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de los Reyes, Benildo G,Mohanty, Bijayalaxmi,Yun, Song Joong,Park, Myoung-Ryoul,Lee, Dong-Yup Springer US 2015 Rice Vol.8 No.-
<P>Dissecting the upstream regulatory architecture of rice genes and their cognate regulator proteins is at the core of network biology and its applications to comparative functional genomics. With the rapidly advancing comparative genomics resources in the genus <I>Oryza</I>, a reference genome annotation that defines the various cis-elements and trans-acting factors that interface each gene locus with various intrinsic and extrinsic signals for growth, development, reproduction and adaptation must be established to facilitate the understanding of phenotypic variation in the context of regulatory networks. Such information is also important to establish the foundation for mining non-coding sequence variation that defines novel alleles and epialleles across the enormous phenotypic diversity represented in rice germplasm. This review presents a synthesis of the state of knowledge and consensus trends regarding the various cis-acting and trans-acting components that define spatio-temporal regulation of rice genes based on representative examples from both foundational studies in other model and non-model plants, and more recent studies in rice. The goal is to summarize the baseline for systematic upstream sequence annotation of the rapidly advancing genome sequence resources in <I>Oryza</I> in preparation for genus-wide functional genomics. Perspectives on the potential applications of such information for gene discovery, network engineering and genomics-enabled rice breeding are also discussed.</P>
Alexander De Los Reyes,Elizabeth Ann Prieto,Karim Omambac,Jeremy Porquez,Lorenzo Lopez Jr.,Karl Cedric Gonzales,John Daniel Vasquez,Mae Agatha Tumanguil,Joselito Muldera,Kohji Yamamoto,Masahiko Tani,A 한국물리학회 2017 Current Applied Physics Vol.17 No.4
We investigate the effects of an externally applied magnetic field on the terahertz (THz) emission of Gallium Manganese Arsenide (GaMnAs) films grown via molecular beam epitaxy (MBE). Results show that low Mn-doping in GaMnAs resulted to increased THz emission as compared with a SI-GaAs substrate. Further increase in Mn-doping content resulted to a comparably less THz emission, which is attributed to reduced crystallinity and higher free-carrier absorption. Under an external magnetic field, the contributions of the Bup and Bdown-related THz emission were observed to be asymmetric: possibly due to intrinsic magnetic properties of GaMnAs.
Mathematical model and intervention strategies for mitigating tuberculosis in the Philippines
Kim, Soyoung,de los Reyes V, Aurelio A.,Jung V, Eunok Elsevier 2018 Journal of theoretical biology Vol.443 No.-
<P><B>Abstract</B></P> <P>Tuberculosis (TB) is the sixth leading cause of morbidity and mortality in the Philippines. Although significant progress has been made in the detection and cure of TB under the Directly Observed Treatment Short Course, battling against the disease is still a burdensome task. It demands a concerted effort for specific and effective interventions. In this work, a mathematical TB model fitted to the Philippine data is developed to understand its transmission dynamics. Different control strategies such as distancing, latent case finding, case holding, active case finding controls, and combinations thereof are investigated within the framework of optimal control theory. This study proposes optimal control strategies for reducing the number of high-risk latent and infectious TB patients with minimum intervention implementation costs. Results suggest that distancing control is the most efficient control strategy when a single intervention is utilized. However, full scale employment of the distancing control measure is a daunting task. This burden can be circumvented by the combination of other control interventions. Our noble finding in this study is that enhancing active case finding control instead of case holding control together with distancing and latent case finding control is shown to have significant potential for curtailing the spread of TB in the Philippines.</P> <P><B>Highlights</B></P> <P> <UL> <LI> A mathematical model for Tuberculosis transmission is developed based on Philippine data. </LI> <LI> Optimal control theory is applied to suggest efficient and cost-effective intervention strategies for mitigating TB spread. </LI> <LI> Active case finding control plays a significant role complementing other control measures. </LI> </UL> </P>
Mohanty, Bijayalaxmi,Takahashi, Hirokazu,de los Reyes, Benildo G.,Wijaya, Edward,Nakazono, Mikio,Lee, Dong-Yup Springer US 2016 Rice Vol.9 No.1
<P><B>Background</B></P><P>Rice is the only crop that germinates and elongates the coleoptile under complete submergence. It has been shown that <I>alcohol dehydrogenase 1 (ADH1)-</I>deficient mutant of rice with <I>reduced alcohol dehydrogenase activity</I> (<I>rad</I>) and reduced ATP level, is viable with much reduced coleoptile elongation under such condition. To understand the altered transcriptional regulatory mechanism of this mutant, we aimed to establish possible relationships between gene expression and <I>cis</I>-regulatory information content.</P><P><B>Findings</B></P><P>We performed promoter analysis of the publicly available differentially expressed genes in <I>ADH1</I> mutant. Our results revealed that a crosstalk between a number of key transcription factors (TFs) and different phytohormones altered transcriptional regulation leading to the survival of the mutant. Amongst the key TFs identified, we suggest potential involvement of MYB, bZIP, ARF and ERF as transcriptional activators and WRKY, ABI4 and MYC as transcriptional repressors of coleoptile elongation to maintain metabolite levels for the cell viability. Out of the repressors, WRKY TF is most likely playing a major role in the alteration of the physiological implications associated with the cell survival.</P><P><B>Conclusions</B></P><P>Overall, our analysis provides a possible transcriptional regulatory mechanism underlying the survival of the <I>rad</I> mutant under complete submergence in an energy crisis condition and develops hypotheses for further experimental validation.</P><P><B>Electronic supplementary material</B></P><P>The online version of this article (doi:10.1186/s12284-016-0124-3) contains supplementary material, which is available to authorized users.</P>
Cafe Arven I.,De Los Reyes Alexander,Lopez Lorenzo,Husay Horace Andrew,Faustino Maria Angela,Mag-usara Valynn Katrine,Tani Masahiko,Salvador Arnel,Somintac Armando,Estacio Elmer 한국물리학회 2023 Current Applied Physics Vol.50 No.-
We demonstrate the use of the terahertz time-domain spectroscopy (THz-TDS) as a complementary tool in detecting the naturally formed oxide (NFO) layer on a copper metal surface. The THz emission from Cu-metal sheets having NFO were compared with Cu-sheets that were rapidly oxidized between temperatures ranges from 100 ◦C to 500 ◦C for 2 h. Raman spectroscopy and scanning electron microscopy were initially utilized as standard techniques for characterizing the oxide layer. However, the two performed standard techniques could not provide distinguishable results between the NFO and the thin oxide layer grown at temperatures below 200 ◦C. The THz-TDS provides clear results for non-destructive detection of the NFO on the Cu-surface. Excitation-power dependence and magnetic field dependence measurements revealed that the dominant THz emission mechanism is diffusion for CuxO formed below 300 ◦C and drift for thicker oxides grown at temperatures greater than 400 ◦C. The carrier diffusion and carrier drift mechanism are also dependent on the absorption efficiency and structural properties of the oxide layer that was formed. No THz radiation mechanism originating form nonlinear optical process was observed.
Hannah Bardolaza,Jessica Afalla,Alexander De Los Reyes,Deborah Anne Lumantas,John Daniel Vasquez,Joselito Muldera,Valynn Katrine Mag-usara,Armando Somintac,Arnel Salvador,Masahiko Tani,Elmer Estacio 한국물리학회 2019 Current Applied Physics Vol.19 No.6
An externally applied magnetic field was used to induce increased photocarrier transport along the high mobility channel in GaAs/AlGaAs modulation-doped heterostructures (MDH). The terahertz (THz) emission from GaAs/ AlGaAs MDH increases with increasing magnetic field, applied parallel to the heterojunction. The THz emission enhancement factors due to the magnetic field in MDH are higher than in undoped GaAs/AlGaAs heterojunction and in bulk SI-GaAs. This demonstrates that properly utilizing the high-mobility channel for carrier transport promises to be a viable design consideration for efficient THz photoconductive antenna (PCA) devices. Moreover, it was observed that for MDH, as well as for an undoped GaAs/AlGaAs heterojunction, the enhancement for one magnetic field direction is greater than the enhancement for the opposite direction. This is in contrast to the symmetric enhancement with magnetic field direction observed in a bulk SI-GaAs. An analysis of photocarrier trajectories under an external magnetic field supports the explanation that the enhancement asymmetry with magnetic field direction in MDH is due to the cycloid motion of electrons as affected by the GaAs/AlGaAs interface.
Park, Myoung Ryoul,Baek, So-Hyeon,de los Reyes, Benildo G.,Yun, Song Joong,Hasenstein, Karl H. Elsevier 2012 Journal of plant physiology Vol.169 No.2
<P><B>Abstract</B></P><P>Phosphorus (P) is a structural component of nucleic acids and phospholipids and plays important roles in plant growth and development. P accumulation was significantly reduced (about 35%) in rice leaves from plants grown under low (32μM) P compared to 320μMP grown plants. Genome response to low P was examined using the rice 60K oligonucleotide DNA microarrays. At the threshold significance of |log<SUB>2</SUB>| fold>2.0, 21,033 genes (about 33.7% of all genes on the microarray) were affected by P deficiency. Among all genes on the microarray, 4271 genes were sorted into 51 metabolic pathways. Low P affected 1494 (35.0%) genes and the largest category of genes was related to sucrose degradation to ethanol and lactate pathway. To survey the role of P in rice, 25 pathways were selected based on number of affected genes. Among these pathways, cytosolic glycolysis contained the least number of upregulated but most down-regulated genes. Low P decreased glucose, pyruvate and chlorophyll, and genes related to carbon metabolism and chlorophyllide <I>a</I> biosynthesis. However, sucrose and starch levels increased. These results indicate that P nutrition affects diverse metabolic pathways mostly related to glucose, pyruvate, sucrose, starch, and chlorophyll <I>a</I>.</P>
Choi, Dong-Geun,Yoo, Nam-Hee,Yu, Chang-Yeon,De Los Reyes, Benildo,Yun, Song-Joong Korean Society for Biochemistry and Molecular Biol 2004 Journal of biochemistry and molecular biology Vol.37 No.5
All members of R. glutinosa show the unique characteristic of intrinsic tolerance to paraquat (PQ). Antioxidant enzymes have been proposed to be the primary mechanism of PQ resistance in several plant species. Therefore, the antioxidant enzyme systems of R. glutinosa were evaluated by comparatively analyzing cellular antioxidant enzyme levels, and their responses of oxidative stresses and hormones. The levels of ascorbate peroxidase (APX), glutathione reductase (GR), non-specific peroxidase (POX), and superoxide dismutase (SOD) were 7.3-, 4.9-, 2.7- and 1.6-fold higher in PQ-tolerant R. glutinosa than in PQ-susceptible soybeans. However, the activity of catalase (CAT) was about 12-fold higher in the soybeans. The activities of antioxidant enzymes reduced after PQ treatment in the two species, with the exception of POX and SOD in R. glutinosa, which increased by about 40%. Interestingly, the activities of APX, SOD and POX in R. glutinosa, relative to those in soybeans, were further increased by 49, 67 and 93% after PQ treatment. The considerably higher intrinsic levels, and increases in the relative activities of antioxidant enzymes in R. glutinosa under oxidative stress support the possible role of these enzymes in the PQ tolerance of R. glutinosa. However, the relatively lower levels of SOD versus PQ tolerance, and the mixed responses of antioxidant enzymes to stresses and hormones, suggest a possible alternative mechanism(s) for PQ tolerance in R. glutinosa.