The Experts below are selected from a list of 2220 Experts worldwide ranked by ideXlab platform
Uzzal Mohammad - One of the best experts on this subject based on the ideXlab platform.
-
Avalanche ISFET Sensing Chip for DNA Sequencing
UNM Digital Repository, 2016Co-Authors: Uzzal MohammadAbstract:DNA sequencing is a fundamental tool for biological science, aimed primarily at uncovering the genetic contributions to diseases. The first Human DNA sequence, which employed conventional fluorescent-based Sanger Sequencing method, took many years to complete at a cost of over three billion dollars. In one survey, it shows that Human Genome Project (HGP) had generated more than $67 billion in U.S. economic output, $20 billion in personal income for Americans and 310 thousand jobs in USA, only during year 2010. The HGP has increased the need for high-throughput, low cost, fast, accurate and inexpensive DNA sequence technique. This demand has forced a fundamental shift away from the conventional Sanger sequencing technique to Next Generation Sequencing (NGS) technique for genome analysis. NGS techniques provide high-throughput; low cost, user-friendly DNA sequencing and they are opening fascinating new opportunities in biomedicine. In near future, as the price of complete DNA sequencing goes further down to a few hundred dollars, we will then have DNA sequence data of millions of people. The enormous DNA sequencing data and corresponding correlation will allow us to figure out which sequences are responsible for which traits. As we relate the sequences of all of these people to their traits, we will be able to connect the dots and learn the genetic equations that define health, disease, longevity, intelligence, and other personality traits. In this dissertation, we propose a new avalanche ion-sensitive field effect transistor (A-ISFET) capable of sensing very weak pH changes during DNA synthesis. This is the first attempt to operate ISFET in avalanche mode. A-ISFET is the core of our proposed highly dense, low-cost and high-throughput DNA sequencing technique. To validate our proposed concept, we have designed, laid-out, fabricated, and successfully tested a test chip with arrays of A-ISFET using TSMC 0.25um CMOS process. Our research also includes the development of data processing circuits and system architectures for fast and efficient data processing. The test chip is used as the verification of this new DNA sequencing concept and the validation of the interfacial circuitry for the synchronization of sensing system. Each of the unit cells in the test chip is accessed through column-select and row-select Signals during readout process. We design a test environment and test setup for correct readout of the sensing data from the chip through proper Synchronizing Signal. A specially milled and shaped structure is used to inlet and outlet the bio-chemical on the gate surface of the A-ISFET arrays. The inlet and outlet is attached to a time-controlled valve to control the flow of liquids on the surface of A-ISFET chip for test and verification of this novel DNA sensing concept. The test chip has been tested both at normal mode and at avalanche mode. Test results show that the sensitivity at avalanche mode is 6 times more than the normal mode of operation. We have developed a model to determine the Signal-to-noise ratio (SNR) of A-ISFET. The model identifies that there is an optimum bias point of A-ISFET to have maximum SNR sensitivity from the sensor. Every electronic device generates its own intrinsic noise, in addition to other induced noise from associated nearby components. We have identified different noise components of A-ISFET and have modeled their respective characteristics with bias change. Different noise components that we find in A-ISFET are thermal noise, flicker noise, shot noise, and dark current noise. This noise modeling of A-ISFET sensor will help us to understand noise sources better and to predict the sensor behavior with change of bias. Using the noise model, we can select a bias point to minimize the noise impact of A-ISFET sensor and maximize its SNR. We also have developed a physical operation-based drain current model for A-ISFET during avalanche operation. Since A-ISFET operates in avalanche region, an accurate model for the breakdown behavior is therefore very important from both circuit design and circuit reliability point of view. The avalanche breakdown can result from impact ionization, a parasitic bipolar transistor, or the punch-through effect. Our developed model of A-ISFET drain current at avalanche region is due to impact ionization. We have validated the drain current model at avalanche through a correlation study among analytical model results, SPICE simulation results, and experimental measured results
-
Avalanche ISFET Sensing Chip for DNA Sequencing
2016Co-Authors: Uzzal MohammadAbstract:DNA sequencing is a fundamental tool for biological science, aimed primarily at uncovering the genetic contributions to diseases. The first Human DNA sequence, which employed conventional fluorescent-based Sanger Sequencing method, took many years to complete at a cost of over three billion dollars. In one survey, it shows that Human Genome Project (HGP) had generated more than $67 billion in U.S. economic output, $20 billion in personal income for Americans and 310 thousand jobs in USA, only during year 2010. The HGP has increased the need for high-throughput, low cost, fast, accurate and inexpensive DNA sequence technique. This demand has forced a fundamental shift away from the conventional Sanger sequencing technique to Next Generation Sequencing (NGS) technique for genome analysis. NGS techniques provide high-throughput; low cost, user-friendly DNA sequencing and they are opening fascinating new opportunities in biomedicine. In near future, as the price of complete DNA sequencing goes further down to a few hundred dollars, we will then have DNA sequence data of millions of people. The enormous DNA sequencing data and corresponding correlation will allow us to figure out which sequences are responsible for which traits. As we relate the sequences of all of these people to their traits, we will be able to connect the dots and learn the genetic equations that define health, disease, longevity, intelligence, and other personality traits. In this dissertation, we propose a new avalanche ion-sensitive field effect transistor (A-ISFET) capable of sensing very weak pH changes during DNA synthesis. This is the first attempt to operate ISFET in avalanche mode. A-ISFET is the core of our proposed highly dense, low-cost and high-throughput DNA sequencing technique. To validate our proposed concept, we have designed, laid-out, fabricated, and successfully tested a test chip with arrays of A-ISFET using TSMC 0.25um CMOS process. Our research also includes the development of data processing circuits and system architectures for fast and efficient data processing. The test chip is used as the verification of this new DNA sequencing concept and the validation of the interfacial circuitry for the synchronization of sensing system. Each of the unit cells in the test chip is accessed through column-select and row-select Signals during readout process. We design a test environment and test setup for correct readout of the sensing data from the chip through proper Synchronizing Signal. A specially milled and shaped structure is used to inlet and outlet the bio-chemical on the gate surface of the A-ISFET arrays. The inlet and outlet is attached to a time-controlled valve to control the flow of liquids on the surface of A-ISFET chip for test and verification of this novel DNA sensing concept. The test chip has been tested both at normal mode and at avalanche mode. Test results show that the sensitivity at avalanche mode is 6 times more than the normal mode of operation. We have developed a model to determine the Signal-to-noise ratio (SNR) of A-ISFET. The model identifies that there is an optimum bias point of A-ISFET to have maximum SNR sensitivity from the sensor. Every electronic device generates its own intrinsic noise, in addition to other induced noise from associated nearby components. We have identified different noise components of A-ISFET and have modeled their respective characteristics with bias change. Different noise components that we find in A-ISFET are thermal noise, flicker noise, shot noise, and dark current noise. This noise modeling of A-ISFET sensor will help us to understand noise sources better and to predict the sensor behavior with change of bias. Using the noise model, we can select a bias point to minimize the noise impact of A-ISFET sensor and maximize its SNR. We also have developed a physical operation-based drain current model for A-ISFET during avalanche operation. Since A-ISFET operates in avalanche region, an accurate model for the breakdown behavior is therefore very important from both circuit design and circuit reliability point of view. The avalanche breakdown can result from impact ionization, a parasitic bipolar transistor, or the punch-through effect. Our developed model of A-ISFET drain current at avalanche region is due to impact ionization. We have validated the drain current model at avalanche through a correlation study among analytical model results, SPICE simulation results, and experimental measured results.Doctor of Philosophy : EngineeringDoctoralUniversity of New Mexico. Dept. of Electrical and Computer EngineeringZarkesh-Ha, PaymanCalhoun, VinceEdwards, JeremySharma, AshwaniSzauter, Pau
Nano Rita - One of the best experts on this subject based on the ideXlab platform.
-
Mechanism and effects of pulsatile GABA secretion from cytosolic pools in the human beta cell.
eScholarship University of California, 2019Co-Authors: Menegaz Danusa, Hagan D Walker, Almaça Joana, Cianciaruso Chiara, Rodriguez-diaz Rayner, Molina Judith, Dolan, Robert M, Becker, Matthew W, Schwalie, Petra C, Nano RitaAbstract:Pancreatic beta cells synthesize and secrete the neurotransmitter γ-aminobutyric acid (GABA) as a paracrine and autocrine Signal to help regulate hormone secretion and islet homeostasis. Islet GABA release has classically been described as a secretory vesicle-mediated event. Yet, a limitation of the hypothesized vesicular GABA release from islets is the lack of expression of a vesicular GABA transporter in beta cells. Consequentially, GABA accumulates in the cytosol. Here we provide evidence that the human beta cell effluxes GABA from a cytosolic pool in a pulsatile manner, imposing a Synchronizing rhythm on pulsatile insulin secretion. The volume regulatory anion channel (VRAC), functionally encoded by LRRC8A or Swell1, is critical for pulsatile GABA secretion. GABA content in beta cells is depleted and secretion is disrupted in islets from type 1 and type 2 diabetic patients, suggesting that loss of GABA as a Synchronizing Signal for hormone output may correlate with diabetes pathogenesis
-
Mechanism and effects of pulsatile GABA secretion from cytosolic pools in the human beta cell
'Springer Science and Business Media LLC', 2019Co-Authors: Menegaz Danusa, Hagan D Walker, Almaça Joana, Cianciaruso Chiara, Rodriguez-diaz Rayner, Molina Judith, Dolan, Robert M, Becker, Matthew W, Schwalie, Petra C, Nano RitaAbstract:Pancreatic beta cells synthesize and secrete the neurotransmitter GABA (gamma-aminobutyric acid) as a paracrine and autocrine Signal to help regulate hormone secretion and islet homeostasis. Islet GABA release has classically been described as a secretory-vesicle-mediated event. Yet, a limitation of the hypothesized vesicular GABA release from islets is the lack of expression of a vesicular GABA transporter in beta cells. Consequentially, GABA accumulates in the cytosol. Here, we provide evidence that the human beta cell effluxes GABA from a cytosolic pool in a pulsatile manner, imposing a Synchronizing rhythm on pulsatile insulin secretion. The volume regulatory anion channel, functionally encoded by LRRC8A or Swell1, is critical for pulsatile GABA secretion. GABA content in beta cells is depleted and secretion is disrupted in islets from patients with type 1 and type 2 diabetes, suggesting that loss of GABA as a Synchronizing Signal for hormone output may correlate with diabetes pathogenesis
Castrucci, Ana Maria De Lauro - One of the best experts on this subject based on the ideXlab platform.
-
Regulation of Melanopsins and Per1 by α-MSH and Melatonin in Photosensitive Xenopus laevis Melanophores
Hindawi Publishing Corporation, 2014Co-Authors: Moraes, Maria Nathália De Carvalho Magalhães, Santos, Luciane Rogéria Dos, Mezzalira, Nathana Fernandes, Poletini, Maristela Oliveira, Castrucci, Ana Maria De LauroAbstract:α-MSH and light exert a dispersing effect on pigment granules of Xenopus laevis melanophores; however, the intracellular Signaling pathways are different. Melatonin, a hormone that functions as an internal Signal of darkness for the organism, has opposite effects, aggregating the melanin granules. Because light functions as an important Synchronizing Signal for circadian rhythms, we further investigated the effects of both hormones on genes related to the circadian system, namely, Per1 (one of the clock genes) and the melanopsins, Opn4x and Opn4m (photopigments). Per1 showed temporal oscillations, regardless of the presence of melatonin or α-MSH, which slightly inhibited its expression. Melatonin effects on melanopsins depend on the time of application: if applied in the photophase it dramatically decreased Opn4x and Opn4m expressions, and abolished their temporal oscillations, opposite to α-MSH, which increased the melanopsins’ expressions. Our results demonstrate that unlike what has been reported for other peripheral clocks and cultured cells, medium changes or hormones do not play a major role in Synchronizing the Xenopus melanophore population. This difference is probably due to the fact that X. laevis melanophores possess functional photopigments (melanopsins) that enable these cells to primarily respond to light, which triggers melanin dispersion and modulates gene expression
-
Regulation of Melanopsins and Per1 by α-MSH and Melatonin in Photosensitive Xenopus laevis Melanophores
New York, 2014Co-Authors: Moraes, Maria Nathália De Carvalho Magalhães, Santos, Luciane Rogéria Dos, Mezzalira, Nathana Fernandes, Poletini, Maristela Oliveira, Castrucci, Ana Maria De LauroAbstract:α-MSH and light exert a dispersing effect on pigment granules of Xenopus laevis melanophores; however, the intracellular Signaling pathways are different. Melatonin, a hormone that functions as an internal Signal of darkness for the organism, has opposite effects, aggregating the melanin granules. Because light functions as an important Synchronizing Signal for circadian rhythms, we further investigated the effects of both hormones on genes related to the circadian system, namely, Per1 (one of the clock genes) and the melanopsins, Opn4x and Opn4m (photopigments). Per1 showed temporal oscillations, regardless of the presence of melatonin or α-MSH, which slightly inhibited its expression. Melatonin effects on melanopsins depend on the time of application: if applied in the photophase it dramatically decreased Opn4x and Opn4m expressions, and abolished their temporal oscillations, opposite to α-MSH, which increased the melanopsins’ expressions. Our results demonstrate that unlike what has been reported for other peripheral clocks and cultured cells, medium changes or hormones do not play a major role in Synchronizing the Xenopus melanophore population. This difference is probably due to the fact that X. laevis melanophores possess functional photopigments (melanopsins) that enable these cells to primarily respond to light, which triggers melanin dispersion and modulates gene expression.The authors acknowledge Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) and Conselho Nacional de Desenvolvimento Tecnológico e Científico (CNPq) Grants. Maria Nathália de Carvalho Magalhães Moraes is a fellow of FAPESP, Nathana Mezzalira is a fellow of CAPES, and Luciane Rogéria dos Santos was a fellow of FAPESP
Jana Kopřivova - One of the best experts on this subject based on the ideXlab platform.
-
the effect of a common daily schedule on human circadian rhythms during the polar day in svalbard a field study
Journal of Circadian Rhythms, 2019Co-Authors: Kamila Weissova, Jitka Skrabalova, Kateřina Skalova, Zdeňka Bendova, Jana KopřivovaAbstract:All Arctic visitors have to deal with extreme conditions, including a constant high light intensity during the summer season or constant darkness during winter. The light/dark cycle serves as the most potent Synchronizing Signal for the biological clock, and any Arctic visitor attending those regions during winter or summer would struggle with the absence of those entraining Signals. However, the inner clock can be synchronized by other zeitgebers such as physical activity, food intake, or social interactions. Here, we investigated the effect of the polar day on the circadian clock of 10 researchers attending the polar base station in the Svalbard region during the summer season. The data collected in Svalbard was compared with data obtained just before leaving for the expedition (in the Czech Republic 49.8175°N, 15.4730°E). To determine the circadian functions, we monitored activity/rest rhythm with wrist actigraphy followed by sleep diaries, melatonin rhythm in saliva, and clock gene expression (Per1, Bmal1, and Nr1D1) in buccal mucosa samples. Our data shows that the two-week stay in Svalbard delayed melatonin onset but did not affect its rhythmic secretion, and delayed the activity/rest rhythm. Furthermore, the clock gene expression displayed a higher amplitude in Svalbard compared to the amplitude detected in the Czech Republic. We hypothesize that the common daily schedule at the Svalbard expedition strengthens circadian rhythmicity even in conditions of compromised light/dark cycles. To our knowledge, this is the first study to demonstrate peripheral clock gene expression during a polar expedition.
Menegaz Danusa - One of the best experts on this subject based on the ideXlab platform.
-
Mechanism and effects of pulsatile GABA secretion from cytosolic pools in the human beta cell.
eScholarship University of California, 2019Co-Authors: Menegaz Danusa, Hagan D Walker, Almaça Joana, Cianciaruso Chiara, Rodriguez-diaz Rayner, Molina Judith, Dolan, Robert M, Becker, Matthew W, Schwalie, Petra C, Nano RitaAbstract:Pancreatic beta cells synthesize and secrete the neurotransmitter γ-aminobutyric acid (GABA) as a paracrine and autocrine Signal to help regulate hormone secretion and islet homeostasis. Islet GABA release has classically been described as a secretory vesicle-mediated event. Yet, a limitation of the hypothesized vesicular GABA release from islets is the lack of expression of a vesicular GABA transporter in beta cells. Consequentially, GABA accumulates in the cytosol. Here we provide evidence that the human beta cell effluxes GABA from a cytosolic pool in a pulsatile manner, imposing a Synchronizing rhythm on pulsatile insulin secretion. The volume regulatory anion channel (VRAC), functionally encoded by LRRC8A or Swell1, is critical for pulsatile GABA secretion. GABA content in beta cells is depleted and secretion is disrupted in islets from type 1 and type 2 diabetic patients, suggesting that loss of GABA as a Synchronizing Signal for hormone output may correlate with diabetes pathogenesis
-
Mechanism and effects of pulsatile GABA secretion from cytosolic pools in the human beta cell
'Springer Science and Business Media LLC', 2019Co-Authors: Menegaz Danusa, Hagan D Walker, Almaça Joana, Cianciaruso Chiara, Rodriguez-diaz Rayner, Molina Judith, Dolan, Robert M, Becker, Matthew W, Schwalie, Petra C, Nano RitaAbstract:Pancreatic beta cells synthesize and secrete the neurotransmitter GABA (gamma-aminobutyric acid) as a paracrine and autocrine Signal to help regulate hormone secretion and islet homeostasis. Islet GABA release has classically been described as a secretory-vesicle-mediated event. Yet, a limitation of the hypothesized vesicular GABA release from islets is the lack of expression of a vesicular GABA transporter in beta cells. Consequentially, GABA accumulates in the cytosol. Here, we provide evidence that the human beta cell effluxes GABA from a cytosolic pool in a pulsatile manner, imposing a Synchronizing rhythm on pulsatile insulin secretion. The volume regulatory anion channel, functionally encoded by LRRC8A or Swell1, is critical for pulsatile GABA secretion. GABA content in beta cells is depleted and secretion is disrupted in islets from patients with type 1 and type 2 diabetes, suggesting that loss of GABA as a Synchronizing Signal for hormone output may correlate with diabetes pathogenesis
