scholarly journals ULI-NChIP assay protocol

2021 ◽  
Author(s):  
Tie-Gang Meng ◽  
Qian Zhou ◽  
Xue-Shan Ma ◽  
Xiao-Yu Liu ◽  
Qing-Ren Meng ◽  
...  
Keyword(s):  
Sample Preparation ◽  
Nuclear Membrane ◽  
Dna Isolation ◽  
Polar Body ◽  
Histone Mark ◽  
Micrococcal Nuclease ◽  
High Quality ◽  
Polar Bodies ◽  
Genome Wide ◽  
Assay Protocol

Abstract This protocol presents ULI-NChIP-seq (ultra-low-input micrococcal nuclease-based native ChIP-seq) assay to generate high quality and complexity genome-wide histone mark profiles from rare oocytes andembryos populations. The procedure of ULI-NChIP-seq assay typically consists of five parts including Binding antibodies to magnatic beads, Chromatin shearing and nuclear membrane solubilization, Magnetic immunoprecipitation, Washes and DNA isolation. Sample preparation involves to remove the zona Pellucida of oocyte and polar body to avoid the genomic contamination of polar bodies.

Quantitative defect studies in semiconductor TEM samples prepared by low angle ion milling

1995 ◽  
Vol 53 ◽  
pp. 512-513
Author(s):  
L. Mulestagno ◽  
J.C. Holzer ◽  
P. Fraundorf
Keyword(s):  
Sample Preparation ◽  
Milling Time ◽  
High Density ◽  
Low Density ◽  
Ion Milling ◽  
High Quality ◽  
Variable Angle ◽  
Major Disadvantage ◽  
Induced Defects

Due to the wealth of information, both analytical and structural that can be obtained from it TEM always has been a favorite tool for the analysis of process-induced defects in semiconductor wafers. The only major disadvantage has always been, that the volume under study in the TEM is relatively small, making it difficult to locate low density defects, and sample preparation is a somewhat lengthy procedure. This problem has been somewhat alleviated by the availability of efficient low angle milling.Using a PIPS® variable angle ion -mill, manufactured by Gatan, we have been consistently obtaining planar specimens with a high quality thin area in excess of 5 × 104 μm2 in about half an hour (milling time), which has made it possible to locate defects at lower densities, or, for defects of relatively high density, obtain information which is statistically more significant (table 1).

scholarly journals High-Quality Genome Resource of the Pathogen of Diaporthe (Phomopsis) phragmitis Causing Kiwifruit Soft Rot

2020 ◽  
Author(s):  
Pu Liu ◽  
Wang Xiaojie ◽  
Dong Hongjie ◽  
Jianbin Lan ◽  
Kuan Liang ◽  
...  
Keyword(s):  
Plant Pathogens ◽  
Management Strategies ◽  
Soft Rot ◽  
Fruit Rot ◽  
Economic Plant ◽  
High Quality ◽  
Total Size ◽  
Genome Wide ◽  
Solid Foundation ◽  
High Quality Genome

Diaporthe spp. are critical plant pathogens that cause wood cankers, wilt, dieback, and fruit rot in a wide variety of economic plant hosts and are regarded as one of the most acute threats faced by kiwifruit industry worldwide. Diaporthe phragmitis strain NJD1 is a highly pathogenic isolate of soft rot of kiwifruit. Here, we present a high-quality genome-wide sequence of D. phragmitis NJD1 that was assembled into 28 contigs containing a total size of 58.33 Mb and N50 length of 3.55 Mb. These results lay a solid foundation for understanding host–pathogen interaction and improving disease management strategies.

scholarly journals Genome‐Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High‐Quality Rice

2018 ◽  
Vol 11 (3) ◽  
pp. 170076 ◽  
Author(s):  
Gastón Quero ◽  
Lucía Gutiérrez ◽  
Eliana Monteverde ◽  
Pedro Blanco ◽  
Fernando Pérez de Vida ◽  
...  
Keyword(s):  
Association Study ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
High Quality ◽  
Breeding Populations ◽  
Genome Wide ◽  
Genomic Regions

scholarly journals An alternative method for Staphylococcus aureus DNA isolation

2008 ◽  
Vol 60 (2) ◽  
pp. 299-306 ◽  
Author(s):  
L. Chapaval ◽  
D.H. Moon ◽  
J.E. Gomes ◽  
F.R. Duarte ◽  
S.M. Tsai
Keyword(s):  
Staphylococcus Aureus ◽  
Genomic Dna ◽  
Dna Isolation ◽  
Environmental Isolates ◽  
Reaction Volume ◽  
High Quality ◽  
Rapid Procedure ◽  
Final Reaction ◽  
Staphylococcal Enterotoxins ◽  
Final Reaction Volume

This study describes a rapid procedure for the isolation of genomic DNA from Staphylococcus aureus that yielded a good amount of high quality DNA for the amplification of staphylococcal enterotoxins genes (A, B, C, D, and E) and the TSST-1 gene as well as enzymatic restriction (HaeIII) from environmental isolates. With this method, it was possible to detect these genes in a sample containing as little as 10(5) cells with positive PCR reactions obtained from approximately 10pg of DNA in a final reaction volume of 25µl.

scholarly journals High similarity among ChEC-seq datasets

2021 ◽  
Author(s):  
Chitvan Mittal ◽  
Matthew J. Rossi ◽  
B. Franklin Pugh
Keyword(s):  
Rna Polymerase Ii ◽  
Transcriptional Regulators ◽  
Micrococcal Nuclease ◽  
High Similarity ◽  
Dna Interactions ◽  
Promoter Regions ◽  
Genome Wide ◽  
A Genome ◽  
Protein Dna Interactions ◽  
Negative Controls

AbstractChEC-seq is a method used to identify protein-DNA interactions across a genome. It involves fusing micrococcal nuclease (MNase) to a protein of interest. In principle, specific genome-wide interactions of the fusion protein with chromatin result in local DNA cleavages that can be mapped by DNA sequencing. ChEC-seq has been used to draw conclusions about broad gene-specificities of certain protein-DNA interactions. In particular, the transcriptional regulators SAGA, TFIID, and Mediator are reported to generally occupy the promoter/UAS of genes transcribed by RNA polymerase II in yeast. Here we compare published yeast ChEC-seq data performed with a variety of protein fusions across essentially all genes, and find high similarities with negative controls. We conclude that ChEC-seq patterning for SAGA, TFIID, and Mediator differ little from background at most promoter regions, and thus cannot be used to draw conclusions about broad gene specificity of these factors.

scholarly journals Genome assembly of the JD17 soybean provides a new reference genome for Comparative genomics

2021 ◽  
Author(s):  
Xinxin Yi ◽  
Jing Liu ◽  
Shengcai Chen ◽  
Hao Wu ◽  
Min Liu ◽  
...  
Keyword(s):  
Nitrogen Fixation ◽  
Genome Assembly ◽  
Reference Genome ◽  
De Novo ◽  
Genomic Analysis ◽  
Comparative Genomic ◽  
High Quality ◽  
Genome Wide ◽  
A Genome ◽  
Cultivated Soybean

Cultivated soybean (Glycine max) is an important source for protein and oil. Many elite cultivars with different traits have been developed for different conditions. Each soybean strain has its own genetic diversity, and the availability of more high-quality soybean genomes can enhance comparative genomic analysis for identifying genetic underpinnings for its unique traits. In this study, we constructed a high-quality de novo assembly of an elite soybean cultivar Jidou 17 (JD17) with chromsome contiguity and high accuracy. We annotated 52,840 gene models and reconstructed 74,054 high-quality full-length transcripts. We performed a genome-wide comparative analysis based on the reference genome of JD17 with three published soybeans (WM82, ZH13 and W05) , which identified five large inversions and two large translocations specific to JD17, 20,984 - 46,912 PAVs spanning 13.1 - 46.9 Mb in size, and 5 - 53 large PAV clusters larger than 500kb. 1,695,741 - 3,664,629 SNPs and 446,689 - 800,489 Indels were identified and annotated between JD17 and them. Symbiotic nitrogen fixation (SNF) genes were identified and the effects from these variants were further evaluated. It was found that the coding sequences of 9 nitrogen fixation-related genes were greatly affected. The high-quality genome assembly of JD17 can serve as a valuable reference for soybean functional genomics research.

scholarly journals Oocyte Positional Recognition for Automatic Manipulation in ICSI

Micromachines ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 429 ◽  
Author(s):  
Mozafar Saadat ◽  
Amir Hajiyavand ◽  
Ajai-pal Singh Bedi
Keyword(s):  
Body Position ◽  
Polar Body ◽  
Recognition System ◽  
Size Measurement ◽  
Transform Method ◽  
Position Detection ◽  
Polar Bodies ◽  
Fitting Method ◽  
Injection Mechanism ◽  
Intracellular Structure

Polar body position detection is a necessary process in the automation of micromanipulation systems specifically used in intracytoplasmic sperm injection (ICSI) applications. The polar body is an intracellular structure, which accommodates the chromosomes, and the injection must not only avoid this structure but be at the furthest point away from it. This paper aims to develop a vision recognition system for the recognition of the oocyte and its polar body in order to be used to inform the automated injection mechanism to avoid the polar body. The novelty of the paper is its capability to determine the position and orientation of the oocyte and its polar body. The gradient-weighted Hough transform method was employed for the detection of the location of the oocyte and its polar body. Moreover, a new elliptical fitting method was employed for size measurement of the polar bodies and oocytes for the allowance of morphological variance of the oocytes and their polar bodies. The proposed algorithm has been designed to be adaptable with typical commercial inverted microscopes with different criteria. The successful experimental results for this algorithm produce maximum errors of 5% for detection and 10% for reporting respectively.

Memoirs: The Germ-Cell Cycle in Phytophaga destructor Say

1935 ◽  
Vol s2-77 (308) ◽  
pp. 585-604
Author(s):  
MARGOT E. METEALFE
Keyword(s):  
Germ Cells ◽  
Growth Stage ◽  
Germ Line ◽  
Polar Body ◽  
Metaphase Plate ◽  
Body Formation ◽  
Polar Bodies ◽  
Complicated Process ◽  
Female Pronucleus ◽  
Polar Body Formation

1. The somatic cells in both sexes of Phytophaga destructor Say contain four pairs of V-shaped chromosomes, the sex-group being indistinguishable in size or form. 2. The germ-cells in both sexes contain eight pairs of chromosomes. 3. The maturation of the egg follows the normal course of development, eight bivalents being formed. After polar body formation the female pronucleus has eight chromosomes. The polar bodies are never extruded from the egg. 4. Spermatogenesis is a complicated process, the details of which have not been satisfactorily determined. The growth stage appears to take place before the last spermatogonial division. No pairing of chromosome has been observed, and apparently no metaphase plate is formed at meiosis. Eeduction is effected by the expulsion of two buds each containing four chromosomes. Thus only one sperm is produced from each spermatocyte. 5. One or more sperms may enter the egg at fertilization. 6. The germ-line is differentiated from the soma at the eightcell stage. 7. At the fifth cleavage the somatic nuclei eliminate half their number of chromosomes, and are left with eight chromosomes. 8. Migration of the germ nuclei takes place at the sixteencell stage. 9. The relation of the chromosome numbers in the somatic and germ lines is discussed.

Cytological characterisation of the mutant phenotypes produced during early embryogenesis by null and loss-of-function alleles of the gammaTub37C gene in Drosophila

1999 ◽  
Vol 112 (5) ◽  
pp. 659-667 ◽  
Author(s):  
S. Llamazares ◽  
G. Tavosanis ◽  
C. Gonzalez
Keyword(s):  
Polar Body ◽  
Nuclear Proliferation ◽  
Early Embryogenesis ◽  
Drosophila Embryo ◽  
Loss Of Function ◽  
Female Meiosis ◽  
Polar Bodies ◽  
Early Drosophila Embryo ◽  
Gamma Tubulin ◽  
Mutant Phenotypes

We have studied the mutant phenotypes brought about during early embryogenesis by mutation in the gammaTub37C gene, one of the two isoforms of gamma-tubulin that have been identified in Drosophila. We have focused our attention on fs(2)TW1(1) and fs(2)TW1(RU34), a null and a hypomorph allele of this gene, whose sequences we report in this work. We have found that the abnormal meiotic figures observed in mutant stage 14 oocytes are not observed in laid oocytes or fertilised embryos, suggesting that these abnormal meiotic figures are not terminally arrested. We have also concluded that both null and hypomorph alleles lead to a total arrest of nuclear proliferation during early embryogenesis. This is in contrast to their effect on female meiosis-I where hypomorph alleles display a much weaker phenotype. Finally, we have observed that null and hypomorph alleles lead to some distinct phenotypes. Unfertilised laid oocytes and fertilised embryos deficient for gammaTub37C do not contain polar bodies and have a few bipolar microtubule arrays. In contrast, oocytes and embryos from weaker alleles do not have these microtubule arrays, but do contain polar bodies, or polar-body-like structures. These results indicate that gammaTub37C is essential for nuclear proliferation in the early Drosophila embryo.

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