keyword
MENU ▼
Read by QxMD icon Read
search

Consumer genomics

keyword
https://www.readbyqxmd.com/read/28938154/massively-parallel-sequencing-of-forensic-strs-and-snps-using-the-illumina-%C3%A2-forenseq%C3%A2-dna-signature-prep-kit-on-the-miseq-fgx%C3%A2-forensic-genomics-system
#1
Fei Guo, Jiao Yu, Lu Zhang, Jun Li
The ForenSeq™ DNA Signature Prep Kit (ForenSeq Kit) is designed to detect more than 200 forensically relevant markers in a single reaction on the MiSeq FGx™ Forensic Genomics System (MiSeq FGx System), including Amelogenin, 27 autosomal short tandem repeats (A-STRs), 7 X chromosomal STRs (X-STRs), 24 Y chromosomal STRs (Y-STRs) and 94 identity-informative single nucleotide polymorphisms (iSNPs) with the option to contain 22 phenotypic-informative SNPs (pSNPs) and 56 ancestry-informative SNPs (aSNPs). In this study, we evaluated the MiSeq FGx System on three major parts: methodological optimization (DNA extraction, sample quantification, library normalization, diluted libraries concentration, and sample-to-cell arrangement), massively parallel sequencing (MPS) performance (depth of coverage, sequence coverage ratio, and allele coverage ratio), and ForenSeq Kit characteristics (repeatability and concordance, sensitivity, mixture, stability and case-type samples)...
September 8, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28936982/optimization-and-quality-control-of-genome-wide-hi-c-library-preparation
#2
Xiang-Yuan Zhang, Chao He, Bing-Yu Ye, De-Jian Xie, Ming-Lei Shi, Yan Zhang, Wen-Long Shen, Ping Li, Zhi-Hu Zhao
Highest-throughput chromosome conformation capture (Hi-C) is one of the key assays for genome- wide chromatin interaction studies. It is a time-consuming process that involves many steps and many different kinds of reagents, consumables, and equipments. At present, the reproducibility is unsatisfactory. By optimizing the key steps of the Hi-C experiment, such as crosslinking, pretreatment of digestion, inactivation of restriction enzyme, and in situ ligation etc., we established a robust Hi-C procedure and prepared two biological replicates of Hi-C libraries from the GM12878 cells...
September 20, 2017: Yi Chuan, Hereditas
https://www.readbyqxmd.com/read/28934716/automatic-detection-of-micronuclei-by-cell-microscopic-image-processing
#3
Mohammad Taghi Bahreyni Toossi, Hosein Azimian, Omid Sarrafzadeh, Shokoufeh Mohebbi, Shokouhozaman Soleymanifard
With the development and applications of ionizing radiation in medicine, the radiation effects on human health get more and more attention. Ionizing radiation can lead to various forms of cytogenetic damage, including increased frequencies of micronuclei (MNi) and chromosome abnormalities. The cytokinesis block micronucleus (CBMN) assay is widely used method for measuring MNi to determine chromosome mutations or genome instability in cultured human lymphocytes. The visual scoring of MNi is time-consuming and scorer fatigue can lead to inconsistency...
August 12, 2017: Mutation Research
https://www.readbyqxmd.com/read/28926965/glycemic-responses-glycemic-index-and-glycemic-load-values-of-some-street-foods-prepared-from-plantain-musa-spp-aab-genome-in-c%C3%A3-te-d-ivoire
#4
Camille Adam Kouamé, Nestor Kouakou Kouassi, Denis Yao N'dri, Kingsley Kwadwo Asare Pereko, Maria Cristina Casiraghi, Abodo Jacko Rhedoor, Georges N'guessan Amani
The glycemic index (GI) and glycemic load (GL) of four culinary preferences including five local street dishes prepared from three varieties of plantain at different maturity stages was determined. The GI was obtained following ISO/FDI 26642:2010 protocol, and the GL was calculated from test foods' GI, considering the amount of available carbohydrate in the traditional portion size. GI values were 44 for Klaclo (with Ameletiha variety at all black stage), 39 for Aloco (with Agnrin variety at full yellow stage), 39 for Aloco (with Agnrin variety at full yellow with black spots stage); 45 for Chips (with Ameletiha variety at green stage) and 89 for Banane braisée (with Afoto variety at light green stage)...
September 16, 2017: Foods (Basel, Switzerland)
https://www.readbyqxmd.com/read/28926213/whole-genome-amplification-and-sequencing-of-a-daphnia-resting-egg
#5
Justin B Lack, Lawrence J Weider, Punidan D Jeyasingh
Resting eggs banks are unique windows that allow us to directly observe shifts in population genetics, and phenotypes over time as natural populations evolve. Although a variety of planktonic organisms also produce resting stages, the keystone freshwater consumer, Daphnia, is a well-known model for paleogenetics and resurrection ecology. Nevertheless, paleogenomic investigations are limited largely because resting eggs do not contain enough DNA for genomic sequencing. In fact, genomic studies even on extant populations include a laborious preparatory phase of batch culturing dozens of individuals to generate sufficient genomic DNA...
September 19, 2017: Molecular Ecology Resources
https://www.readbyqxmd.com/read/28922761/rapid-mapping-and-cloning-of-the-virescent-1-gene-in-cotton-by-bulked-segregant-analysis-next-generation-sequencing-and-virus-induced-gene-silencing-strategies
#6
Jiankun Zhu, Jiedan Chen, Fengkai Gao, Chenyu Xu, Huaitong Wu, Kun Chen, Zhanfeng Si, Hu Yan, Tianzhen Zhang
Map-based gene cloning is a vital strategy for the identification of the quantitative trait loci or genes underlying important agronomic traits. The conventional map-based cloning method is powerful but generally time-consuming and labor-intensive. In this context, we introduce an improved bulked segregant analysis method in combination with a virus-induced gene silencing (VIGS) strategy for rapid and reliable gene mapping, identification and functional verification. This method was applied to a multiple recessive marker line of upland cotton, Texas 582 (T582), and identified unique genomic positions harboring mutant loci, showing the reliability and efficacy of this method...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28922752/current-understanding-of-the-pathways-of-flavonoid-biosynthesis-in-model-and-crop-plants
#7
Takayuki Tohge, Leonardo Perez de Souza, Alisdair R Fernie
Flavonoids are a signature class of secondary metabolites formed from a relatively simple collection of scaffolds. They are extensively decorated by chemical reactions including glycosylation, methylation, and acylation. They are present in a wide variety of fruits and vegetables and as such in Western populations it is estimated that 20-50 mg of flavonoids are consumed daily per person. In planta they have demonstrated to contribute to both flower color and UV protection. Their consumption has been suggested to presenta wide range of health benefits...
July 10, 2017: Journal of Experimental Botany
https://www.readbyqxmd.com/read/28913805/real-time-pcr-for-the-detection-of-precise-transgene-copy-number-in-wheat
#8
Angelica Giancaspro, Agata Gadaleta, Antonio Blanco
Despite the unceasing advances in genetic transformation techniques, the success of common delivery methods still lies on the behavior of the integrated transgenes in the host genome. Stability and expression of the introduced genes are influenced by several factors such as chromosomal location, transgene copy number and interaction with the host genotype. Such factors are traditionally characterized by Southern blot analysis, which can be time-consuming, laborious, and often unable to detect the exact copy number of rearranged transgenes...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28905710/cleavage-speed-and-blastomere-number-in-dba-2j-compared-with-c57bl-6j-mouse-embryos
#9
Hirofumi Nishizono, Kyosuke Uno, Hiroyuki Abe
DBA/2J mice are among the oldest and most important inbred strains still used in many research fields. However, this strain has reproductive problems, which may consume considerable time and effort during experiments requiring a large population. Because the quality of DBA/2J embryos has not yet been described in detail, we compared DBA/2J mice with the reproductively efficient C57BL/6J strain. Compared with C57BL/6J embryos, DBA/2J embryos had a slower cleavage speed (mean ± 1 SD; first cleavage: C57BL/6J, 16...
January 1, 2017: Journal of the American Association for Laboratory Animal Science: JAALAS
https://www.readbyqxmd.com/read/28903467/development-and-characterization-of-a-synthetic-dna-nuversa-to-be-used-as-a-standard-in-quantitative-polymerase-chain-reactions-for-molecular-pneumococcal-serotyping
#10
Fuminori Sakai, Griffin Sonaty, David Watson, Keith P Klugman, Jorge E Vidal
Identification of Streptococcus pneumoniae and its more than 90 serotypes is routinely conducted by culture and Quellung reactions. Quantitative polymerase chain reactions (qPCRs) have been developed for molecular detection, including a pan-pneumococcus lytA assay, and assays targeting 79 serotypes. Reactions require genomic DNA from every target to prepare standards, which can be time consuming. In this study, we have developed a synthetic DNA molecule as a surrogate for genomic DNA and present new single-plex qPCR reactions to increase molecular detection to 94 pneumococcal serotypes...
September 15, 2017: FEMS Microbiology Letters
https://www.readbyqxmd.com/read/28900766/diversity-and-distribution-of-cyp-gene-family-in-bactrian-camel
#11
Surong Hasi, Jirimutu Yao, Siriguleng Yu, Yanan Tian
Cytochrome P450 (CYP) enzymes belong to a superfamily of monooxygenases which are phase I enzymes responsible for the first pass metabolism of about 90% of drugs in animals. However, these enzymes are often polymorphic and metabolism of the same drug in different species or different individuals is influenced by genetic and non-genetic factors. Bactrian camels are capable of survival in harsh living environments, being able to consume diets that are often toxic to other mammals and can tolerate extreme water and food deprivation...
September 12, 2017: Functional & Integrative Genomics
https://www.readbyqxmd.com/read/28899409/alcohol-consumption-and-breast-tumor-gene-expression
#12
Jun Wang, Yujing J Heng, A Heather Eliassen, Rulla M Tamimi, Aditi Hazra, Vincent J Carey, Christine B Ambrosone, Victor P de Andrade, Adam Brufsky, Fergus J Couch, Tari A King, Francesmary Modugno, Celine M Vachon, David J Hunter, Andrew H Beck, Susan E Hankinson
BACKGROUND: Alcohol consumption is an established risk factor for breast cancer and the association generally appears stronger among estrogen receptor (ER)-positive tumors. However, the biological mechanisms underlying this association are not completely understood. METHODS: We analyzed messenger RNA (mRNA) microarray data from both invasive breast tumors (N = 602) and tumor-adjacent normal tissues (N = 508) from participants diagnosed with breast cancer in the Nurses' Health Study (NHS) and NHSII...
September 12, 2017: Breast Cancer Research: BCR
https://www.readbyqxmd.com/read/28895521/rhizobium-esperanzae-sp-nov-a-n2-fixing-root-symbiont-of-phaseolus-vulgaris-from-mexican-soils
#13
Andrey Barbosa Cordeiro, Renan Augusto Ribeiro, Luisa Caroline Ferraz Helene, Mariangela Hungria
Common bean (Phaseolus vulgaris L.) is the most important legume consumed worldwide; its genetic origins lie in the Mesoamerican (main centre) and Andean regions. It is promiscuous in establishing root-nodule symbioses; however, in the centres of origin/domestication, the predominant association is with Rhizobium etli. We have previously identified a new lineage (PEL-3) comprising three strains (CNPSo 661, CNPSo 666 and CNPSo 668T) isolated from root nodules of common bean in Mexico, and that have now been analysed in more detail...
September 12, 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28887856/cassava-brown-streak-disease-historical-timeline-current-knowledge-and-future-prospects
#14
REVIEW
Katie R Tomlinson, Andy M Bailey, Titus Alicai, Sue Seal, Gary D Foster
Cassava is the second most important staple food crop in terms of per capita calories consumed in Africa and holds potential for climate change adaptation. Unfortunately, productivity in East and Central Africa is severely constrained by two viral diseases: cassava mosaic disease (CMD) and cassava brown streak disease (CBSD). CBSD was first reported in 1936 from northeast Tanzania. For approximately seventy years CBSD was restricted to coastal East Africa and so had a relatively low impact on food security compared to CMD...
September 8, 2017: Molecular Plant Pathology
https://www.readbyqxmd.com/read/28884224/transfection-of-embryonated-muscovy-duck-eggs-with-a-recombinant-plasmid-is-suitable-for-rescue-of-infectious-muscovy-duck-parvovirus
#15
Jianye Wang, Yu Huang, Jueyi Ling, Zhixiang Wang, Guoqiang Zhu
For members of the family Parvoviridae, rescue of infectious virus from recombinant plasmid is usually done in cultured cells. In this study, the whole genome of the pathogenic Muscovy duck parvovirus (MDPV) strain YY was cloned into the pBluescript II (SK) vector, generating recombinant plasmid pYY. With the aid of a transfection reagent, pYY plasmid was inoculated into 11-day-old embryonated Muscovy duck eggs via the chorioallantoic membrane route, resulting in the successful rescue of infectious virus and death of the embryos...
September 7, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28882611/generation-and-crispr-cas9-editing-of-transformed-progenitor-b-cells-as-a-pseudo-physiological-system-to-study-dna-repair-gene-function-in-v-d-j-recombination
#16
Hélène Lenden Hasse, Chloé Lescale, Joy J Bianchi, Wei Yu, Marie Bedora-Faure, Ludovic Deriano
Antigen receptor gene assembly is accomplished in developing lymphocytes by the V(D)J recombination reaction, which can be separated into two steps: DNA cleavage by the recombination-activating gene (RAG) nuclease and joining of DNA double strand breaks (DSBs) by components of the nonhomologous end joining (NHEJ) pathway. Deficiencies for NHEJ factors can result in immunodeficiency and a propensity to accumulate genomic instability, thus highlighting the importance of identifying all players in this process and deciphering their functions...
September 4, 2017: Journal of Immunological Methods
https://www.readbyqxmd.com/read/28881969/chromatin-accessibility-prediction-via-convolutional-long-short-term-memory-networks-with-k-mer-embedding
#17
Xu Min, Wanwen Zeng, Ning Chen, Ting Chen, Rui Jiang
Motivation: Experimental techniques for measuring chromatin accessibility are expensive and time consuming, appealing for the development of computational approaches to predict open chromatin regions from DNA sequences. Along this direction, existing methods fall into two classes: one based on handcrafted k -mer features and the other based on convolutional neural networks. Although both categories have shown good performance in specific applications thus far, there still lacks a comprehensive framework to integrate useful k -mer co-occurrence information with recent advances in deep learning...
July 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28878819/construction-of-an-easy-to-use-crispr-cas9-system-by-patching-a-newly-designed-exit-circuit
#18
Qiang Tang, Chunbo Lou, Shuang-Jiang Liu
BACKGROUND: Plasmid-borne genetic editing tools, including the widely used CRISPR-Cas9 system, have greatly facilitated bacterial programming to obtain novel functionalities. However, the lack of effective post-editing plasmid elimination methods impedes follow-up genetic manipulation or application. Conventional strategies including exposure to physical and chemical treatments, or exploiting temperature-sensitive replication origins have several drawbacks (e.g., they are limited for efficiency and are time-consuming)...
2017: Journal of Biological Engineering
https://www.readbyqxmd.com/read/28874473/revitalization-of-a-forward-genetic-screen-identifies-three-new-regulators-of-fungal-secondary-metabolism-in-the-genus-aspergillus
#19
Brandon T Pfannenstiel, Xixi Zhao, Jennifer Wortman, Philipp Wiemann, Kurt Throckmorton, Joseph E Spraker, Alexandra A Soukup, Xingyu Luo, Daniel L Lindner, Fang Yun Lim, Benjamin P Knox, Brian Haas, Gregory J Fischer, Tsokyi Choera, Robert A E Butchko, Jin-Woo Bok, Katharyn J Affeldt, Nancy P Keller, Jonathan M Palmer
The study of aflatoxin in Aspergillus spp. has garnered the attention of many researchers due to aflatoxin's carcinogenic properties and frequency as a food and feed contaminant. Significant progress has been made by utilizing the model organism Aspergillus nidulans to characterize the regulation of sterigmatocystin (ST), the penultimate precursor of aflatoxin. A previous forward genetic screen identified 23 A. nidulans mutants involved in regulating ST production. Six mutants were characterized from this screen using classical mapping (five mutations in mcsA) and complementation with a cosmid library (one mutation in laeA)...
September 5, 2017: MBio
https://www.readbyqxmd.com/read/28871270/in-vivo-assembly-in-escherichia-coli-of-transformation-vectors-for-plastid-genome-engineering
#20
Yuyong Wu, Lili You, Shengchun Li, Meiqi Ma, Mengting Wu, Lixin Ma, Ralph Bock, Ling Chang, Jiang Zhang
Plastid transformation for the expression of recombinant proteins and entire metabolic pathways has become a promising tool for plant biotechnology. However, large-scale application of this technology has been hindered by some technical bottlenecks, including lack of routine transformation protocols for agronomically important crop plants like rice or maize. Currently, there are no standard or commercial plastid transformation vectors available for the scientific community. Construction of a plastid transformation vector usually requires tedious and time-consuming cloning steps...
2017: Frontiers in Plant Science
keyword
keyword
10003
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"