william seffens | Morehouse School of Medicine (original) (raw)
Papers by william seffens
We used degenerate oligodeoxyribonucleotides derived from the N-terminal sequence of the s-triazi... more We used degenerate oligodeoxyribonucleotides derived from the N-terminal sequence of the s-triazine hydrolase fromRhodococcus corallinusNRRL B-15444R in an amplification reaction to isolate a DNA segment containing a 57-bp fragment from the trzA gene. By using the nucleotide sequence of this fragment, a nondegenerate oligodeoxyribonucleotide was synthesized and used to screen a genomic library ofR. corallinus DNA for fragments containing trzA. A 5.3-kb PstI fragment containing trzA was cloned, and the nucleotide sequence of a 2,450-bp region containingtrzAwas determined. NotrzAexpression was detected inEscherichia coli or several other gram-negative bacteria. The trzA gene was subcloned into a Rhodococcus-E. coli shuttle vector, pBS305, and transformed into severalRhodococcusstrains. Expression oftrzAwas demonstrated in all Rhodococcus transformants. Rhodococcus sp. strain TE1, which possesses the catabolic gene (atrA) for the N-dealkylation of the herbicides atrazine and simazine, ...
International journal of molecular sciences, Jan 8, 2016
RNAs have been shown to exhibit differential enrichment between nuclear, cytoplasmic, and exosome... more RNAs have been shown to exhibit differential enrichment between nuclear, cytoplasmic, and exosome fractions. A current fundamental question asks why non-coding RNA partition into different spatial compartments. We report on the analysis of cellular compartment models with miRNA data sources for spatial-mechanistic modeling to address the broad area of multi-scalar cellular communication by miRNAs. We show that spatial partitioning of miRNAs is related to sequence similarity to the overall transcriptome. This has broad implications in biological informatics for gene regulation and provides a deeper understanding of nucleotide sequence structure and RNA language meaning for human pathologies resulting from changes in gene expression.
Bioinformatics and Biology Insights, 2016
Health-care initiatives are pushing the development and utilization of clinical data for medical ... more Health-care initiatives are pushing the development and utilization of clinical data for medical discovery and translational research studies. Machine learning tools implemented for Big Data have been applied to detect patterns in complex diseases. This study focuses on hypertension and examines phenotype data across a major clinical study called Minority Health Genomics and Translational Research Repository Database composed of self-reported African American (AA) participants combined with related cohorts. Prior genome-wide association studies for hypertension in AAs presumed that an increase of disease burden in susceptible populations is due to rare variants. But genomic analysis of hypertension, even those designed to focus on rare variants, has yielded marginal genome-wide results over many studies. Machine learning and other nonparametric statistical methods have recently been shown to uncover relationships in complex phenotypes, genotypes, and clinical data. We trained neural networks with phenotype data for missing-data imputation to increase the usable size of a clinical data set. Validity was established by showing performance effects using the expanded data set for the association of phenotype variables with case/control status of patients. Data mining classification tools were used to generate association rules.
Medicine & Science in Sports & Exercise, 2015
Gecco, 1999
This paper demonstrates the ability of genetic programming to evolve analog circuits that perform... more This paper demonstrates the ability of genetic programming to evolve analog circuits that perform digital functions and mixed analog-digital circuits. The evolved circuits include two purely digital circuits (a 100 nano-second NAND circuit and a two-instruction arithmetic logic unit circuit) and one mixed-signal circuit, namely a three-input digital-to-analog converter.
American journal of hypertension, Jan 11, 2016
Apelin is an adipokine directly associated with adiposity, insulin resistance, and decreased bloo... more Apelin is an adipokine directly associated with adiposity, insulin resistance, and decreased blood pressure. Urinary 8-isoprostane is a marker of chronic oxidative endothelial stress. Visfatin, an adipokine that acts by binding and activating the insulin receptor, has been associated with hypertension. As severe hypertension (SH) is highly prevalent among African Americans (AA), we aimed to assess the association of these biomarkers with SH status. A sample of 250 AA participants (134 normotensive controls and 116 with SH (including 98 treatment controlled, SCH: severe controlled hypertension, and 18 treatment resistant, SRH: severe resistant hypertension)) from the Minority Health Genomics and Translational Research Bio-Repository Database (MH-GRID) in metro Atlanta had blood analyzed for apelin and visfatin and urine for 8-isoprostane. T-tests, sex-specific age-adjusted correlation coefficients, and multivariable logistic regression models were used to assess the association of bi...
2006 IEEE International Conference on Granular Computing, 2006
We performed a comparative study of Human, Mouse, and Arabidopsis genes to determine if mRNA seco... more We performed a comparative study of Human, Mouse, and Arabidopsis genes to determine if mRNA secondary structure increases with more complex organisms. Calculating the secondary structures of a large number of genes in a transcriptome has a high degree of parallelism, and is suitable to implement on multiple computers. The analysis in this investigation was done on a cluster of
PloS one, 2014
Proper spindle positioning and orientation are essential for accurate mitosis which requires dyna... more Proper spindle positioning and orientation are essential for accurate mitosis which requires dynamic interactions between microtubule and actin filament (F-actin). Although mounting evidence demonstrates the role of F-actin in cortical cytoskeleton dynamics, it remains elusive as to the structure and function of F-actin-based networks in spindle geometry. Here we showed a ring-like F-actin structure surrounding the mitotic spindle which forms since metaphase and maintains in MG132-arrested metaphase HeLa cells. This cytoplasmic F-actin structure is relatively isotropic and less dynamic. Our computational modeling of spindle position process suggests a possible mechanism by which the ring-like F-actin structure can regulate astral microtubule dynamics and thus mitotic spindle orientation. We further demonstrated that inhibiting Plk1, Mps1 or Myosin, and disruption of microtubules or F-actin polymerization perturbs the formation of the ring-like F-actin structure and alters spindle po...
BioMed Research International, 2014
Serous subtype of ovarian cancer is considered to originate from fallopian epithelium mucosa that... more Serous subtype of ovarian cancer is considered to originate from fallopian epithelium mucosa that has been exposed to physiological changes resulting from ovulation. Ovulation influences an increased in inflammation of epithelial ovarian cells as results of constant exposure of cells to ROS. The imbalance between ROS and antioxidant capacities, as well as a disruption of redox signaling, causes a wide range of damage to DNA, proteins, and lipids. This study applied spectrophotometric, dinitrophenylhydrazone (DNPH) assay, two-dimensional gel electrophoresis, and Western blot analyses to assess the levels of oxidatively modified proteins in 100 primary serous epithelial ovarian carcinoma and normal/surrounding tissues. These samples were obtained from 56 Caucasian and 44 African-American patients within the age range of 61 ± 10 years. Analyses showed that the levels of reactive protein carbonyl groups increased as stages progressed to malignancy. Additionally, the levels of protein carbonyls in serous ovarian carcinoma among African Americans are 40% ( < 0.05) higher relative to Caucasian at similar advanced stages. Results suggest that oxidative stress is involved in the modification of carbonyl protein groups, leading to increased aggressiveness of epithelial ovarian tumors and may contribute to the disease's invasiveness among African Americans.
Lecture Notes in Computer Science, 2007
APRS is an abbreviation for Automatic Packet Reporting System, and is a method of broadcasting GP... more APRS is an abbreviation for Automatic Packet Reporting System, and is a method of broadcasting GPS positioning information in real time from packet radio-equipped stations. It was designed in the early 90’s, but it has seen growth in the last few years due to user-friendly software such as WinAPRS or UI-View, and Kenwood’s APRS enabled radio transceivers becoming available. APRS
Journal of Protein Chemistry, 1994
Developmental Genetics, 1990
Extensive studies of gene expression programs in carrot somatic embryos identified a gene, design... more Extensive studies of gene expression programs in carrot somatic embryos identified a gene, designated Dc3, that serves as a reliable molecular marker for the acquisition of embryogenic potential by carrot cells in culture. The complete sequence of a carrot genomic region, DcG3, encoding a Dc3-like mRNA, was determined. The DcG3 transcription unit contains a single intron and encodes mRNA that is expressed at high levels in embryonic tissue but is undetectable in somatic tissue of carrot. The predicted protein sequence of DcG3 is 163 amino acids and includes two approximately 50 amino acid direct repeats which in turn include additional repetitive elements with an unusual distribution of charged amino acids. Dc3 and Dc3-like mRNAs are encoded by a small divergent gene family. Furthermore, similarities of the Dc3 gene family with genes from other plant species that are expressed in response to environmental and developmental cues suggest a possible role in seed desiccation and possibly in more general water-stress responses in plants. Analysis of transgenic tobacco containing a beta-glucuronidase (GUS) reporter gene fused to a 1.7 kb 5' upstream element of DcG3 defined a promoter/enhancer complex that confers developmentally and environmentally regulated expression of GUS activity. Thus, DcG3 is phylogenetically conserved together with the trans-acting factors required for its regulated expression in transgenic tobacco.
Electronic Journal of Biotechnology, 1998
A neural network (NN) was trained on amino and nucleic acid sequences to test the NN's ability to... more A neural network (NN) was trained on amino and nucleic acid sequences to test the NN's ability to predict a nucleic acid sequence given only an amino acid sequence. A multi-layer backpropagation network of one hidden layer with 5 to 9 neurons was used. Different network configurations were used with varying numbers of input neurons to represent amino acids, while a constant representation was used for the output layer representing nucleic acids. In the besttrained network, 93% of the overall bases, 85% of the degenerate bases, and 100% of the fixed bases were correctly predicted from randomly selected test sequences. The training set was composed of 60 human sequences in a window of 10 to 25 codons at the coding sequence start site. Different NN configurations involving the encoding of amino acids under increasing window sizes were evaluated to predict the behavior of the NN with a significantly larger training set. This genetic data analysis effort will assist in understanding human gene structure. Benefits include computational tools that could predict more reliably the backtranslation of amino acid sequences useful for Degenerate PCR cloning, and may assist the identification of human gene coding sequences (CDS) from open reading frames in DNA databases.
Advances in Bioinformatics and Its Applications - Proceedings of the International Conference, 2005
Journal of Biological Systems, 2002
We used degenerate oligodeoxyribonucleotides derived from the N-terminal sequence of the s-triazi... more We used degenerate oligodeoxyribonucleotides derived from the N-terminal sequence of the s-triazine hydrolase fromRhodococcus corallinusNRRL B-15444R in an amplification reaction to isolate a DNA segment containing a 57-bp fragment from the trzA gene. By using the nucleotide sequence of this fragment, a nondegenerate oligodeoxyribonucleotide was synthesized and used to screen a genomic library ofR. corallinus DNA for fragments containing trzA. A 5.3-kb PstI fragment containing trzA was cloned, and the nucleotide sequence of a 2,450-bp region containingtrzAwas determined. NotrzAexpression was detected inEscherichia coli or several other gram-negative bacteria. The trzA gene was subcloned into a Rhodococcus-E. coli shuttle vector, pBS305, and transformed into severalRhodococcusstrains. Expression oftrzAwas demonstrated in all Rhodococcus transformants. Rhodococcus sp. strain TE1, which possesses the catabolic gene (atrA) for the N-dealkylation of the herbicides atrazine and simazine, ...
International journal of molecular sciences, Jan 8, 2016
RNAs have been shown to exhibit differential enrichment between nuclear, cytoplasmic, and exosome... more RNAs have been shown to exhibit differential enrichment between nuclear, cytoplasmic, and exosome fractions. A current fundamental question asks why non-coding RNA partition into different spatial compartments. We report on the analysis of cellular compartment models with miRNA data sources for spatial-mechanistic modeling to address the broad area of multi-scalar cellular communication by miRNAs. We show that spatial partitioning of miRNAs is related to sequence similarity to the overall transcriptome. This has broad implications in biological informatics for gene regulation and provides a deeper understanding of nucleotide sequence structure and RNA language meaning for human pathologies resulting from changes in gene expression.
Bioinformatics and Biology Insights, 2016
Health-care initiatives are pushing the development and utilization of clinical data for medical ... more Health-care initiatives are pushing the development and utilization of clinical data for medical discovery and translational research studies. Machine learning tools implemented for Big Data have been applied to detect patterns in complex diseases. This study focuses on hypertension and examines phenotype data across a major clinical study called Minority Health Genomics and Translational Research Repository Database composed of self-reported African American (AA) participants combined with related cohorts. Prior genome-wide association studies for hypertension in AAs presumed that an increase of disease burden in susceptible populations is due to rare variants. But genomic analysis of hypertension, even those designed to focus on rare variants, has yielded marginal genome-wide results over many studies. Machine learning and other nonparametric statistical methods have recently been shown to uncover relationships in complex phenotypes, genotypes, and clinical data. We trained neural networks with phenotype data for missing-data imputation to increase the usable size of a clinical data set. Validity was established by showing performance effects using the expanded data set for the association of phenotype variables with case/control status of patients. Data mining classification tools were used to generate association rules.
Medicine & Science in Sports & Exercise, 2015
Gecco, 1999
This paper demonstrates the ability of genetic programming to evolve analog circuits that perform... more This paper demonstrates the ability of genetic programming to evolve analog circuits that perform digital functions and mixed analog-digital circuits. The evolved circuits include two purely digital circuits (a 100 nano-second NAND circuit and a two-instruction arithmetic logic unit circuit) and one mixed-signal circuit, namely a three-input digital-to-analog converter.
American journal of hypertension, Jan 11, 2016
Apelin is an adipokine directly associated with adiposity, insulin resistance, and decreased bloo... more Apelin is an adipokine directly associated with adiposity, insulin resistance, and decreased blood pressure. Urinary 8-isoprostane is a marker of chronic oxidative endothelial stress. Visfatin, an adipokine that acts by binding and activating the insulin receptor, has been associated with hypertension. As severe hypertension (SH) is highly prevalent among African Americans (AA), we aimed to assess the association of these biomarkers with SH status. A sample of 250 AA participants (134 normotensive controls and 116 with SH (including 98 treatment controlled, SCH: severe controlled hypertension, and 18 treatment resistant, SRH: severe resistant hypertension)) from the Minority Health Genomics and Translational Research Bio-Repository Database (MH-GRID) in metro Atlanta had blood analyzed for apelin and visfatin and urine for 8-isoprostane. T-tests, sex-specific age-adjusted correlation coefficients, and multivariable logistic regression models were used to assess the association of bi...
2006 IEEE International Conference on Granular Computing, 2006
We performed a comparative study of Human, Mouse, and Arabidopsis genes to determine if mRNA seco... more We performed a comparative study of Human, Mouse, and Arabidopsis genes to determine if mRNA secondary structure increases with more complex organisms. Calculating the secondary structures of a large number of genes in a transcriptome has a high degree of parallelism, and is suitable to implement on multiple computers. The analysis in this investigation was done on a cluster of
PloS one, 2014
Proper spindle positioning and orientation are essential for accurate mitosis which requires dyna... more Proper spindle positioning and orientation are essential for accurate mitosis which requires dynamic interactions between microtubule and actin filament (F-actin). Although mounting evidence demonstrates the role of F-actin in cortical cytoskeleton dynamics, it remains elusive as to the structure and function of F-actin-based networks in spindle geometry. Here we showed a ring-like F-actin structure surrounding the mitotic spindle which forms since metaphase and maintains in MG132-arrested metaphase HeLa cells. This cytoplasmic F-actin structure is relatively isotropic and less dynamic. Our computational modeling of spindle position process suggests a possible mechanism by which the ring-like F-actin structure can regulate astral microtubule dynamics and thus mitotic spindle orientation. We further demonstrated that inhibiting Plk1, Mps1 or Myosin, and disruption of microtubules or F-actin polymerization perturbs the formation of the ring-like F-actin structure and alters spindle po...
BioMed Research International, 2014
Serous subtype of ovarian cancer is considered to originate from fallopian epithelium mucosa that... more Serous subtype of ovarian cancer is considered to originate from fallopian epithelium mucosa that has been exposed to physiological changes resulting from ovulation. Ovulation influences an increased in inflammation of epithelial ovarian cells as results of constant exposure of cells to ROS. The imbalance between ROS and antioxidant capacities, as well as a disruption of redox signaling, causes a wide range of damage to DNA, proteins, and lipids. This study applied spectrophotometric, dinitrophenylhydrazone (DNPH) assay, two-dimensional gel electrophoresis, and Western blot analyses to assess the levels of oxidatively modified proteins in 100 primary serous epithelial ovarian carcinoma and normal/surrounding tissues. These samples were obtained from 56 Caucasian and 44 African-American patients within the age range of 61 ± 10 years. Analyses showed that the levels of reactive protein carbonyl groups increased as stages progressed to malignancy. Additionally, the levels of protein carbonyls in serous ovarian carcinoma among African Americans are 40% ( < 0.05) higher relative to Caucasian at similar advanced stages. Results suggest that oxidative stress is involved in the modification of carbonyl protein groups, leading to increased aggressiveness of epithelial ovarian tumors and may contribute to the disease's invasiveness among African Americans.
Lecture Notes in Computer Science, 2007
APRS is an abbreviation for Automatic Packet Reporting System, and is a method of broadcasting GP... more APRS is an abbreviation for Automatic Packet Reporting System, and is a method of broadcasting GPS positioning information in real time from packet radio-equipped stations. It was designed in the early 90’s, but it has seen growth in the last few years due to user-friendly software such as WinAPRS or UI-View, and Kenwood’s APRS enabled radio transceivers becoming available. APRS
Journal of Protein Chemistry, 1994
Developmental Genetics, 1990
Extensive studies of gene expression programs in carrot somatic embryos identified a gene, design... more Extensive studies of gene expression programs in carrot somatic embryos identified a gene, designated Dc3, that serves as a reliable molecular marker for the acquisition of embryogenic potential by carrot cells in culture. The complete sequence of a carrot genomic region, DcG3, encoding a Dc3-like mRNA, was determined. The DcG3 transcription unit contains a single intron and encodes mRNA that is expressed at high levels in embryonic tissue but is undetectable in somatic tissue of carrot. The predicted protein sequence of DcG3 is 163 amino acids and includes two approximately 50 amino acid direct repeats which in turn include additional repetitive elements with an unusual distribution of charged amino acids. Dc3 and Dc3-like mRNAs are encoded by a small divergent gene family. Furthermore, similarities of the Dc3 gene family with genes from other plant species that are expressed in response to environmental and developmental cues suggest a possible role in seed desiccation and possibly in more general water-stress responses in plants. Analysis of transgenic tobacco containing a beta-glucuronidase (GUS) reporter gene fused to a 1.7 kb 5' upstream element of DcG3 defined a promoter/enhancer complex that confers developmentally and environmentally regulated expression of GUS activity. Thus, DcG3 is phylogenetically conserved together with the trans-acting factors required for its regulated expression in transgenic tobacco.
Electronic Journal of Biotechnology, 1998
A neural network (NN) was trained on amino and nucleic acid sequences to test the NN's ability to... more A neural network (NN) was trained on amino and nucleic acid sequences to test the NN's ability to predict a nucleic acid sequence given only an amino acid sequence. A multi-layer backpropagation network of one hidden layer with 5 to 9 neurons was used. Different network configurations were used with varying numbers of input neurons to represent amino acids, while a constant representation was used for the output layer representing nucleic acids. In the besttrained network, 93% of the overall bases, 85% of the degenerate bases, and 100% of the fixed bases were correctly predicted from randomly selected test sequences. The training set was composed of 60 human sequences in a window of 10 to 25 codons at the coding sequence start site. Different NN configurations involving the encoding of amino acids under increasing window sizes were evaluated to predict the behavior of the NN with a significantly larger training set. This genetic data analysis effort will assist in understanding human gene structure. Benefits include computational tools that could predict more reliably the backtranslation of amino acid sequences useful for Degenerate PCR cloning, and may assist the identification of human gene coding sequences (CDS) from open reading frames in DNA databases.
Advances in Bioinformatics and Its Applications - Proceedings of the International Conference, 2005
Journal of Biological Systems, 2002
Introduction: Biomedical research aimed toward a deeper understanding of yoga’s benefits and phys... more Introduction: Biomedical research aimed toward a deeper understanding of yoga’s benefits and physiological mechanisms has become an active area of study. To decrease disparity between populations who can readily access yoga classes and therapies, benefits of yoga could be implemented in an exergame format at clinical or home environments. This platform could be installed with low cost hardware using the Cloud for analytics and data collection. Purpose: Objective was to analyze yoga posture alignment using a 3D room sensor to produce a physical activity exergame for specific groups, such as young adults. This research utilizes gesture analysis software to provide skill improvement feedback to students in a yoga course setting. Methods: We measured yoga posture alignment over the course of a 10-week period using Kinect SDK 2.0. A convenience sample of 20 undergraduate students with minimal yoga experience were recruited under an IRB approved protocol. Results: Five yoga postures were captured from seven yoga teachers, as a gold standard for comparison and used for training supervised machine learning algorithms. Default settings in Kinect Visual Gesture Builder produced solutions with high True Positives (99.5%) and low False Positives (0.03%) for most yoga postures sampled. Depth stream and skeleton coordinates for the 20 participants were acquired and analyzed against this trained solution. Analysis showed sensitivity for True Positives was greatest for “Side Bend” (0.496) and “Upward Salute” (0.141) and most postures had specificities for True Negatives near 1.0. Based on these results the higher the gesture score, the closer the postures were to the “gold standard”. Discussion: Gesture analysis for yoga alignment training may be a useful tool for the development of home and clinical yoga therapy for hard to reach populations. The exergame developed here provides a tool that scores the performance of yoga postures and improvement. Prior research has shown that even short-term yoga based lifestyle interventions were efficacious in weight loss, inflammation and stress and positively influenced cardiovascular risk factors. Conclusion: Our plans are to target special populations, study the potential effects of body mass and age on posture alignment, and assess breathing, heart rate and limb stretch.