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Journal of Applied Genetics

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https://www.readbyqxmd.com/read/30232619/reference-gene-validation-for-normalization-of-rt-qpcr-assay-associated-with-germination-and-survival-of-rice-under-hypoxic-condition
#1
Dhananjay Kumar, Prasanta Kumar Das, Bidyut Kumar Sarmah
Study on expression of genes for the traits associated with hypoxia tolerance during the germination demands robust choice of reference genes for transcript data normalization and gene validation through real-time quantitative polymerase chain reaction (RT-qPCR). However, reliability and stability of reference genes across different rice germplasms under hypoxic condition have not been accessed yet. Stability performance of reference genes such as eukaryotic elongation factor 1 α (eEF1α), ubiquitin 10 (UBQ10), glyceraldehyde 3-phosphate dehydrogenase (GAPDH), 18S ribosomal RNA (18SrRNA), 25S ribosomal RNA (25SrRNA), β-tublin (β-TUB), actin11 (ACT11), ubiquitin C (UBC), eukaryotic elongation factor 4 α (eIF4α), and ubiquitin5 (UBQ5) was accessed through statistical algorithms like geNorm, NormFinder, Comparative ΔCt method, BestKeeper, and RefFinder in three rice germplasms (KHO, RKB, and IR-64) with varied level of tolerance to hypoxic condition during germination...
September 20, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30209687/do-gwas-and-studies-of-heterozygotes-for-npc1-and-or-npc2-explain-why-npc-disease-cases-are-so-rare
#2
REVIEW
Robert P Erickson
Early onset Niemann-Pick C diseases are extremely rare, especially Niemann-Pick C2. Perhaps unusually for autosomal recessive diseases, heterozygotes for mutations in NPC1 manifest many biological variations. NPC2 deficiency has large effects on fertility. These features of NPC1 and NPC2 are reviewed in regard to possible negative selection for heterozygotes carrying null and hypomorphic alleles.
September 13, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30203143/myofibrillar-myopathy-in-the-genomic-context
#3
REVIEW
Jakub Piotr Fichna, Aleksandra Maruszak, Cezary Żekanowski
Myofibrillar myopathy (MFM) is a group of inherited muscular disorders characterized by myofibril dissolution and abnormal accumulation of degradation products. The diagnosis of muscular disorders based on clinical presentation is difficult due to phenotypic heterogeneity and overlapping symptoms. In addition, precise diagnosis does not always explain the disease etiopathology or the highly variable clinical course even among patients diagnosed with the same type of myopathy. The advent of high-throughput next-generation sequencing (NGS) has provided a successful and cost-effective strategy for identification of novel causative genes in myopathies, including MFM...
September 10, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30159773/the-influence-of-al-3-on-dna-methylation-and-sequence-changes-in-the-triticale-%C3%A3-triticosecale-wittmack-genome
#4
Niedziela Agnieszka
Abiotic stressors such as drought, salinity, and exposure to heavy metals can induce epigenetic changes in plants. In this study, liquid chromatography (RP-HPLC), methylation amplified fragment length polymorphisms (metAFLP), and methylation-sensitive amplification polymorphisms (MSAP) analysis was used to investigate the effects of aluminum (Al) stress on DNA methylation levels in the crop species triticale. RP-HPLC, but not metAFLP or MSAP, revealed significant differences in methylation between Al-tolerant (T) and non-tolerant (NT) triticale lines...
August 30, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30145696/correction-to-novel-1q22-q23-1-duplication-in-a-patient-with-lambdoid-and-metopic-craniosynostosis-muscular-hypotonia-and-psychomotor-retardation
#5
Anna Sowińska-Seidler, Ewelina M Olech, Magdalena Socha, Dawid Larysz, Aleksander Jamsheer
This article was originally published electronically on 29 May 2018 with incorrect copyright line in the Publisher's internet portal (currently SpringerLink). The copyright line of the article should be "
August 25, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30145695/elevated-expression-of-p53-in-early-colon-polyps-in-a-pig-model-of-human-familial-adenomatous-polyposis
#6
Agata Sikorska, Tatiana Flisikowska, Monika Stachowiak, Alexander Kind, Angelika Schnieke, Krzysztof Flisikowski, Marek Switonski
Familial adenomatous polyposis (FAP) is a hereditary predisposition to formation of colon polyps that can progress to colorectal cancer (CRC). The severity of polyposis varies substantially within families bearing the same germline mutation in the adenomatous polyposis coli (APC) tumour suppressor gene. The progressive step-wise accumulation of genetic events in tumour suppressor genes and oncogenes leads to oncogenic transformation, with driver alterations in the tumour protein p53 (TP53) gene playing a key role in advanced stage CRC...
August 25, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30088231/htert-promoter-methylation-status-in-peripheral-blood-leukocytes-as-a-molecular-marker-of-head-and-neck-cancer-progression
#7
Agnieszka Sobecka, Wiktoria Blaszczak, Wojciech Barczak, Pawel Golusinski, Blazej Rubis, Michal M Masternak, Wiktoria M Suchorska, Wojciech Golusinski
Cancer cells, including head and neck cancer cell carcinoma (HNSCC), are characterized by an increased telomerase activity. This enzymatic complex is active in approximately 80-90% of all malignancies, and is regulated by various factors, including methylation status of hTERT gene promoter. hTERT methylation pattern has been thoroughly studied so far. It was proved that hTERT is aberrantly methylated in tumor tissue versus healthy counterparts. However, such effect has not yet been investigated in PBLs (peripheral blood leukocytes) of cancer patients...
August 7, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30047032/disease-not-genetic-but-infectious-multiple-tuberculomas-and-fibrinous-pericarditis-as-symptoms-pathognomonic-for-tuberculosis-of-frederic-chopin
#8
Michał Witt, Artur Szklener, Wojciech Marchwica, Tadeusz Dobosz
Chopin's heart, generally enlarged, presented morphologic features pathognomonic for fibrinous pericarditis presumably of tubercular origin: multiple nodular hyalinization foci-tuberculomas and fibrillary coating covering the whole surface of pericardium ("frosted heart"). We show that these features differ significantly from post mortem-formed inorganic crystalline deposits, mold colonies, or fat deposits known from various preserved anatomical objects stored for a long period of time. In our opinion, these pathologies fully justify the claim that chronic cavernous pulmonary, laryngeal, and intestinal tuberculosis presents itself as the most plausible diagnosis of Frederic Chopin and that rapidly progressing tubercular pericarditis became the immediate cause of his death...
July 25, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30039242/identification-and-expression-of-genes-in-response-to-cassava-bacterial-blight-infection
#9
Piengtawan Tappiban, Supajit Sraphet, Nattaya Srisawad, Duncan R Smith, Kanokporn Triwitayakorn
Cassava bacterial blight (CBB) caused by Xanthomonas axonopodis pv. manihotis (or XAM) is a serious disease of cassava (Manihot esculenta Crantz). In this study, quantitative trait loci (QTL) associated with CBB infection were identified in the F1 progenies of a cross between the "Huay Bong 60" and "Hanatee" cassava cultivars. The phenotype of disease severity was observed at 7, 10, and 12 days after inoculation (DAI). A total of 12 QTL were identified, of which 5, 6, and 1 were detected in 7, 10, and 12 DAI samples, respectively...
July 23, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30014258/an-ems-induced-new-sequence-variant-tems5032-in-the-coding-region-of-srs3-gene-leads-to-shorter-grain-length-in-rice-oryza-sativa-l
#10
Umakanta Ngangkham, Manoj Nath, Prasad Dokku, S V Amitha Mithra, Srinivasan Ramamurthy, Nagendra K Singh, R P Sharma, Trilochan Mohapatra
Grain shape and size influence yield and consumer preferences in rice. In the present study, we characterized and mapped a short and bold grained mutant and named it as TEMS5032, as the mutant is a result of EMS-induced transition from C to T at the 5032nd bp of SRS3 gene, which is known to affect grain size in rice. The substitution led to creation of a stop codon in the motor domain of SRS3, a kinesin 13 family gene, translating into a truncated protein product. However, transcription of this gene remained unaffected in TEMS5032 compared to the wild type, N22...
July 17, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29978277/transcriptome-analysis-reveals-candidate-genes-involved-in-splay-leg-syndrome-in-piglets
#11
Tao Wu, Xu Zhang, Mi Tian, Qiangqiang Tao, Liang Zhang, Yueyun Ding, Xiaodong Zhang, Zongjun Yin
Splay leg is frequently observed in newborn piglets and leads to economic loss as well as welfare concerns. However, the etiology and pathogenesis of splay leg syndrome in piglets are still poorly understood. The aims of this paper were to characterize changes in the transcriptome of splay leg piglets and identify candidate genes responsible for this disease. We chose three splay leg piglets and their healthy full sibs, and constructed six RNA libraries using skeletal muscle samples from both groups and identified the differentially expressed genes between the two groups using RNA-seq...
July 6, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29938393/possible-association-of-the-tert-promoter-polymorphisms-rs2735940-rs7712562-and-rs2853669-with-diabetes-mellitus-in-obese-elderly-polish-population-results-from-the-national-polsenior-study
#12
Ewa Gutmajster, Jerzy Chudek, Aleksandra Augusciak-Duma, Malgorzata Szwed, Aleksandra Szybalska, Malgorzata Mossakowska, Monika Puzianowska-Kuznicka, Andrzej Wiecek, Aleksander L Sieron
One of the markers of aging is lymphocyte telomere length (LTL), which is affected by genetic constitution of the organism and environmental conditions, such as development and diseases, including diabetes. The relationship of the later seems to be bilateral. The enzyme responsible for the maintenance of telomere length is a subunit of telomerase-telomerase reverse transcriptase (TERT). The aims of the present study were to (1) determine the influence of the TERT promoter sequence SNP variants on relative telomere length (RTL) in an elderly Polish population and (2) explore the potential associations of the SNPs with the type 2 diabetes mellitus (T2DM) in the obese individuals...
June 25, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29971754/population-analysis-of-magnaporthe-oryzae-by-using-endogenous-repetitive-dna-sequences-and-mating-type-alleles-in-different-districts-of-karnataka-india
#13
D Jagadeesh, M K Prasanna Kumar, N S Devaki
Rice is the staple food crop of more than 60% of the population of the world. This crop suffers from blast disease caused by Magnaporthe oryzae. Information on the mating-type allele distribution and diversity of the pathogen population for the state of Karnataka, India is scanty. With this background, a total of 72 isolates of M. oryzae from rice in different districts of Karnataka were examined for identifying sexual mating alleles MAT1, MAT2 and understanding the genetic diversity based on DNA fingerprint of pot2, an inverted repeat transposon...
August 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29951891/molecular-characterization-of-microtubule-associated-protein-1-light-chain-3b-in-megalobrama-amblycephala-fed-with-high-fat-berberine-diets
#14
Wei-Na Xu, Dan-Hong Chen, Wen-Bin Liu, Jian-Xiong Xu, Shuo-Shuo Yang
This study tested the effect of berberine on autophagy-related protein of Megalobrama amblycephala fed with high fat diet under different feeding modes. The full-length complementary DNA (cDNA) of microtubule-associated protein 1-light chain 3B (LC3B) was 1871 bp with an open reading frame of 378 bp encoding 125 amino acids. High homology at nucleotide and amino acid sequences to carp LC3B was revealed though sequence analysis. LC3B was mainly (P < 0.05) expressed in hepatopancreas but lower in several peripheral tissues, including gill, intestine, kidney, and spleen...
August 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29946990/genome-wide-association-study-of-body-weight-in-wenshang-barred-chicken-based-on-the-slaf-seq-technology
#15
REVIEW
Fuwei Li, Haixia Han, Qiuxia Lei, Jinbo Gao, Jie Liu, Wei Liu, Yan Zhou, Huimin Li, Dingguo Cao
Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models...
August 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29845577/novel-1q22-q23-1-duplication-in-a-patient-with-lambdoid-and-metopic-craniosynostosis-muscular-hypotonia-and-psychomotor-retardation
#16
Anna Sowińska-Seidler, Ewelina M Olech, Magdalena Socha, Dawid Larysz, Aleksander Jamsheer
Craniosynostosis (CS) refers to the group of craniofacial malformations characterized by the premature closure of one or more cranial sutures. The disorder is clinically and genetically heterogeneous and occurs usually as an isolated trait, but can also be syndromic. In 30-60% of patients, CS is caused by known genetic factors; however, in the rest of the cases, causative molecular lesions remain unknown. In this paper, we report on a sporadic male patient affected by complex CS (metopic and unilateral lambdoid synostosis), muscular hypotonia, psychomotor retardation, and facial dysmorphism...
August 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29725989/survey-of-potential-factors-involved-in-the-low-frequency-of-cp5-and-cp8-expression-in-staphylococcus-aureus-isolates-from-mastitis-of-dairy-cattle-from-argentina-chile-and-uruguay
#17
Maria Belen Ambroggio, Melina Soledad Perrig, Cecilia Camussone, Nazarena Pujato, Alicia Bertón, Edgardo Gianneechini, Silvia Alvarez, Ivan Sergio Marcipar, Luis Fernando Calvinho, Maria Sol Barbagelata
Staphylococcus aureus produces capsular polysaccharides (CPs) both in vivo and under defined culture conditions being serotypes 5 and 8 the most prevalent. S. aureus isolates that fail to produce CP5 or CP8 are defined as non-typeable (NT). Loss of capsule expression, however, may lead to S. aureus persistence in a chronically infected host. The prevalence of NT strains of S. aureus isolated from bovine mastitis varies according to the geographic origin of the strain. The aims of this work were to detect phenotypically and genotypically the capsular profile of 144 S...
August 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29721857/correction-to-identification-of-novel-mutations-in-ffpe-lung-adenocarcinomas-using-deparray-sorting-technology-and-next-generation-sequencing
#18
Ji Won Lee, Jong-Yeon Shin, Jeong-Sun Seo
In the original article, part of Table 1 headings and entries were missing. The correct Table is as shown below. The original article has been corrected.
August 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29705927/single-nucleotide-polymorphism-rs11614913-associated-with-cc-genotype-in-mir-196a2-is-overrepresented-in-laryngeal-squamous-cell-carcinoma-but-not-salivary-gland-tumors-in-polish-population
#19
Marcin Skalski, Adam Ustaszewski, Katarzyna Jaskiewicz, Katarzyna Kiwerska, Malgorzata Wierzbicka, Hanna Klimza, Reidar Grenman, Maciej Giefing
The miRNA-196a2 has shown significance in the development of various neoplasms, including head and neck squamous cell carcinoma (HNSCC). The oncogenic functionality of this miRNA is mediated via its potential to target annexin A1 mRNA, a tumor suppressor gene involved in inhibition of the NF-κB pathway. Interestingly, recent data indicate a susceptibility for aforementioned neoplasms in patients with the CC genotype vs the CT and TT genotypes of the rs11614913 SNP located within the DNA sequence of the miR-196a2 that results in elevated expression of the gene...
August 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/29680930/splicing-mutations-in-human-genetic-disorders-examples-detection-and-confirmation
#20
REVIEW
Abramowicz Anna, Gos Monika
Precise pre-mRNA splicing, essential for appropriate protein translation, depends on the presence of consensus "cis" sequences that define exon-intron boundaries and regulatory sequences recognized by splicing machinery. Point mutations at these consensus sequences can cause improper exon and intron recognition and may result in the formation of an aberrant transcript of the mutated gene. The splicing mutation may occur in both introns and exons and disrupt existing splice sites or splicing regulatory sequences (intronic and exonic splicing silencers and enhancers), create new ones, or activate the cryptic ones...
August 2018: Journal of Applied Genetics
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