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Design Of Analog Cmos Integrated Circuits

The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention. We survey 141 sequenced plant genomes to elucidate consequences of gene and genome duplication, processes central to the evolution of biodiversity. We develop a pipeline named DupGen_finder to identify different modes of gene duplication in plants. Genes derived from whole-genome, tandem, proximal, transposed, or dispersed duplication differ in abundance, selection pressure, expression divergence, and gene conversion rate among genomes. The number of WGD-derived duplicate genes decreases exponentially with increasing age of duplication events—transposed duplication- and dispersed duplication-derived genes declined in parallel. In contrast, the frequency of tandem and proximal duplications showed no significant decrease over time, providing a continuous supply of variants available for adaptation to continuously changing environments. Moreover, tandem and proximal duplicates experienced stronger selective pressure than genes formed by other modes and evolved toward biased functional roles involved in plant self-defense. The rate of gene conversion among WGD-derived gene pairs declined over time, peaking shortly after polyploidization. To provide a platform for accessing duplicated gene pairs in different plants, we constructed the Plant Duplicate Gene Database. We identify a comprehensive landscape of different modes of gene duplication across the plant kingdom by comparing 141 genomes, which provides a solid foundation for further investigation of the dynamic evolution of duplicate genes.

/pdf/gene-duplication-and-evolution-in-recurring-polyploidization-1tk6fsc37e.pdf

Gene duplication and evolution in recurring polyploidization-diploidization cycles in plants.

PLAZA (https://bioinformatics.psb.ugent.be/plaza) is a plant-oriented online resource for comparative, evolutionary and functional genomics. The PLAZA platform consists of multiple independent instances focusing on different plant clades, while also providing access to a consistent set of reference species. Each PLAZA instance contains structural and functional gene annotations, gene family data and phylogenetic trees and detailed gene colinearity information. A user-friendly web interface makes the necessary tools and visualizations accessible, specific for each data type. Here we present PLAZA 4.0, the latest iteration of the PLAZA framework. This version consists of two new instances (Dicots 4.0 and Monocots 4.0) providing a large increase in newly available species, and offers access to updated and newly implemented tools and visualizations, helping users with the ever-increasing demands for complex and in-depth analyzes. The total number of species across both instances nearly doubles from 37 species in PLAZA 3.0 to 71 species in PLAZA 4.0, with a much broader coverage of crop species (e.g. wheat, palm oil) and species of evolutionary interest (e.g. spruce, Marchantia). The new PLAZA instances can also be accessed by a programming interface through a RESTful web service, thus allowing bioinformaticians to optimally leverage the power of the PLAZA platform.

https://biblio.ugent.be/publication/8558157/file/8558161.pdf

PLAZA 4.0 : an integrative resource for functional, evolutionary and comparative plant genomics

We have witnessed an explosion in our understanding of the evolution and structure of plant genomes in recent years. Here, we highlight three important emergent realizations: (1) that the evolutionary history of all plant genomes contains multiple, cyclical episodes of whole-genome doubling that were followed by myriad fractionation processes; (2) that the vast majority of the variation in genome size reflects the dynamics of proliferation and loss of lineage-specific transposable elements; and (3) that various classes of small RNAs help shape genomic architecture and function. We illustrate ways in which understanding these organism-level and molecular genetic processes can be used for crop plant improvement.

/pdf/evolution-of-plant-genome-architecture-arph2a199b.pdf

Evolution of plant genome architecture

We report the first annotated chromosome-level reference genome assembly for pea, Gregor Mendel’s original genetic model. Phylogenetics and paleogenomics show genomic rearrangements across legumes and suggest a major role for repetitive elements in pea genome evolution. Compared to other sequenced Leguminosae genomes, the pea genome shows intense gene dynamics, most likely associated with genome size expansion when the Fabeae diverged from its sister tribes. During Pisum evolution, translocation and transposition differentially occurred across lineages. This reference sequence will accelerate our understanding of the molecular basis of agronomically important traits and support crop improvement.

/pdf/a-reference-genome-for-pea-provides-insight-into-legume-4vzcjuqayo.pdf

A reference genome for pea provides insight into legume genome evolution

Mungbean (Vigna radiata) is a fast-growing, warm-season legume crop that is primarily cultivated in developing countries of Asia. Here we construct a draft genome sequence of mungbean to facilitate genome research into the subgenus Ceratotropis, which includes several important dietary legumes in Asia, and to enable a better understanding of the evolution of leguminous species. Based on the de novo assembly of additional wild mungbean species, the divergence of what was eventually domesticated and the sampled wild mungbean species appears to have predated domestication. Moreover, the de novo assembly of a tetraploid Vigna species (V. reflexo-pilosa var. glabra) provides genomic evidence of a recent allopolyploid event. The species tree is constructed using de novo RNA-seq assemblies of 22 accessions of 18 Vigna species and protein sets of Glycine max. The present assembly of V. radiata var. radiata will facilitate genome research and accelerate molecular breeding of the subgenus Ceratotropis.

/pdf/genome-sequence-of-mungbean-and-insights-into-evolution-6lvhesfomn.pdf

Genome sequence of mungbean and insights into evolution within Vigna species

A cylindrical tightly coupled dipole array antenna (C-TCDA) based on Munk’s planar TCDA theory, the elements of which are placed on the surface of a cylinder, is introduced and analyzed in this study. The explicit field components of the transverse electromagnetic (TEM) waves existing in the C-TCDA for both polarizations are given. Moreover, the embedding impedance characteristics of the CTCDA are presented and compared with those of planar TCDA. Analysis results show that the C-TCDA has similar impedance characteristics to the planar TCDA and thus can be implemented in a similar manner. The design of a dual-polarized omnidirectional octagonal TCDA, which has a 3.08:1 bandwidth (from 0.73 GHz to 2.25 GHz) with a voltage standing wave radiation (VSWR) of less than 2 and a low gain variation of less than 1.8 dB at broadside for both polarizations, is also proposed. When scanning up to ±30° in the θdirection, the array operates in the same frequency band with a VSWR of less than 2.05 and a low gain variation of less than 2 dB for

/pdf/cylindrical-tightly-coupled-dipole-array-antenna-32qbhohu9w.pdf

Cylindrical Tightly Coupled Dipole Array Antenna

In this paper, a modified subspace projection method for non-parallel measurement through-the-wall radar imaging is proposed. The proposed modified subspace projection method includes equivalent time delay and normalization to remove wall clutter. Synthetic data are obtained using a finite-difference time-domain forward solver to verify the validity of the proposed method. The target-to-clutter ratio of the delayed-sum migration image after the proposed method was improved 21.6 dB compared to the conventional subspace projection method.

http://ael.snu.ac.kr/paper_file/Eucap임영준%20논문.pdf

Wall clutter mitigation using a modified subspace projection method for non-parallel measurement through-the-wall radar imaging

In this paper, we propose the design of switched line True time delay (TTD) using cascaded switches, which removes off-switch resonance. Conventional switched lines with two different delay-time difference, 15ps and 270p, are presented to indicate that off-switch resonances can be observed in switched lines using switches with a fair isolation of 15dB. Switched line with cascaded switches is designed and fabricated to show the resonance can be eliminated. All designs are conducted in consideration of matching. The measured results are in agreement with the simulation results in CST Design Studio.

Minyoung Yoon

Papers

Genome sequence of mungbean and insights into evolution within Vigna species

Cylindrical Tightly Coupled Dipole Array Antenna

Wall clutter mitigation using a modified subspace projection method for non-parallel measurement through-the-wall radar imaging

Avoidance of off-switch resonance in true time delay line using cascaded switches

Design Optimizaion of Gm-C Filters via Geometric Programming