Engineering Commons^™

Human Microbiome Transfer In The Built Environment Differs Based On Occupants, Objects, And Buildings, Andrew J. Hoisington, Christopher E. Stamper, Katherine L. Bates, Maggie A. Stanislawski, Michael C. Flux, Teodor T. Postolache, Christopher A. Lowry, Lisa A. Brenner

Faculty Publications

Compared to microbiomes on other skin sites, the bacterial microbiome of the human hand has been found to have greater variability across time. To increase understanding regarding the longitudinal transfer of the hand microbiome to objects in the built environment, and vice versa, 22 participants provided skin microbiome samples from their dominant hands, as well as from frequently and infrequently touched objects in their office environments. Additional longitudinal samples from home environments were obtained from a subset of 11 participants. We observed stability of the microbiomes of both the hand and built environments within the office and home settings; however, …

Dataset For Effects Of Single-Session Practice Structure On Motor Skill Acquisition And Alpha And Beta Eeg Oscillations, Audrey Porter, Ronald V. Croce, Wayne Smith

Faculty Publications

Although it is known that practicing a motor skill updates the associated internal model, it is still unclear as to how cortical oscillations linked with the motor skill change under differing practice schedules. The current study investigated α- and β-power changes associated with motor skill acquisition. Firstly, we investigated the behavioral effects of practice on motor learning and retention during repetitive (RP) and variable (VP) practice schedules on an anticipation timing task. Secondly, we investigated changes in cortical α (10-13 HZ) and β (15-30 Hz) event-related synchronization and dyssynchronization (ERS/ERD) under RP and VP during early (EP) and late …

Effects Of Temperature And Antioxidants On The Oxidation Of Biodiesel Derived From Waste Vegetable Oil, Randy L. Maglinao, Torrey J. Wagner, Keegan Duff

Faculty Publications

Biodiesel offers several environmental benefits and improvements to some fuel performance properties, but its poor oxidative stability has been a major concern. Currently, the accepted practice to improve biodiesel oxidative stability is the addition of antioxidants; numerous antioxidants have been studied but their effectiveness in inhibiting biodiesel oxidation is difficult to predict due to variation with resonance stability, solubility, reactivity, and volatility. To improve prediction efforts, this study explored the Rapid Small-Scale Oxidation Test (RSSOT) as a means to investigate how biodiesel oxidation is affected by antioxidant concentration and temperature, and compared its results with the oxidative stability index test. …

On-Site And External Energy Harvesting In Underground Wireless, Usman Raza, Abdul Salam

Faculty Publications

Energy efficiency is vital for uninterrupted long-term operation of wireless underground communication nodes in the field of decision agriculture. In this paper, energy harvesting and wireless power transfer techniques are discussed with applications in underground wireless communications (UWC). Various external wireless power transfer techniques are explored. Moreover, key energy harvesting technologies are presented that utilize available energy sources in the field such as vibration, solar, and wind. In this regard, the Electromagnetic(EM)- and Magnetic Induction(MI)-based approaches are explained. Furthermore, the vibration-based energy harvesting models are reviewed as well. These energy harvesting approaches lead to design of an efficient wireless underground …

A New Ectotherm 3d Tracking And Behavior Analytics System Using A Depth-Based Approach With Color Validation, With Preliminary Data On Kihansi Spray Toad (Nectophrynoides Asperginis) Activity, Philip Bal, Damian Lyons, Avishai Shuter

Faculty Publications

The Kihansi spray toad (Nectophrynoides asperginis), classified as Extinct in the Wild by the IUCN, is being bred at the Wildlife Conservation Society’s (WCS) Bronx Zoo as part of an effort to successfully reintroduce the species into the wild. Thousands of toads live at the Bronx Zoo presenting an opportunity to learn more about their behaviors for the first time, at scale. It is impractical to perform manual observations for long periods of time. This paper reports on the development of a RGB-D tracking and analytics approach that allows researchers to accurately and efficiently gather information about the toads’ behavior. …

Internet Of Things In Agricultural Innovation And Security, Abdul Salam

Faculty Publications

The agricultural Internet of Things (Ag-IoT) paradigm has tremendous potential in transparent integration of underground soil sensing, farm machinery, and sensor-guided irrigation systems with the complex social network of growers, agronomists, crop consultants, and advisors. The aim of the IoT in agricultural innovation and security chapter is to present agricultural IoT research and paradigm to promote sustainable production of safe, healthy, and profitable crop and animal agricultural products. This chapter covers the IoT platform to test optimized management strategies, engage farmer and industry groups, and investigate new and traditional technology drivers that will enhance resilience of the farmers to the …

Internet Of Things In Water Management And Treatment, Abdul Salam

Faculty Publications

The goal of the water security IoT chapter is to present a comprehensive and integrated IoT based approach to environmental quality and monitoring by generating new knowledge and innovative approaches that focus on sustainable resource management. Mainly, this chapter focuses on IoT applications in wastewater and stormwater, and the human and environmental consequences of water contaminants and their treatment. The IoT applications using sensors for sewer and stormwater monitoring across networked landscapes, water quality assessment, treatment, and sustainable management are introduced. The studies of rate limitations in biophysical and geochemical processes that support the ecosystem services related to water quality …

Cgste11 Mediates Cross Tolerance To Multiple Environmental Stressors In Candida Glabrata, Mian Huang, Jibran Khan, Manpreet Kaur, Julian Daniel Torres Vanega, Orlando Andres Aguilar Patiño, Anand Ramasubramanian, Katy Kao

Faculty Publications

Candida glabrata is a human commensal and an opportunistic human fungal pathogen. It is more closely related to the model yeast Saccharomyces cerevisiae than other Candida spp. Compared with S. cerevisiae, C. glabrata exhibits higher innate tolerance to various environmental stressors, including hyperthermal stress. Here we investigate the molecular mechanisms of C. glabrata adaptation to heat stress via adaptive laboratory evolution. We show that all parallel evolved populations readily adapt to hyperthermal challenge (from 47 °C to 50 °C) and exhibit convergence in evolved phenotypes with extensive cross-tolerance to various other environmental stressors such as oxidants, acids, and alcohols. Genome …

Subsurface Mimo: A Beamforming Design In Internet Of Underground Things For Digital Agriculture Applications, Abdul Salam

Faculty Publications

In underground (UG) multiple-input and multiple-output (MIMO), the transmit beamforming is used to focus energy in the desired direction. There are three different paths in the underground soil medium through which the waves propagates to reach at the receiver. When the UG receiver receives a desired data stream only from the desired path, then the UG MIMO channel becomes three path (lateral, direct, and reflected) interference channel. Accordingly, the capacity region of the UG MIMO three path interference channel and degrees of freedom (multiplexing gain of this MIMO channel requires careful modeling). Therefore, expressions are required for the degree of …

A Theoretical Model Of Underground Dipole Antennas For Communications In Internet Of Underground Things, Abdul Salam, Mehmet C. Vuran, Xin Dong, Christos Argyropoulos, Suat Irmak

Faculty Publications

The realization of Internet of Underground Things (IOUT) relies on the establishment of reliable communication links, where the antenna becomes a major design component due to the significant impacts of soil. In this paper, a theoretical model is developed to capture the impacts of change of soil moisture on the return loss, resonant frequency, and bandwidth of a buried dipole antenna. Experiments are conducted in silty clay loam, sandy, and silt loam soil, to characterize the effects of soil, in an indoor testbed and field testbeds. It is shown that at subsurface burial depths (0.1-0.4m), change in soil moisture impacts …

Photosynthetic Performance And Anti-Oxidative Response Of Cornus Controversa Seedlings Under Cadmium And Lead Stress, Xinyu Huang, Yonglei Jiang, Xiaomao Cheng, Lilan Deng, Xuncheng Liu

Faculty Publications

The photosynthetic efficiency of Cornus controversa leaves was decreased significantly under Cd treatment while it was not affected by Pb exposure. Cd decreased while Pb treatment increased the chlorophyll contents of Cornus controversa leaves. Furthermore, the peroxidase (GPX) activities were decreased after Cd treatment while elevated by Pb exposure in Cornus controvera seedlings. In addition, both Cd and Pb exposures increased the malondialdehyde (MDA) and proline contents and elevated the superoxide dismutase (SOD) activities of Cornus controvera seedlings. Collectively, these results indicated that Cornus controversa may be more tolerant to Pb than Cd toxicity. This finding will contribute to the …

Runoff Of Silvicultural Herbicides Applied Using Best Management Practices, Matthew W. Mcbroom, Jeff Louch, R Scott Beasley, Mingteh Chang, George G. Ice

Faculty Publications

Nine small (2.2 to 2.9 ha) and four large (70 to 135 ha) watersheds in East Texas, USA, were instrumented to compare herbicide runoff under different silvicultural systems with best management practices (BMPs). Two treatments were evaluated: conventional, with clearcutting, aerial herbicide site preparation, and hand-applied banded herbaceous release; and intensive, in which subsoiling, aerial fertilization, and a second-year aerial herbicide application were added. Herbicides were applied as operational tank mixes. The highest imazapyr concentration found in stream water was 39 mg L^‑1 during the first storm after application (23 days after treatment, DAT) and in-stream concentrations …

Complex Of Myoglobin With Phenol Bound In A Proximal Cavity, Xiao Huang, Chunxue Wang, Lesa R. Celeste, Leslie L. Lovelace, Shengfang Sun, John H. Dawson, Lukasz Lebioda

Faculty Publications

Sperm whale myoglobin (Mb) has weak dehaloperoxidase activity and catalyzes the peroxidative dehalogenation of 2,4,6-trichlorophenol (TCP) to 2,6-dichloroquinone. Crystals of Mb and of its more active G65T variant were used to study the binding of TCP, 4-iodophenol (4-IP) and phenol. The structures of crystals soaked overnight in a 10 mM solution of phenol revealed that a phenol molecule binds in the proximal cavity, forming a hydrogen bond to the hydroxyl of Tyr146 and hydrophobic contacts which include interactions with C and C of the proximal histidine His93. The phenol position corresponds to the strongest xenon binding site, Xe1. It …

Structures Of Human Thymidylate Synthase R163k With Dump, Fdump And Glutathione Show Asymmetric Ligand Binding, Lydia M. Gibson, Lesa R. Celeste, Leslie L. Lovelace, Lukasz Lebioda

Faculty Publications

Thymidylate synthase (TS) is a well validated target in cancer chemotherapy. Here, a new crystal form of the R163K variant of human TS (hTS) with five subunits per asymmetric part of the unit cell, all with loop 181-197 in the active conformation, is reported. This form allows binding studies by soaking crystals in artificial mother liquors containing ligands that bind in the active site. Using this approach, crystal structures of hTS complexes with FdUMP and dUMP were obtained, indicating that this form should facilitate high-throughput analysis of hTS complexes with drug candidates. Crystal soaking experiments using oxidized glutathione revealed that …

Genome3d: A Viewer-Model Framework For Integrating And Visualizing Multi-Scale Epigenomic Information Within A Three-Dimensional Genome, Thomas M. Asbury, Matt Mitman, Jijun Tang, W. Jim Zheng

Faculty Publications

Background
New technologies are enabling the measurement of many types of genomic and epigenomic information at scales ranging from the atomic to nuclear. Much of this new data is increasingly structural in nature, and is often difficult to coordinate with other data sets. There is a legitimate need for integrating and visualizing these disparate data sets to reveal structural relationships not apparent when looking at these data in isolation.

Results
We have applied object-oriented technology to develop a downloadable visualization tool, Genome3D, for integrating and displaying epigenomic data within a prescribed three-dimensional physical model of the human genome. In order …

Using Jackknife To Assess The Quality Of Gene Order Phylogenies, Jian Shi, Yiwei Zhang, Haiwei Luo, Jijun Tang

Faculty Publications

Background
In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with a large number of states, traditional bootstrap procedures cannot be applied. Researchers began to use a jackknife resampling method to assess the quality of gene order phylogenies.

Results
In this paper, we design and conduct a set of experiments to validate the performance of this jackknife procedure and provide discussions on how to conduct it properly. Our results show that jackknife is very useful to …

Gene Order Phylogeny And The Evolution Of Methanogens, Haiwei Luo, Zhiyi Sun, William Arndt, Jian Shi, Robert Friedman, Jijun Tang

Faculty Publications

Methanogens are a phylogenetically diverse group belonging to Euryarchaeota. Previously, phylogenetic approaches using large datasets revealed that methanogens can be grouped into two classes, “Class I” and “Class II”. However, some deep relationships were not resolved. For instance, the monophyly of “Class I” methanogens, which consist of Methanopyrales, Methanobacteriales and Methanococcales, is disputable due to weak statistical support. In this study, we use MSOAR to identify common orthologous genes from eight methanogen species and a Thermococcale species (outgroup), and apply GRAPPA and FastME to compute distance-based gene order phylogeny. The gene order phylogeny supports two classes of methanogens, but it …

Gene Order Phylogeny Of The Genus Prochlorococcus, Haiwei Luo, Jian Shi, William Arndt, Jijun Tang, Robert Friedman

Faculty Publications

Background
Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. This character was used to resolve the evolutionary history within the genus Prochlorococcus, a group of marine cyanobacteria.

Methodology/Principal Findings
Orthologous gene sets and their genomic positions were identified from 12 species of Prochlorococcus and 1 outgroup species of Synechococcus. From this data, inversion and breakpoint distance-based phylogenetic trees were computed by GRAPPA and FastME. Statistical support of the resulting topology was obtained by application of a 50% jackknife resampling technique. The result was consistent and congruent with nucleotide sequence-based and gene-content based …

Improving Reversal Median Computation Using Commuting Reversals And Cycle Information, William Arndt, Jijun Tang

Faculty Publications

In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. Methods for reconstructing phylogeny from genome rearrangements include distance-based methods, MCMC methods, and direct optimization methods. The latter, pioneered by Sankoff and extended with the software suites GRAPPA and MGR, is the most accurate approach, but is very limited due to the difficulty of its scoring procedure—it must solve multiple instances of the reversal median problem to compute the score of a given tree. The reversal median problem is known to be NP-hard and all …

Multi-Break Rearrangements And Breakpoint Re-Uses: From Circular To Linear Genomes, Max A. Alekseyev

Faculty Publications

Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions, fissions, and translocations, 3-break rearrangements represent a natural generalization of transpositions. Alekseyev and Pevzner (2007a, 2008a) studied multi-break rearrangements in circular genomes and further applied them to the analysis of chromosomal evolution in mammalian genomes. In this paper, we extend these results to the more difficult case of linear genomes. In particular, we give lower bounds for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion …

Phylogenetic Reconstruction From Transpositions, Feng Yue, Meng Zhang, Jijun Tang

Faculty Publications

Background
Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangement of these entities through computational means. As a result, genome rearrangement data has attracted increasing attentions from both biologists and computer scientists as a new type of data for phylogenetic analysis. The main events of genome rearrangements include inversions, transpositions and transversions. To date, GRAPPA and MGR are the most accurate …

Gene Rearrangement Analysis And Ancestral Order Inference From Chloroplast Genomes With Inverted Repeat, Feng Yue, Liying Cui, Claude W. Depamphilis, Bernard M.E. Moret, Jijun Tang

Faculty Publications

Background
Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction.

Results
We extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR …

Are There Rearrangement Hotspots In The Human Genome?, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

In a landmark paper, Nadeau and Taylor [18] formulated the random breakage model (RBM) of chromosome evolution that postulates that there are no rearrangement hotspots in the human genome. In the next two decades, numerous studies with progressively increasing levels of resolution made RBM the de facto theory of chromosome evolution. Despite the fact that RBM had prophetic prediction power, it was recently refuted by Pevzner and Tesler [4], who introduced the fragile breakage model (FBM), postulating that the human genome is a mosaic of solid regions (with low propensity for rearrangements) and fragile regions (rearrangement hotspots). However, the rebuttal …

Whole Genome Duplications And Contracted Breakpoint Graphs, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

The genome halving problem, motivated by the whole genome duplication events in molecular evolution, was solved by El-Mabrouk and Sankoff in the pioneering paper [SIAM J. Comput., 32 (2003), pp. 754–792]. The El-Mabrouk–Sankoff algorithm is rather complex, inspiring a quest for a simpler solution. An alternative approach to the genome halving problem based on the notion of the contracted breakpoint graph was recently proposed in [M. A. Alekseyev and P. A. Pevzner, IEEE/ACM Trans. Comput. Biol. Bioinformatics, 4 (2007), pp. 98–107]. This new technique reveals that while the El-Mabrouk–Sankoff result is correct in most cases, it does not hold in …

Colored De Bruijn Graphs And The Genome Halving Problem, Max A. Alekseyev, Pavel A. Pevzner

Faculty Publications

Breakpoint graph analysis is a key algorithmic technique in studies of genome rearrangements. However, breakpoint graphs are defined only for genomes without duplicated genes, thus limiting their applications in rearrangement analysis. We discuss a connection between the breakpoint graphs and de Bruijn graphs that leads to a generalization of the notion of breakpoint graph for genomes with duplicated genes. We further use the generalized breakpoint graphs to study the Genome Halving Problem (first introduced and solved by Nadia El-Mabrouk and David Sankoff). The El-Mabrouk-Sankoff algorithm is rather complex, and, in this paper, we present an alternative approach that is based …

Adaptive Evolution Of Chloroplast Genome Structure Inferred Using A Parametric Bootstrap Approach, Liying Cui, Jim Leebens-Mack, Li-San Wang, Jijun Tang, Linda Rymarquis, David B. Stern, Claude W. Depamphilis

Faculty Publications

Background
Genome rearrangements influence gene order and configuration of gene clusters in all genomes. Most land plant chloroplast DNAs (cpDNAs) share a highly conserved gene content and with notable exceptions, a largely co-linear gene order. Conserved gene orders may reflect a slow intrinsic rate of neutral chromosomal rearrangements, or selective constraint. It is unknown to what extent observed changes in gene order are random or adaptive. We investigate the influence of natural selection on gene order in association with increased rate of chromosomal rearrangement. We use a novel parametric bootstrap approach to test if directional selection is responsible for the …

Structure Of Human Thymidylate Synthase Under Low-Salt Conditions, Leslie L. Lovelace, Wladek Minor, Lukasz Lebioda

Faculty Publications

Human thymidylate synthase, a target in cancer chemotherapy, was crystallized from PEG 3350 with 30 mM ammonium sulfate (AS) in the crystallization medium. The crystals are isomorphous with the high-salt crystals (~2.0 M AS) and the structure has been solved and refined (R = 22.6%, Rfree = 24.3%) at 1.8 Å resolution. The high- and low-AS-concentration structures are quite similar, with loop 181-197 is in the inactive conformation. Also, residues 95-106 and 129-135 (eukaryotic inserts region) show high mobility as assessed by poor electron density and high values of crystallographic temperature factors (residues 1-25 and 108-129 are disordered in both …

Growth And Transport Properties Of Complementary Germanium Nanowire Field Effect Transistors, Andrew B. Greytak, Lincoln J. Lauhon, Mark S. Gudiksen, Charles M. Lieber

Faculty Publications

n- and p-type Ge nanowires were synthesized by a multistep process in which axial elongation, via vapor–liquid–solid (VLS) growth, and doping were accomplished in separate chemical vapor deposition steps. Intrinsic, single-crystal, Ge nanowires prepared by Au nanocluster-mediated VLS growth were surface-doped in situ using diborane or phosphine, and then radial growth of an epitaxial Ge shell was used to cap the dopant layer. Field-effect transistors prepared from these Ge nanowires exhibited on currents and transconductances up to 850 µA/µm and 4.9 µA/V, respectively, with device yields of >85%.