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January 2018

Jan 23
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Genome Characterization of Oleaginous Aspergillus oryzae BCC7051: A Potential Fungal-Based Platform for Lipid Production

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Curr Microbiol. 2018 Jan;75(1):57-70. doi: 10.1007/s00284-017-1350-7. Epub 2017 Sep 1.

Thammarongtham C, Nookaew I, Vorapreeda T, Srisuk T, Land ML, Jeennor S, Laoteng K

Abstract

The selected robust fungus, Aspergillus oryzae strain BCC7051 is of interest for biotechnological production of lipid-derived products due to its capability to accumulate high amount of intracellular lipids using various sugars and agro-industrial substrates. Here, we report the genome sequence of the oleaginous A. oryzae BCC7051. The obtained reads were de novo assembled into 25 scaffolds spanning of 38,550,958 bps with predicted 11,456 protein-coding genes. By synteny mapping, a large rearrangement was found in two scaffolds of A. oryzae BCC7051 as compared to the reference RIB40 strain. The genetic relationship between BCC7051 and other strains of A. oryzae in terms of aflatoxin production was investigated, indicating that the A. oryzae BCC7051 was categorized into group 2 nonaflatoxin-producing strain. Moreover, a comparative analysis of the structural genes focusing on the involvement in lipid metabolism among oleaginous yeast and fungi revealed the presence of multiple isoforms of metabolic enzymes responsible for fatty acid synthesis in BCC7051. The alternative routes of acetyl-CoA generation as oleaginous features and malate/citrate/pyruvate shuttle were also identified in this A. oryzae strain. The genome sequence generated in this work is a dedicated resource for expanding genome-wide study of microbial lipids at systems level, and developing the fungal-based platform for production of diversified lipids with commercial relevance.

PMID: 28865010 DOI: 10.1007/s00284-017-1350-7

Jan 23
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Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

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mSystems, 3:e00070-17. https://doi.org/10.1128/ mSystems.00070-17.
DOI: 10.1128/mSystems.00070-17

Abiotic Stresses Shift Belowground Populus-Associated Bacteria Toward a Core Stress Microbiome

Collin M. Timm, Kelsey R. Carter, Alyssa A. Carrell, Se-Ran Jun, Sara S. Jawdy, Jessica M. Vélez, Lee E. Gunter, Zamin Yang, Intawat Nookaew, Nancy L. Engle, Tse-Yuan S. Lu, Christopher W. Schadt, Timothy J. Tschaplinski, Mitchel J. Doktycz, Gerald A. Tuskan, Dale A. Pelletier, David J. Weston

ABSTRACT

Adverse growth conditions can lead to decreased plant growth, productivity, and survival, resulting in poor yields or failure of crops and biofeedstocks. In some cases, the microbial community associated with plants has been shown to alleviate plant stress and increase plant growth under suboptimal growing conditions. A systematic understanding of how the microbial community changes under these conditions is required to understand the contribution of the microbiome to water utilization, nutrient uptake, and ultimately yield. Using a microbiome inoculation strategy, we studied how the belowground microbiome of Populus deltoides changes in response to diverse environmental conditions, including water limitation, light limitation (shading), and metal toxicity. While plant responses to treatments in terms of growth, photosynthesis, gene expression and metabolite profiles were varied, we identified a core set of bacterial genera that change in abundance in response to host stress. The results of this study indicate substantial structure in the plant microbiome community and identify potential drivers of the phytobiome response to stress.

IMPORTANCE: The identification of a common “stress microbiome” indicates tightly controlled relationships between the plant host and bacterial associates and a conserved structure in bacterial communities associated with poplar trees under different growth conditions. The ability of the microbiome to buffer the plant from extreme environmental conditions coupled with the conserved stress microbiome observed in this study suggests an opportunity for future efforts aimed at predictably modulating the microbiome to optimize plant growth.

Jan 20
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Gender Differences in the Pathogenesis and Management of Heart Disease

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Chapter 7 in the book “Gender Differences in the Pathogenesis and Management of Heart Disease”, Springer/Nature publishing company, in the press (January 2018).   ISBN:978-3-319-71134-8

Adriana Cabal, Trudy M. Wassenaar, and David W. Ussery

Abstract

The literature was reviewed to search for consistently reported differences in the gut microbiome between females and males, in an attempt to relate such changes to different risks of cardiovascular disease that exist between the genders. Although multiple publications were identified that reported gender differences in the gut microbiome, none of the described observations were consistent. Apparently, the variation in gut microbiome between populations under study, as a result of differences in geography, life style, diet, age, genetics and possible other factors is more extensive than the variation between males and females. However, we summarize a number of findings on gender differences reported for cardiovascular diseases that may have a link to the microbiome, for instance the presence of irritable bowel disease (IBD) which is a risk factor for cardiovascular disease, coincides with a dysbiosis of the gut microbiome, and is more common in females than males. Other microbiome-related gender differences may pose a greater risk for males, so that, overall, there is no known positive or negative generally applicable effect of a ‘female-type’ or ‘male-type’ microbiome that would have a significant effect on risk or severity of cardiovascular diseases.

Jan 16
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Distinctive molecular signature and activated signaling pathways in aortic smooth muscle cells of patients with myocardial infarction

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http://www.atherosclerosis-journal.com/article/S0021-9150(18)30024-8/fulltext
DOI: http://dx.doi.org/10.1016/j.atherosclerosis.2018.01.024

Atherosclerosis, manuscript in the press, accepted 16 January, 2028

Thidathip Wongsurawat, Chin Cheng Woo, Antonis Giannakakis, Xiao Yun Lin, Esther Sok Hwee Cheow, Chuen Neng Lee, Mark Richards, Siu Kwan Sze, Intawat Nookaew, Vladimir A. Kuznetsov’Correspondence information about the author Vladimir A. Kuznetsov, Vitaly Sorokin

Abstract

Background and aims: We aim to identify significant transcriptome alterations of vascular smooth muscle cells (VSMCs) in the aortic wall of myocardial infarction (MI) patients. Providing a robust transcriptomic signature, we aim to highlight the most likely aberrant pathway(s) in MI VSMCs. Methods and results: Laser-captured microdissection (LCM) was used to obtain VSMCs from aortic wall tissues harvested during coronary artery bypass surgery. Microarray gene analysis was applied to analyse VSMCs from 17 MI and 19 non-MI patients. Prediction Analysis of Microarray (PAM) identified 370 genes that significantly discriminated MI and non-MI samples and were enriched in genes responsible for muscle development, differentiation and phenotype regulation. Incorporation of gene ontology (GO) led to the identification of a 21-gene VSMCs-associated classifier that discriminated between MI and non-MI patients with 92% accuracy. The mass spectrometry-based iTRAQ analysis of the MI and non-MI samples revealed 94 proteins significantly differentiating these tissues. Ingenuity Pathway Analysis (IPA) of 370 genes revealed top pathways associated with hypoxia signaling in the cardiovascular system. Enrichment analysis of these proteins suggested an activation of the superoxide radical degradation pathway. An integrated transcriptome-proteome pathway analysis revealed that superoxide radical degradation pathway remained the most implicated pathway. The intersection of the top candidate molecules from the transcriptome and proteome highlighted superoxide dismutase (SOD1) overexpression

Conclusions: We provided a novel 21-gene VSMCs-associated MI classifier in reference to significant VSMCs transcriptome alterations that, in combination with proteomics data, suggests the activation of superoxide radical degradation pathway in VSMCs of MI patients.

Jan 13
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Complete genomic and transcriptional landscape analysis using third-generation sequencing: a case study of Saccharomyces cerevisiae CEN.PK113-7D

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Introduction:

The genome of the most well studied eukaryotic model organism, Saccharomyces cerevisiae strain S288c, was sequenced and released in 1996; it was the first complete, high quality genome sequence of an eukaryal organism (1). Since then, the development ofDNAsequencing technologies has yielded scientific breakthroughs that enable us to obtain and analyze genomic DNA sequences at a faster, more economical pace (2).

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Jan 08
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Assessing the utility of metabarcoding for diet analyses of the omnivorous wild pig (Sus scrofa)

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http://onlinelibrary.wiley.com/doi/10.1002/ece3.3638/full

Ecology and Evolution, (2018), 8:185-196. DOI: 10.1002/ece3.3638

Michael S. Robeson II, Kamil Khanipov, George Golovko, Samantha M. Wisely, Michael D. White, Michael Bodenchuck, Timothy J. Smyser, Yuriy Fofanov, Noah Fierer, Antoinette J. Piaggio

Abstract

Wild pigs (Sus scrofa) are an invasive species descended from both domestic swine and Eurasian wild boar that was introduced to North America during the early 1500s. Wild pigs have since become the most abundant free-ranging exotic ungulate in the United States. Large and ever-increasing populations of wild pigs negatively impact agricul- ture, sport hunting, and native ecosystems with costs estimated to exceed $1.5 bil- lion/year within the United States. Wild pigs are recognized as generalist feeders, able to exploit a broad array of locally available food resources, yet their feeding behaviors remain poorly understood as partially digested material is often unidentifiable through traditional stomach content analyses. To overcome the limitation of stomach content analyses, we developed a DNA sequencing-based protocol to describe the plant and animal diet composition of wild pigs. Additionally, we developed and evaluated block- ing primers to reduce the amplification and sequencing of host DNA, thus providing greater returns of sequences from diet items. We demonstrate that the use of block- ing primers produces significantly more sequencing reads per sample from diet items, which increases the robustness of ascertaining animal diet composition with molecular tools. Further, we show that the overall plant and animal diet composition is signifi- cantly different between the three areas sampled, demonstrating this approach is suit- able for describing differences in diet composition among the locations.

 

KEYWORDS

blocking primer, CO1, diet, feral swine, metabarcoding, trnL

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