Qunfeng Dong

Loyola University Chicago

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David E. Nelson

University School

Xiang Gao

Guangxi University

Evelyn Toh

Indiana University – Purdue University Indianapolis

Huaiying Lin

University of Chicago

Alan J. Wolfe

Loyola University Chicago

Linda Brubaker

University of California, San Diego

Claudia Vilo

University of Antofagasta

George M. Weinstock

Jackson Laboratory

Kashi V. Revanna

Loyola University Chicago

Elizabeth R. Mueller

Loyola University Medical Center

Cooperative Institutions

Indiana University

Indiana University Bloomington

Indiana University – Purdue University Indianapolis

Indiana University School of Medicine

Loyola University Chicago

Stanford University

Loyola University Medical Center

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University of Washington

University of California, San Diego

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POSTER: “Pseudomonas fluorescens Strain NCIMB 11764, a unique bacterium with cyanide adaptation features”

Claudia Vilo Daniel A. Kunz Xiang Gao Qunfeng Dong

Cyanide is a potent poison that can be found naturally in some environments, and released as a waste in human activities. Cyanide waste is indeed a public health and an environmental concern. Its removal is an important issue, which has been addressed by chemical-physical methods or by alternatives such as bioremediation, which utilize organisms that can degrade cyanide. Pseudomonas fluorescens NCIMB11764 (Pf11764) bacterium is capable of utilize cyanide as its sole nitrogen source. However, the complete pathways involved in its metabolism are unclear. Therefore, to learn more about the unique genetic features of Pf11764, we characterized the bacterium's genome using next-generation sequencing technology. Our main objectives were to characterize and identify the genes involved in cyanide degradation and to study potential resistance pathways present in this genome.

Pseudomonas fluorescens

Strain (injury)

10.1109/iccabs.2013.6629209

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Towards Robust Firewalls Using Approximate Packet Classification

Qunfeng Dong Dheeraj Agrawal Zihui Ge Jia Wang Jianming Wu

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Erratum for Vilo et al., Draft Genome Sequence of Cupriavidus sp. Strain SK-3, a 4-Chlorobiphenyl- and 4-Chlorobenzoic Acid-Degrading Bacterium

Genome Announcements (2014)

Claudia Vilo Michael J. Benedik Matthew O. Ilori Qunfeng Dong

Volume 2, no. 4, [e00664-14][1], 2014. Page 1: The article title should read as given above and the word “clorobenzoic” should read “chlorobenzoic” in the abstract and main text. [1]: /lookup/doi/10.1128/genomeA.00664-14

Strain (injury)

10.1128/genomea.00756-14

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Citations (1)

Household air pollution and the lung microbiome of healthy adults in Malawi: a cross-sectional study

PMC (2016)

Jamie Rylance Anstead Kankwatira David E. Nelson Evelyn Toh Richard B. Day

Domestic combustion of biomass fuels, such as wood, charcoal, crop residue and dung causes Household Air Pollution (HAP). These inhaled particulates affect more than half of the world’s population, causing respiratory problems such as infection and inflammatory lung disease. We examined whether the presence of black carbon in alveolar macrophages was associated with alterations in the lung microbiome in a Malawi population. Bronchoalveolar lavage samples from 44 healthy adults were sequenced using 16S rDNA amplification to assess microbial diversity, richness and relative taxa abundance. Individuals were classified as high or low particulate exposure as determined by questionnaire and the percentage of black carbon within their alveolar macrophages. Subjects in the low and high particulate groups did not differ in terms of source of fuels used for cooking or lighting. There was no difference in alpha or beta diversity by particulate group. Neisseria and Streptococcus were significantly more abundant in samples from high particulate exposed individuals, and Tropheryma was found less abundant. Petrobacter abundance was higher in people using biomass fuel for household cooking and lighting, compared with exclusive use of electricity. Healthy adults in Malawi exposed to higher levels of particulates have higher abundances of potentially pathogenic bacteria (Streptococcus, Neisseria) within their lung microbiome. Domestic biomass fuel use was associated with an uncommon environmental bacterium (Petrobacter) associated with oil-rich niches.

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The human urobiome

Mammalian Genome (2021)

Linda Brubaker Catherine Putonti Qunfeng Dong Alan J. Wolfe

Human genetics

10.1007/s00335-021-09862-8

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Sexual Behavior Shapes the Adult Male Genitourinary Microbiome

SSRN Electronic Journal (2022)

Evelyn Toh Yue Xing Xiang Gao Stephen J. Jordan Teresa A. Batteiger

The origin, composition, and significance of the distal male urethral microbiome are unclear, but vaginal microbiome dysbioses have been linked to new sex partners and several urogynecological syndromes. We characterized 110 urethral specimens from men without urethral symptoms, infections, or inflammation using shotgun metagenomics. Characteristic Lactic acid bacteria and Corynebacteria spp. were detected in most of the specimens. In contrast, several vaginal dysbiosis associated microorganisms were detected only in specimens from the men who reported vaginal intercourse. Sexual behavior, but no other evaluated behavioral, demographic, or clinical variables, contributed strongly to the observed inter-specimen variance in urethral microbiome composition. Thus, the male urethra supports a core microbiome that is established independent of but which can be reshaped by sexual exposures. Overall, we show urogenital microbiology and sexual behavior are inexorably intertwined and hypothesize that the male urethra may be a silent reservoir for several important female urogenital pathobionts and pathogens.

10.2139/ssrn.4023681

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Computational Identification of Related Proteins

Humana Press eBooks (2005)

Qunfeng Dong Volker Brendel

Molecular sequences that share a high degree of similarity often are thought to have evolved from common ancestral genes. Closely related protein sequences will presumably correspond to similar three-dimensional structures and conserved biological functions (although the reverse is not necessarily true: similar structures and conserved functions do not imply that the corresponding protein sequences will be similar; reviewed in ref. 1). These assumptions provide the basis for computational gene annotation. Typically, the first step in characterizing a novel gene is to compare its sequence against known sequences in available databases and to predict its origin and function by copying the annotation of those previously characterized sequences. This approach has been highly successful and is probably the only practical method applicable to large-scale annotation efforts at present. It should be pointed out, however, that this practice is not without its limitations (and is also unsatisfactory from the more theoretical perspective of those who wish to determine structure and function from primary sequence; for a provocative editorial on this subject, see ref. 2). The intrinsic problems of transitive propagation of historical annotation errors have been discussed elsewhere (bi3) and are all too familiar to any biologist who has looked into the databases only to find puzzling annotations that make no sense with current knowledge.

Copying

Identification

Similarity (geometry)

Sequence (biology)

10.1007/978-1-59259-890-8_51

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PlantGDB, plant genome database and analysis tools

Nucleic Acids Research (2003)

Qunfeng Dong

PlantGDB ( http://www.plantgdb.org/ ) is a database of molecular sequence data for all plant species with significant sequencing efforts. The database organizes EST sequences into contigs that represent tentative unique genes. Contigs are annotated and, whenever possible, linked to their respective genomic DNA. Genome sequence fragments are assembled similarly. The goal of the PlantGDB web site is to establish the basis for identifying sets of genes common to all plants or specific to particular species by integrating a number of bioinformatics tools that facilitate gene prediction and cross‐ species comparisons. For species with large‐scale genome sequencing efforts, PlantGDB provides genome browsing capabilities that integrate all available EST and cDNA evidence for current gene models (for Arabidopsis thaliana , see the AtGDB site at http://www.plantgdb.org/AtGDB/ ).

10.1093/nar/gkh046

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Citations (219)

Journal of Global Optimization (2003)

Qunfeng Dong

Data set

10.1023/a:1023221624213

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Citations (57)

Practical network coding in wireless networks

Qunfeng Dong Jianming Wu Wenjun Hu Jon Crowcroft

Network coding is seen as a promising technique to improve network throughput. In this paper, we study two important problems in localized network coding in wireless networks, which only requires each node to know about and coordinate with one-hop neighbors. In particular, we first establish a condition that is both necessary and sufficient for useful coding to be possible. We show this condition is much weaker than expected, and hence allows a variety of coding schemes to suit different network conditions and application preferences. Based on the understanding we establish, we are able to design a robust coding technique called loop coding that can improve network throughput and TCP throughput simultaneously.

Linear network coding

10.1145/1287853.1287891

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Citations (70)