soils than in the oil palm phyllosphere.

scholarly journals Comparative genomics analyses of lifestyle transitions at the origin of an invasive fungal pathogen in the genus Cryphonectria

2020 ◽  
Author(s):  
Lea Stauber ◽  
Simone Prospero ◽  
Daniel Croll
Keyword(s):  
Fungal Pathogens ◽  
Gene Clusters ◽  
Sister Group ◽  
Gene Content ◽  
Valuable Insight ◽  
Protein Length ◽  
The Family ◽  
Cysteine Content ◽  
High Degree ◽  
Insight Into

AbstractEmerging fungal pathogens are a threat to forest and agroecosystems, as well as animal and human health. How pathogens evolve from non-pathogenic ancestors is still poorly understood making the prediction of future outbreaks challenging. Most pathogens have evolved lifestyle adaptations, which were enabled by specific changes in the gene content of the species. Hence, understanding transitions in the functions encoded by genomes gives valuable insight into the evolution of pathogenicity. Here, we studied lifestyle evolution in the genus Cryphonectria, including the prominent invasive pathogen C. parasitica, the causal agent of chestnut blight on Castanea species. We assembled and compared the genomes of pathogenic and putatively non-pathogenic Cryphonectria species, as well as sister group pathogens in the family Cryphonectriaceae (Diaporthales, Ascomycetes) to investigate the evolution of genome size and gene content. We found a striking loss of genes associated with carbohydrate metabolism (CAZymes) in C. parasitica compared to other Cryphonectriaceae. Despite substantial CAZyme gene loss, experimental data suggests that C. parasitica has retained wood colonization abilities shared with other Cryphonectria species. Putative effectors substantially varied in number, cysteine content and protein length among species. In contrast, secondary metabolite gene clusters show a high degree of conservation within the genus. Overall, our results underpin the recent lifestyle transition of C. parasitica towards a more pathogenic lifestyle. Our findings suggest that a CAZyme loss may have promoted pathogenicity of C. parasitica on chestnuts. Analyzing gene complements underlying key nutrition modes can facilitate the detection of species with the potential to emerge as pathogens.

Study of the resistor material of an automotive spark plug by use of the charge-up effect along with elemental mapping in an electron microprobe

1991 ◽  
Vol 49 ◽  
pp. 742-743
Author(s):  
D. R. Liu ◽  
S. S. Shinozaki ◽  
J. S. Park ◽  
B. N. Juterbock
Keyword(s):  
Electron Microprobe ◽  
Present Report ◽  
Coated Sample ◽  
Valuable Insight ◽  
Elemental Mapping ◽  
Spark Plug ◽  
Carbon Coated ◽  
Electron Image ◽  
Electron Imaging ◽  
Insight Into

The electric and thermal properties of the resistor material in an automotive spark plug should be stable during its service lifetime. Containing many elements and many phases, this material has a very complex microstructure. Elemental mapping with an electron microprobe can reveal the distribution of all relevant elements throughout the sample. In this work, it is demonstrated that the charge-up effect, which would distort an electron image and, therefore, is normally to be avoided in an electron imaging work, could be used to advantage to reveal conductive and resistive zones in a sample. Its combination with elemental mapping can provide valuable insight into the underlying conductivity mechanism of the resistor.This work was performed in a CAMECA SX-50 microprobe. The spark plug used in the present report was a commercial product taken from the shelf. It was sectioned to expose the cross section of the resistor. The resistor was known not to contain the precious metal Au as checked on the carbon coated sample. The sample was then stripped of carbon coating and re-coated with Au.

Differentiation Of Clarias Batrachus, C. Gariepinus And Heteropneustes Fossilis By Pcr-Sequencing Of Mitochondrial 16s Rrna Gene

2015 ◽  
Vol 41 (1) ◽  
pp. 51-58
Author(s):  
Mohammad Shamimul Alam ◽  
Hawa Jahan ◽  
Rowshan Ara Begum ◽  
Reza M Shahjahan
Keyword(s):  
16S Rrna ◽  
16S Rrna Gene ◽  
Fish Larva ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Rrna Gene ◽  
Valuable Insight ◽  
Multiple Sequence ◽  
Pcr Rflp ◽  
Alternative Means

Heteropneustesfossilis, Clariasbatrachus and C. gariepinus are three major catfishes ofecological and economic importance. Identification of these fish species becomes aproblem when the usual external morphological features of the fish are lost or removed,such as in canned fish. Also, newly hatched fish larva is often difficult to identify. PCRsequencingprovides accurate alternative means of identification of individuals at specieslevel. So, 16S rRNA genes of three locally collected catfishes were sequenced after PCRamplification and compared with the same gene sequences available from othergeographical regions. Multiple sequence alignment of the 16S rRNA gene fragments ofthe catfish species has revealed polymorphic sites which can be used to differentiate thesethree species from one another and will provide valuable insight in choosing appropriaterestriction enzymes for PCR-RFLP based identification in future. Asiat. Soc. Bangladesh, Sci. 41(1): 51-58, June 2015

Quantum Mechanical Interpretation of the Ultra-Low Energy Methyl-Rotation Dynamics in Porous Metal-Organic Frameworks Probed by Low-Frequency Vibrational Spectroscopy and ab initio Simulations

2018 ◽  
Author(s):  
Qi Li ◽  
Adam J. Zaczek ◽  
Timothy M. Korter ◽  
J. Axel Zeitler ◽  
Michael T. Ruggiero
Keyword(s):  
Ab Initio ◽  
Metal Organic Frameworks ◽  
Low Frequency ◽  
Rotor Dynamics ◽  
Quantum Mechanical ◽  
Valuable Insight ◽  
Void Space ◽  
Ab Initio Simulations ◽  
Metal Organic ◽  
Insight Into

<div>Understanding the nature of the interatomic interactions present within the pores of metal-organic frameworks</div><div>is critical in order to design and utilize advanced materials</div><div>with desirable applications. In ZIF-8 and its cobalt analogue</div><div>ZIF-67, the imidazolate methyl-groups, which point directly</div><div>into the void space, have been shown to freely rotate - even</div><div>down to cryogenic temperatures. Using a combination of ex-</div><div>perimental terahertz time-domain spectroscopy, low-frequency</div><div>Raman spectroscopy, and state-of-the-art ab initio simulations,</div><div>the methyl-rotor dynamics in ZIF-8 and ZIF-67 are fully charac-</div><div>terized within the context of a quantum-mechanical hindered-</div><div>rotor model. The results lend insight into the fundamental</div><div>origins of the experimentally observed methyl-rotor dynamics,</div><div>and provide valuable insight into the nature of the weak inter-</div><div>actions present within this important class of materials.</div>

Phylogeny of actin and tubulin gene homologs in diverse eukaryotic species

2019 ◽  
Vol 79 (01S) ◽  
Author(s):  
Pawan Kumar Jayaswal ◽  
Asheesh Shanker ◽  
Nagendra Kumar Singh
Keyword(s):  
Evolutionary Relationship ◽  
Genomic Data ◽  
Gene Clusters ◽  
Species Trees ◽  
Model Species ◽  
Tubulin Gene ◽  
Tubulin Genes ◽  
Eukaryotic Species ◽  
Relationship Of ◽  
Insight Into

Actin and tubulin are cytoskeleton proteins, which are important components of the celland are conserved across species. Despite their crucial significance in cell motility and cell division the distribution and phylogeny of actin and tubulin genes across taxa is poorly understood. Here we used publicly available genomic data of 49 model species of plants, animals, fungi and Protista for further understanding the distribution of these genes among diverse eukaryotic species using rice as reference. The highest numbers of rice actin and tubulin gene homologs were present in plants followed by animals, fungi and Protista species, whereas ten actin and nine tubulin genes were conserved in all 49 species. Phylogenetic analysis of 19 actin and 18 tubulin genes clustered them into four major groups each. One each of the actin and tubulin gene clusters was conserved across eukaryotic species. Species trees based on the conserved actin and tubulin genes showed evolutionary relationship of 49 different taxa clustered into plants, animals, fungi and Protista. This study provides a phylogenetic insight into the evolution of actin and tubulin genes in diverse eukaryotic species.

A Review of Phytochemical and Pharmacological Studies of Inula Species

2020 ◽  
Vol 16 (5) ◽  
pp. 557-567
Author(s):  
Aparoop Das ◽  
Anshul Shakya ◽  
Surajit Kumar Ghosh ◽  
Udaya P. Singh ◽  
Hans R. Bhat
Keyword(s):  
Bacterial Infections ◽  
Chemical Constituents ◽  
Valuable Insight ◽  
Important Ingredient ◽  
Pharmacological Activities ◽  
Medicinal Uses ◽  
The Family ◽  
Pharmacological Studies ◽  
Perennial Herbs ◽  
Insight Into

Background: Plants of the genus Inula are perennial herbs of the family Asteraceae. This genus includes more than 100 species, widely distributed throughout Europe, Africa and Asia including India. Many of them are indicated in traditional medicine, e.g., in Ayurveda. This review explores chemical constituents, medicinal uses and pharmacological actions of Inula species. Methods: Major databases and research and review articles retrieved through Scopus, Web of Science, and Medline were consulted to obtain information on the pharmacological activities of the genus Inula published from 1994 to 2017. Results: Inula species are used either alone or as an important ingredient of various formulations to cure dysfunctions of the cardiovascular system, respiratory system, urinary system, central nervous system and digestive system, and for the treatment of asthma, diabetes, cancers, skin disorders, hepatic disease, fungal and bacterial infections. A range of phytochemicals including alkaloids, essential and volatile oils, flavonoids, terpenes, and lactones has been isolated from herbs of the genus Inula, which might possibly explain traditional uses of these plants. Conclusion: The present review is focused on chemical constituents, medicinal uses and pharmacological actions of Inula species and provides valuable insight into its medicinal potential.

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