Residue coevolution: modeling and interpretation

Coevolution between amino acid residues and its context-dependence are important for exploring protein structure and function, and critical for understanding protein structural and functional evolution. Coevolution has long been ignored because of its complexity and the lack of computing power. In the research presented here, I developed an efficient coevolution analysis methodology based on likelihood comparisons of statistical models. Likelihood ratios and Bayes factors, calculated using the Markov chain Monte Carlo algorithm, were employed as the statistics. Two types of models, 2-state and 3-state, were developed to allow for the context-dependence of coevolution. Computer programs implementing this methodology were coded in C/C++ and were run on the Beowulf clusters of our laboratory and the super computers of LSU. Using these programs and custom Perl scripts, residue coevolution in cytochrome c oxidase and photolyases/cryptochromes protein superfamily was analyzed. I found that pairwise coevolution between residues is highly dependent on protein tertiary structures and functions. I detected extensive coevolving pairs in all our analyses, and these pairs were primary localized in regions of known structural and/or functional importance. I also found that coevolution is related to evolutionary rate and concentrated in moderately conserved sites. In supporting the importance of functional constraints, I detected a non-negligible coevolutionary signal between complex subunits and stronger coevolution in proteins of functional importance. I also found that the interaction between subunits can serve as a local coevolutionary constraint on one subunit rather than driving coevolution between two subunits. Based on coevolutionary patterns, I suggested that a domain without any previously supposed function actually operates as a folding core in the proteins of photolyase/cryptochrome superfamily. The coevolutionary patterns also provided clues regarding the functional evolution of electron transfer in this superfamily. I also found that coevolving sites with double substitutions along a branch tend to occur only at physically contacting sites, and that salt-bridge stabilization and secondary structure stabilization are important forces of residue coevolution. The methodology and programs developed in this research are powerful tools for coevolutionary analysis, which can provide valuable information for characterization of protein structural/functional domains and exploration of protein structural/functional evolution

DC-Informative Joint Color-Frequency Modulation for Visible Light Communications

In this paper, we consider the problem of constellation design for a visible light communication (VLC) system using red/green/blue light-emitting diodes (RGB LED), and propose a method termed DC-informative joint color-frequency modulation (DCI-JCFM). This method jointly utilizes available diversity resources including different optical wavelengths, multiple baseband subcarriers, and adaptive DC-bias. Constellation is designed in a high dimensional space, where the compact sphere packing advantage over lower dimensional counterparts is utilized. Taking into account multiple practical illumination constraints, a non-convex optimization problem is formulated, seeking the least error rate with a fixed spectral efficiency. The proposed scheme is compared with a decoupled scheme, where constellation is designed separately for each LED. Notable gains for DCI-JCFM are observed through simulations where balanced, unbalanced and very unbalanced color illuminations are considered.Comment: submitted to Journal of Lightwave Technology, Aug. 5th 201

Volume-based non-continuum modeling of bone functional adaptation

BACKGROUND: Bone adapts to mechanical strain by rearranging the trabecular geometry and bone density. The common finite element methods used to simulate this adaptation have inconsistencies regarding material properties at each node and are computationally demanding. Here, a volume-based, non-continuum formulation is proposed as an alternative. Adaptive processes corresponding to various external mechanical loading conditions are simulated for the femur. RESULTS: Bone adaptations were modeled for one-legged stance, abduction and adduction. One-legged stance generally results in higher bone densities than the other two loading cases. The femoral head and neck are the regions where densities change most drastically under different loading conditions while the distal area always contains the lowest densities regardless of the loading conditions. In the proposed formulation, the inconsistency of material densities or strain energy densities, which is a common problem to finite element based approaches, is eliminated. The computational task is alleviated through introduction of the quasi-binary connectivity matrix and linearization operations in the Jacobian matrix and is therefore computationally less demanding. CONCLUSION: The results demonstrated the viability of the proposed formulation to study bone functional adaptation under mechanical loading

Uso de la tecnología de comunicación para el trabajo en casa durante el tiempo fuera del trabajo y el conflicto trabajo-familia: los roles del apoyo familiar y el desapego psicológico

This article studies the influence of communication technology use for work at home during off-job time on work-family conflict based on work-family border theory, and highlights the roles of psychological detachment and family support. Based on 423 samples, we use regression analysis to test hypotheses. The results show that communication technology use for work at home during off-job time is positively related to employee’s work-family conflict, including time-based conflict and strain-based conflict. Besides, family support moderates the impact of communication technology use for work at home on employee’s work-family conflict. Furthermore, psychological detachment mediates the moderating effect of family support on the relationship between communication technology use for work at home and employee’s work-family conflict. Theoretical and practical implications, limitations, and future studies are discussed.Este estudio analiza la influencia del uso de las tecnologías de la comunicación para el trabajo en casa durante el tiempo fuera del trabajo en el conflicto trabajo-familia. Nuestro análisis se basa en la teoría de los límites entre trabajo y familia. Por otra parte, este estudio destaca los roles de desapego psicológico y apoyo familiar. Sobre la base de 423 participantes, utilizamos el análisis de regresión para probar nuestras hipótesis. Los resultados muestran que el uso de la tecnología de comunicación para trabajar en casa durante el tiempo fuera del trabajo se relaciona positivamente con el conflicto entre el trabajo y la familia, incluyendo los conflictos basados en el tiempo y la tensión. El apoyo de la familia modera el efecto del uso de las tecnologías de la comunicación para el trabajo en casa durante el tiempo fuera del trabajo en el conflicto laboral-familiar del empleado. Además, el desapego psicológico media el efecto moderador del apoyo familiar sobre la relación entre el uso de las tecnologías de la comunicación para el trabajo en casa durante el tiempo fuera del trabajo y el conflicto entre el trabajo y la familia

Map-Assisted Power Allocation and Constellation Design for mmWave WDM with OAM in Short-Range LOS Environment

We consider a system that integrates positioning and single-user millimeter wave (mmWave) communication, where the communication part adopts wavelength division multiplexing (WDM) and orbital angular momentum (OAM). This paper addresses the power allocation and high dimensional constellation design in short-range line-of-sight (LOS) environment, with stable communication links. We propose a map-assisted method to reduce transmission delay and online computing overhead. We explore the possibility of using a few patterns in the maps, and investigate its performance loss. For power allocation, we first characterize the performance loss outside the OAM beam regions with only plane waves, and figure out that the loss is always small. However, in OAM beam regions, the performance loss has similar characteristics only at some specific positions. Based on numerical results, we illustrate that a few patterns can be adopted for all receiver locations in the map. We also investigate high dimensional constellation design, and prove that a fixed constellation can be adopted for the positions where the channel matrices are sufficiently close to be proportional. Similarly, we figure out that the constellation design for all receiver locations can be represented by a few constellation sets

Trichinella spiralis: Adaptation and parasitism

Publication of the genome from the clade I organism, Trichinella spiralis, has provided us an avenue to address more holistic problems in parasitology; namely the processes of adaptation and the evolution of parasitism. Parasitism among nematodes has evolved in multiple, independent events. Deciphering processes that drive species diversity and adaptation are keys to understanding parasitism and advancing control strategies. Studies have been put forth on morphological and physiological aspects of parasitism and adaptation in nematodes; however, data is now coming available to investigate adaptation, host switching and parasitism at the genomic level. Herein we compare proteomic data from the clade I parasite, Trichinella spiralis with data from Brugia malayi (clade III), Meloidogyne hapla and Meloidogyne incognita (clade IV), and free-living nematodes belonging to the genera Caenorhabditis and Pristionchus (clade V). We explore changes in protein family birth/death and expansion/reduction over the course of metazoan evolution using Homo sapiens, Drosophila melanogaster and Saccharomyces cerevisiae as out- groups for the phylum Nematoda. We further examine relationships between these changes and the ability and/or result of nematodes adapting to their environments. Data are consistent with gene loss occurring in conjunction with nematode specialization resulting from parasitic worms acclimating to well-defined, environmental niches. We observed evidence for independent, lateral gene transfer events involving conserved genes that may have played a role in the evolution of nematode parasitism. In general, parasitic nematodes gained proteins through duplication and lateral gene transfer, and lost proteins through random mutation and deletions. Data suggest independent acquisition rather than ancestral inheritance among the Nematoda followed by selective gene loss over evolutionary time. Data also show that parasitism and adaptation affected a broad range of proteins, especially those involved in sensory perception, metabolism, and transcription/translation. New protein gains with functions related to regu- lating transcription and translation, and protein family expansions with functions related to morphology and body development have occurred in association with parasitism. Further gains occurred as a result of lateral gene transfer and in particular, with the cyanase protein family In contrast, reductions and/or losses have occurred in protein families with functions related to metabolic process and signal trans- duction. Taking advantage of the independent occurrences of parasitism in nematodes, which enabled us to distinguish changes associated with parasitism from species specific niche adaptation, our study provides valuable insights into nematode parasitism at a proteome level using T. spiralis as a benchmark for early adaptation to or acquisition of parasitism

Intestine of Zebrafish: Regionalization, Characterization and Stem Cells

Ph.DDOCTOR OF PHILOSOPH