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Journal of Applied Genetics

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https://www.readbyqxmd.com/read/30417315/the-ftsa-gene-as-a-molecular-marker-for-phylogenetic-studies-in-bradyrhizobium-and-identification-of-bradyrhizobium-japonicum
#1
Michał Kalita, Wanda Małek
The use of ftsA gene sequences for taxonomic studies of the genus Bradyrhizobium bacteria was assessed. The ftsA gene codes for an actin-like protein involved in prokaryotic cell division. Up to now, this gene has not been used as a phylogenetic marker for analysis of bacteria establishing root nodule symbiosis with Fabaceae plants. In this study, the ftsA gene sequences obtained for bradyrhizobia forming N2 fixing symbiosis with four Genisteae tribe plants growing in Poland and most of the type strains of the genus Bradyrhizobium species were analyzed and evaluated as molecular markers for phylogenetic studies of these bacteria for the first time...
November 11, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30414053/mapping-of-qtl-associated-with-seed-longevity-in-durum-wheat-triticum-durum-desf
#2
Mian Abdur Rehman Arif, Andreas Börner
Regeneration cycle of seeds kept at genebanks is determined by seed longevity. Information about longevity of species is important for storage periods, germination test intervals, and reproduction cycles. Seed longevity is different between species and depends on the storage conditions. It also differs between genotypes of a species providing the basis of genetic analyses of seed longevity. Studies in hexaploid wheat and barley have identified numerous quantitative trait locus (QTL) linked to the trait. Seed longevity in durum wheat, however, has not been attempted so far...
November 9, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30368734/genome-wide-regulatory-gene-derived-ssrs-reveal-genetic-differentiation-and-population-structure-in-fiber-flax-genotypes
#3
Dipnarayan Saha, Rajeev Singh Rana, Shantanab Das, Subhojit Datta, Jiban Mitra, Sylvie J Cloutier, Frank M You
We designed a set of 580 simple sequence repeat markers; 506 from transcription factor-coding genes, and 74 from long non-coding RNAs and designated them as regulatory gene-derived simple sequence repeat (ReG-SSR) markers. From this set, we could anchor 559 ReG-SSR markers on 15 flax chromosomes with an average marker distance of 0.56 Mb. Thirty-one polymorphic ReG-SSR primers, amplifying SSR loci length of at least 20 bp were chosen from 134 screened primers. This primer set was used to characterize a diversity panel of 93 flax accessions...
October 27, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30353473/genetic-diversity-linkage-disequilibrium-and-population-structure-in-a-panel-of-brazilian-rice-accessions
#4
Eduardo Venske, Cássia Fernanda Stafen, Victoria Freitas de Oliveira, Luciano Carlos da Maia, Ariano Martins de Magalhães Junior, Kenneth L McNally, Antonio Costa de Oliveira, Camila Pegoraro
Narrowing of genetic diversity and the quantitative nature of most agronomic traits is a challenge for rice breeding. Genome-wide association studies have a great potential to identify important variation in loci underlying quantitative and complex traits; however, before performing the analysis, it is important to assess parameters of the genotypic data and population under study, to improve the accuracy of the genotype-phenotype associations. The aim of this study was to access the genetic diversity, linkage disequilibrium, and population structure of a working panel of Brazilian and several introduced rice accessions, which are currently being phenotyped for a vast number of traits to undergo association mapping...
October 23, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30353472/karyotype-analysis-of-eight-cultivated-allium-species
#5
Farzaneh Pordel Maragheh, Daniel Janus, Magdalena Senderowicz, Kamil Haliloglu, Bozena Kolano
The karyotypes of Allium, a genus that comprises many crops and ornamental plants, are relatively poorly studied. To extend our knowledge on karyotype structure of the genus, the chromosomal organization of rRNA genes and CMA/DAPI bands was studied. Fluorescence in situ hybridization using 5S and 35S rDNA probes and banding methods (silver staining and CMA3 /DAPI staining) were used to analyze the karyotypes of eight cultivated Allium L. species. Analyzed Allium taxa revealed three different basic chromosome numbers (x = 7, 8, 9) and three different ploidy levels (diploid, triploid, and tetraploid)...
October 23, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30328055/5-flanking-variants-of-equine-casein-genes-csn1s1-csn1s2-csn2-csn3-and-their-relationship-with-gene-expression-and-milk-composition
#6
Jakub Cieslak, Lukasz Wodas, Alicja Borowska, Piotr Pawlak, Grazyna Czyzak-Runowska, Jacek Wojtowski, Kamila Puppel, Beata Kuczynska, Mariusz Mackowski
Genes encoding casein proteins are important candidates for milk composition traits in mammals. In the case of the domestic horse, our knowledge of casein genes is limited mainly to coding sequence variants. This study involved screening for polymorphism in 5'-flanking regions of four genes encoding equine caseins (CSN1S1, CSN1S2, CSN2, and CSN3) and making a preliminary assessment of their effect on the gene expression (on the mRNA and protein levels) and milk composition traits in selected horse breeds. Altogether, 23 polymorphisms (21 described previously SNPs and two novel InDels) were found in the studied sequences, the majority of which are common in various horse breeds...
October 16, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30284681/structural-and-copy-number-chromosome-abnormalities-in-canine-cutaneous-mast-cell-tumours
#7
Miluse Vozdova, Svatava Kubickova, Halina Cernohorska, Jan Fröhlich, Petr Fictum, Jiri Rubes
Mast cell tumours (MCTs) are the most common skin tumours in dogs. Their clinical behaviour is variable and their aetiology remains largely unknown. We performed a metaphase fluorescence in situ hybridisation (FISH) with whole chromosome painting probes, and interphase FISH with BAC probes for 14 cancer-related genes to reveal clonal structural chromosome rearrangements and copy number variants (CNVs) in canine cutaneous MCTs. The metaphase FISH performed in three MCTs revealed several clonal monosomies and trisomies and two different chromosome rearrangements...
October 4, 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30284680/homozygous-2p11-2-deletion-supports-the-implication-of-elmod3-in-hearing-loss-and-reveals-the-potential-association-of-capg-with-asd-id-etiology
#8
Saida Lahbib, Claire S Leblond, Mariem Hamza, Béatrice Regnault, Laure Lemée, Alexandre Mathieu, Hager Jaouadi, Rahma Mkaouar, Ilhem Ben Youssef-Turki, Ahlem Belhadj, Ichraf Kraoua, Thomas Bourgeron, Sonia Abdelhak
Autism spectrum disorder (ASD) is a set of neurodevelopmental conditions characterized by early-onset difficulties in social communication and unusually restricted, repetitive behavior and interests. Parental consanguinity may lead to higher risk of ASD and to more severe clinical presentations in the offspring. Studies of ASD families with high inbreeding enable the identification of inherited variants of this disorder particularly those with an autosomal recessive pattern of inheritance. In our study, using copy number variants (CNV) analysis, we identified a rare homozygous deletion in 2p11...
October 4, 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
#9
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/30145696/correction-to-novel-1q22-q23-1-duplication-in-a-patient-with-lambdoid-and-metopic-craniosynostosis-muscular-hypotonia-and-psychomotor-retardation
#10
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/30269313/the-molecular-and-phenotypic-characterization-of-fructophilic-lactic-acid-bacteria-isolated-from-the-guts-of-apis-mellifera-l-derived-from-a-polish-apiary
#11
Artur Pachla, Magdalena Wicha, Aneta A Ptaszyńska, Grzegorz Borsuk, Łucja Łaniewska -Trokenheim, Wanda Małek
This paper describes taxonomic position, phylogeny, and phenotypic properties of 14 lactic acid bacteria (LAB) originating from an Apis mellifera guts. Based on the 16S rDNA and recA gene sequence analyses, 12 lactic acid bacteria were assigned to Lactobacillus kunkeei and two others were classified as Fructobacillus fructosus. Biochemically, all isolated lactic acid bacteria showed typical fructophilic features and under anaerobic conditions grew well on fructose, but poorly on glucose. Fast growth of bacteria on glucose was noted in the presence of oxygen or fructose as external electron acceptors...
November 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30259345/efficient-construction-of-streptococcus-anginosus-mutants-in-strains-of-clinical-origin
#12
Katarzyna Obszańska, Izabella Kern-Zdanowicz, Izabela Sitkiewicz
Streptococcus anginosus group (SAG) is Gram-positive bacteria responsible for a number of purulent human infections such as brain and liver abscesses, which have been on the rise for last few decades. Although some virulence factors of SAG are described, they are mostly undefined and there are almost no methods for genetic manipulations of clinical SAG. Therefore, we presented various approaches to produce engineered strains of this poorly known group of streptococci. We developed a procedure of transformation characterized by transformation efficiency at the level of 104 per 1 μg DNA for certain strains...
November 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30255485/breaking-bad-news-in-genetic-counseling-problems-and-communication-tools
#13
REVIEW
Magdalena M Witt, Katarzyna A Jankowska
Breaking bad news is a common problem for clinical geneticists in their daily work. Just like doctors of other specialties, e.g., oncologists, they can use proven communication tools instead of relying only on professional sense. The latter is, of course, always the most important for experienced doctors, but the use of protocols such as SPIKES and EMPATHY facilitates both the delineation of difficult information and the process of its transmission. The article gives an overview of the best tools of this type available to medical professionals dealing with genetic counseling...
November 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30251238/genomic-prediction-ability-for-beef-fatty-acid-profile-in-nelore-cattle-using-different-pseudo-phenotypes
#14
Hermenegildo Lucas Justino Chiaia, Elisa Peripolli, Rafael Medeiros de Oliveira Silva, Fabiele Loise Braga Feitosa, Marcos Vinícius Antunes de Lemos, Mariana Piatto Berton, Bianca Ferreira Olivieri, Rafael Espigolan, Rafael Lara Tonussi, Daniel Gustavo Mansan Gordo, Lucia Galvão de Albuquerque, Henrique Nunes de Oliveira, Adrielle Mathias Ferrinho, Lenise Freitas Mueller, Sabrina Kluska, Humberto Tonhati, Angélica Simone Cravo Pereira, Ignacio Aguilar, Fernando Baldi
The aim of the present study was to compare the predictive ability of SNP-BLUP model using different pseudo-phenotypes such as phenotype adjusted for fixed effects, estimated breeding value, and genomic estimated breeding value, using simulated and real data for beef FA profile of Nelore cattle finished in feedlot. A pedigree with phenotypes and genotypes of 10,000 animals were simulated, considering 50% of multiple sires in the pedigree. Regarding to phenotypes, two traits were simulated, one with high heritability (0...
November 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30244407/identification-novel-lqt-syndrome-associated-variants-in-polish-population-and-genotype-phenotype-correlations-in-eight-families
#15
Małgorzata Szperl, Urszula Kozicka, Agnieszka Kosiec, Piotr Kukla, Marta Roszczynko, Elżbieta Katarzyna Biernacka
Congenital long QT syndrome (LQTS) is a primary cardiac channelopathy. Genetic testing has not only diagnostic but also prognostic and therapeutic implications. At present, 15 genes have been associated with the disease, with most mutations located in 3 major LQTS-susceptibility genes. During a routine genetic screening for KCNQ1, KCNH2 and SCN5A genes in index cases with LQTS, seven novel variants in KCNH2 and SCN5A genes were found. Genotype-phenotype correlations were analysed in these patients and their families...
November 2018: Journal of Applied Genetics
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
#16
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...
November 2018: Journal of Applied Genetics
https://www.readbyqxmd.com/read/30203143/myofibrillar-myopathy-in-the-genomic-context
#17
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...
November 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
#18
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...
November 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
#19
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...
November 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
#20
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...
November 2018: Journal of Applied Genetics
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