Genome-wide identification of internal reference genes for normalization of gene expression values during endosperm development in wheat.
Abstract Internal reference genes that are stably expressed are essential for normalization in comparative expression analyses. However, gene expression varies significantly among species, organisms, tissues, developmental stages, stresses, and treatments. Therefore, identification of stably expressed reference genes in developmental endosperm of bread wheat is important for expression analysis of endosperm genes. As the first study to systematically screen for reference genes across different developmental stages of wheat endosperm, nine genes were selected from among 76 relatively stable genes based on high-thro...
Source: J Appl Genet - July 11, 2019 Category: Genetics & Stem Cells Authors: Mu J, Chen L, Gu Y, Duan L, Han S, Li Y, Yan Y, Li X Tags: J Appl Genet Source Type: research

Relevance of solute carrier family 5 transporter defects to inherited and acquired human disease.
De Paepe B Abstract The solute carrier (SLC) group of membrane transport proteins is crucial for cells via their control of import and export of vital molecules across the cellular membrane. Defects in these transporters with narrow substrate specificities cause monogenic disorders, giving us essential clues of their precise roles in cellular functioning. The SLC5 family in particular has been linked to various human diseases, of mild and severe phenotype as well as high and low prevalence. In this review, we describe the effects on health of SLC5 dysfunction and dysregulation by summarizing findings in patients ...
Source: J Appl Genet - July 8, 2019 Category: Genetics & Stem Cells Authors: Cannizzaro M, Jarošová J, De Paepe B Tags: J Appl Genet Source Type: research

Efflux pumps as an additional source of resistance to trichothecenes in Fusarium proliferatum and Fusarium oxysporum isolates.
Abstract Role of efflux-mediated toxin resistance to trichothecenes is known in trichothecene-producing species. However, the role of trichothecene efflux pump homologues in non-producing fusaria such as F. oxysporum and F. proliferatum was not investigated in detail. Analysis of the homologues of trichothecene efflux pump from multiple fungal species allowed us to uncover and catalogue functional gene copies of conserved structure. Putative Tri12 candidates in Fusarium oxysporum and F. proliferatum were characterised via expression profiling in response to different trigger compounds, providing supporting evidenc...
Source: J Appl Genet - June 27, 2019 Category: Genetics & Stem Cells Authors: Popiel D, Dawidziuk A, Koczyk G Tags: J Appl Genet Source Type: research

MicroRNA transcriptome analysis of poly I:C-stimulated and PRRSV-infected porcine alveolar macrophages.
Abstract Porcine reproductive and respiratory syndrome virus (PRRSV) causes severe reproductive failure in sows, respiratory diseases, and high mortality in piglets, which results in serious economic losses to the swine industry worldwide. Previous studies have described that PRRSV could suppress the host immune system and had antiapoptotic activity in its initial phase of infection. Polyinosinic-polycytidylic acid (poly I:C), a synthesized analogue of viral double-strand RNA, activates innate immunity responses and induces apoptosis in cells. Therefore, we performed miRNA transcriptome analysis of poly I:C-stimul...
Source: J Appl Genet - June 22, 2019 Category: Genetics & Stem Cells Authors: Wu J, Ji Z, Qiao M, Peng X, Wu H, Song Z, Zhao H, Liu G, Li F, Mei S Tags: J Appl Genet Source Type: research

Prediction of key regulators and downstream targets of E. coli induced mastitis.
Abstract Mastitis, an inflammatory response of mammary glands to invading bacteria, is one of the most economically costly diseases affecting dairy animals. Escherichia coli can be introduced as a major etiological agent of bovine mastitis in well-managed dairy farms. It is of great significance to understand the regulatory mechanisms by which the disease can be controlled. High-throughput technologies combined with novel computational systems biology tools have provided new opportunities for a better understanding of the molecular mechanisms that underlie disease. In the current study, the results of microarray m...
Source: J Appl Genet - June 11, 2019 Category: Genetics & Stem Cells Authors: Sharifi S, Pakdel A, Ebrahimie E, Aryan Y, Ghaderi Zefrehee M, Reecy JM Tags: J Appl Genet Source Type: research

A single enzyme PCR-RFLP assay targeting V1-V3 region of 16S rRNA gene for direct identification of Alicyclobacillus acidoterrestris from other Alicyclobacillus species.
In conclusion, a single enzyme PCR-RFLP assay was developed and showed rapid, inexpensive and direct identification of Alicyclobacillus isolates. The application of this method will be useful to identify this contaminant in fruit juices. PMID: 31001785 [PubMed - as supplied by publisher] (Source: J Appl Genet)
Source: J Appl Genet - April 19, 2019 Category: Genetics & Stem Cells Authors: Sourri P, Doulgeraki AI, Tassou CC, Nychas GE Tags: J Appl Genet Source Type: research

Zebrafish breeding program: genetic parameters estimates for growth traits.
The objective of this study was to evaluate the genetic parameters of two generations of zebrafish breeding program. The base population was formed by crossing individuals of six commercial stocks of zebrafish, resulting in a nucleus with 60 families. Two generations were evaluated, with a total of 780 and 781 individuals for the first and second generation, respectively. The selection was made based on the mean genetic value of each family, followed by mass selection of the breeders. Mathematical models that considered the fixed (age, density in the larval stage, sex, and generation) and random (animal additive genetics, ...
Source: J Appl Genet - April 17, 2019 Category: Genetics & Stem Cells Authors: Lewandowski V, Sary C, Casetta J, Seccatto Garcia AL, Lopes de Oliveira CA, Pereira Ribeiro R, Vargas Mendez LD Tags: J Appl Genet Source Type: research

Copy number variation of bovine SHH gene is associated with body conformation traits in Chinese beef cattle.
Abstract Sonic Hedgehog (Shh) regulates many key developmental processes during vertebrate limb development, fat formation, and skeletal tissue regeneration. Current whole genome sequencing data have identified a copy number variation mapping to bovine Sonic Hedgehog gene (SHH-CNV). The object of this study was to characterize the SHH-CNV distributions in 648 individuals from 11 Chinese cattle populations and further to investigate the associations of the copy number changes with gene expression and cattle growth traits. The SHH-CNV showed a high variance within Chinese indigenous yellow cattle. Compared to yak an...
Source: J Appl Genet - April 17, 2019 Category: Genetics & Stem Cells Authors: Liu M, Li B, Shi T, Huang Y, Liu GE, Lan X, Lei C, Chen H Tags: J Appl Genet Source Type: research

AFLP protocol comparison for microbial diversity fingerprinting.
Abstract Over the last decade, several methods based on genomic DNA have been developed for the identification and genotyping of prokaryotic and eukaryotic organisms. These genomic methods differ regarding taxonomic range, discriminatory power, reproducibility, and ease of interpretation and standardization. The amplified fragment length polymorphism (AFLP) technique is a very powerful DNA fingerprinting technique for DNA of any source or complexity, varying in both size and base composition. In addition, this method shows high discriminatory power and good reproducibility allowing it to be efficient in discrimina...
Source: J Appl Genet - April 15, 2019 Category: Genetics & Stem Cells Authors: Bertani G, Savo Sardaro ML, Neviani E, Lazzi C Tags: J Appl Genet Source Type: research

Comparing assignment-based approaches to breed identification within a large set of horses.
aron;tohl R Abstract Considering the extensive data sets and statistical techniques, animal breeding embodies a branch of machine learning that has a constantly increasing impact on breeding. In our study, information regarding the potential of machine learning and data mining within a large set of horses and breeds is presented. The individual assignment methods and factors influencing the success rate of the procedure are compared at the Czech population scale. The fixation index values ranged from 0.057 (HMS1) to 0.144 (HTG6), and the overall genetic differentiation amounted to 8.9% among the breeds. The highes...
Source: J Appl Genet - April 8, 2019 Category: Genetics & Stem Cells Authors: Putnová L, Štohl R Tags: J Appl Genet Source Type: research

Genetic analysis of drought response of wheat following either chemical desiccation or the use of a rain-out shelter.
Nagel M Abstract Simulating drought stress during the breeding process has been proposed as a way to select varieties under naturally non-stressful conditions. The aim of the study was to characterise the genetic basis of the response of 111 spring wheat (Triticum aestivum L.) varieties and landraces to chemical desiccation and to rain-out shelter drought. The effect of the rain-out shelter was a 15% reduction in plant height, spike length and thousand seed weight (TSW); in contrast, the desiccant treatment induced a 15% reduction in seed number, a 35-72% loss in TSW and a reduction in subsequent germination of 12...
Source: J Appl Genet - April 4, 2019 Category: Genetics & Stem Cells Authors: Tarawneh RA, Szira F, Monostori I, Behrens A, Alqudah AM, Thumm S, Lohwasser U, Röder MS, Börner A, Nagel M Tags: J Appl Genet Source Type: research

Novel data on growth phenotype and causative genotypes in 29 patients with Morquio (Morquio-Brailsford) syndrome from Central-Eastern Europe.
ska A Abstract Mucopolysaccharidosis type IVA, also known as Morquio (Morquio-Brailsford) syndrome results from accumulation of keratan sulfate (KS) and chondroitin-6-sulfate (C6S), whereas the primary cause is mutations in the gene encoding galactosamine (N-acetyl)-6-sulfatase (GALNS). Phenotypically it seems to be a well-defined condition, with two main clinical forms: mild (attenuated) and severe, which are determined based on a combination of symptoms, i.e., enzymatic activity of GALNS, age of onset, and symptom severity. Nevertheless, the natural history of MPSIVA in relation to specific anthropometric parame...
Source: J Appl Genet - March 30, 2019 Category: Genetics & Stem Cells Authors: Jezela-Stanek A, Różdżyńska-Świątkowska A, Kulpanovich A, Ciara E, Marucha J, Tylki-Szymańska A Tags: J Appl Genet Source Type: research

Correction to: Splicing mutations in human genetic disorders: examples, detection, and confirmation.
Abstract The original version on this paper contained an error. The first names and last names of Anna Abramowicz and Monika Gos are inadvertently interchanged and are incorrectly displayed in indexing sites. The correct names are presented above. PMID: 30888641 [PubMed - as supplied by publisher] (Source: J Appl Genet)
Source: J Appl Genet - March 19, 2019 Category: Genetics & Stem Cells Authors: Abramowicz A, Gos M Tags: J Appl Genet Source Type: research

Genotype by environment interaction using AMMI model and estimation of additive and epistasis gene effects for 1000-kernel weight in spring barley (Hordeum vulgare L.).
The objective of this study was to assess genotype by environment interaction for 1000-kernel weight in spring barley lines grown in South Poland by the additive main effects and multiplicative interaction model. The study comprised of 32 spring barley (Hordeum vulgare L.) genotypes (two parental genotypes-breeding line 1 N86 and doubled haploid (DH) line RK63/1, and 30 DH lines derived from F1 hybrids), evaluated at six locations in a randomized complete block design, with three replicates. 1000-kernel weight ranged from 24.35 g (for R63N/42 in 2011) to 61.46 g (for R63N/18 in 2008), with an average of 44.8...
Source: J Appl Genet - March 15, 2019 Category: Genetics & Stem Cells Authors: Bocianowski J, Warzecha T, Nowosad K, Bathelt R Tags: J Appl Genet Source Type: research

High-frequency marker haplotypes in the genomic selection of dairy cattle.
Abstract The aim of this study was to predict the genomic breeding value (DGV) of production, selected conformation and reproductive traits, and somatic cell score of dairy cattle in Poland using high-frequency marker haplotypes. The dataset consisted of phenotypic, genotypic, and pedigree data of 1216 Polish Holstein-Friesian bulls. The genotypic data consisted of 54,000 single-nucleotide polymorphisms (SNPs). The data were divided into two subsets: a test dataset (n = 1064) and a validation dataset (n = 152). Genotypic data were selected using three criteria: the percentage of missing...
Source: J Appl Genet - March 15, 2019 Category: Genetics & Stem Cells Authors: Mucha A, Wierzbicki H, Kamiński S, Oleński K, Hering D Tags: J Appl Genet Source Type: research

New QTL for resistance to Puccinia polysora Underw in maize.
In this study, resistance to SCR was evaluated in a BC1RIL population comprising 118 lines grown under three different field conditions. Combined with a genetic map constructed from 1635 SNP markers obtained from the maize 9.4 K SNP Affymetrix® Axiom® Genotyping Array, single quantitative trait loci (QTL) were mapped on chromosomes 4, 9, and 10, respectively. The QTL on chromosome 4 (qSCR4.08) and chromosome 9 (qSCR9.04) were stable across multiple environments, and each explained more than 10% of the phenotypic variation. The stable QTL detected could be desirable sources of SCR resistance in maize-breeding progra...
Source: J Appl Genet - March 5, 2019 Category: Genetics & Stem Cells Authors: Deng C, Li H, Li Z, Tian Z, Chen J, Chen G, Zhang X, Ding J, Chang Y Tags: J Appl Genet Source Type: research

Co-treatment with probucol does not improve lung pathology in hydroxypropyl- β-cyclodextrin-treated Npc1-/- mice.
Co-treatment with probucol does not improve lung pathology in hydroxypropyl-β-cyclodextrin-treated Npc1-/- mice. J Appl Genet. 2019 Feb 28;: Authors: Erickson RP, Borbon IA Abstract We previously reported the altered pulmonary function and pathology found in the mouse model of infantile Niemann-Pick C1 disease, the Npc1-/- mouse. Despite its salutary properties on brain and liver parameters, we did not find efficacious effects of hydroxypropyl-β-cyclodextrin (HPBCD) on pulmonary pathology. Since we had previously shown the beneficial effects of probucol on the somatic phenotype in the Npc1-/...
Source: J Appl Genet - February 28, 2019 Category: Genetics & Stem Cells Authors: Erickson RP, Borbon IA Tags: J Appl Genet Source Type: research

A novel WDR62 missense mutation in microcephaly with abnormal cortical architecture and review of the literature.
We describe two patients, a boy and a girl, with severe congenital microcephaly, global developmental delay, epilepsy, and failure to thrive. MRI showed hemispherical asymmetry, diffuse pachygyria, thick gray matter, indistinct gray-white matter junction, and corpus callosum and white matter hypoplasia. Whole exome sequencing revealed the same novel homozygous missense mutation, c.668T>C, p.Phe223Ser in exon 6 of the WDR62 gene. The healthy parents were heterozygous for this mutation. The mutation affects a highly conserved region in one of the WD repeats of the WDR62 protein. Haplotype analysis showed genetic relatedne...
Source: J Appl Genet - February 1, 2019 Category: Genetics & Stem Cells Authors: Zombor M, Kalmár T, Nagy N, Berényi M, Telcs B, Maróti Z, Brandau O, Sztriha L Tags: J Appl Genet Source Type: research

Diversifying selection signatures among divergently selected subpopulations of Polish Red cattle.
Abstract Polish Red cattle is one of the few indigenous breeds of European red cattle which is characterized by several desired features, such as high disease resistance, good health, longevity, good fertility, and high nutritional value of milk. Currently, Polish Red cattle population is a subject of two independent breeding programs: (i) improvement program and (ii) genetic resources conservation program. The aim of the improvement program is the genetic progress in terms of milk production and body conformation traits, while the conservation program mainly focuses on protection of the genetic resources of Polis...
Source: J Appl Genet - January 26, 2019 Category: Genetics & Stem Cells Authors: Gurgul A, Jasielczuk I, Semik-Gurgul E, Szmatoła T, Majewska A, Sosin-Bzducha E, Bugno-Poniewierska M Tags: J Appl Genet Source Type: research

Analysis of allele-specific expression of seven candidate genes involved in lipid metabolism in pig skeletal muscle and fat tissues reveals allelic imbalance of ACACA, LEP, SCD, and TNF.
Abstract Analysis of allele-specific expression may help to elucidate the genetic architecture of complex traits including fat deposition in pigs. Here, we used pyrosequencing to investigate the allele proportions of candidate genes (ACACA, ADIPOR1, FASN, LEP, ME1, SCD, and TNF) involved in regulation of lipid metabolism in two fat deposits (subcutaneous and visceral fat) and longissimus dorsi muscle of pigs representing Polish Large White, Polish Landrace, Duroc, and Pietrain breeds. We detected differential allelic expression of ACACA, LEP, SCD, and TNF in all tissues analyzed. To search for putative cis-regulat...
Source: J Appl Genet - January 26, 2019 Category: Genetics & Stem Cells Authors: Stachowiak M, Flisikowski K Tags: J Appl Genet Source Type: research

A crash course in sequencing for a microbiologist.
Abstract For the last 40 years, "Sanger sequencing" allowed to unveil crucial secrets of life. However, this method of sequencing has been time-consuming, laborious and remains expensive even today. Human Genome Project was a huge impulse to improve sequencing technologies, and unprecedented financial and human effort prompted the development of cheaper high-throughput technologies and strategies called next-generation sequencing (NGS) or whole genome sequencing (WGS). This review will discuss applications of high-throughput methods to study bacteria in a much broader context than simply their genom...
Source: J Appl Genet - January 25, 2019 Category: Genetics & Stem Cells Authors: Kozińska A, Seweryn P, Sitkiewicz I Tags: J Appl Genet Source Type: research

Exome sequencing in genomic regions related to racing performance of Quarter Horses.
The objective of this study was to analyze exomes and UTRs in regions previously associated with this trait by GWAS in Quarter Horse racehorses with contrasting maximum speed index (SImax), prospecting causal gene polymorphisms that are related to or are in strong linkage disequilibrium with racing performance. Genotypic and phenotypic records from 360 animals of the racing line of Quarter Horses, previously genotyped with an SNP chip to obtain individual genomic estimated breeding values for performance, were used for the formation and sequencing of two groups of animals with contrasting racing performance (20 animals wit...
Source: J Appl Genet - January 21, 2019 Category: Genetics & Stem Cells Authors: Pereira GL, Malheiros JM, Ospina AMT, Chardulo LAL, Curi RA Tags: J Appl Genet Source Type: research

Meta-analysis of association between Arg326Gln (rs1503185) and Gln276Pro (rs1566734) polymorphisms of PTPRJ gene and cancer risk.
Abstract Protein tyrosine phosphatase receptor type J (PTPRJ, DEP1) is a tumour suppressor gene that negatively regulates such processes as angiogenesis, cell proliferation and migration and is one of the genes important for tumour development. Similar to other phosphatase genes, PTPRJ is also described as an oncogene. Among various genetic changes characteristic for this gene, single nucleotide polymorphisms (SNPs) constituting benign genetic variants that can modulate its function have been described. We focused on Gln276Pro and Arg326Gln missense polymorphisms and performed a meta-analysis using data from 2930 ...
Source: J Appl Genet - January 19, 2019 Category: Genetics & Stem Cells Authors: Laczmanska I, Sasiadek MM Tags: J Appl Genet Source Type: research

Genetics and epigenetics of autism spectrum disorder-current evidence in the field.
Abstract Autism spectrum disorders (ASD) is a heterogenous group of neurodevelopmental disorders characterized by problems in social interaction and communication as well as the presence of repetitive and stereotyped behavior. It is estimated that the prevalence of ASD is 1-2% in the general population with the average male to female ratio 4-5:1. Although the causes of ASD remain largely unknown, the studies have shown that both genetic and environmental factors play an important role in the etiology of these disorders. Array comparative genomic hybridization and whole exome/genome sequencing studies identified co...
Source: J Appl Genet - January 10, 2019 Category: Genetics & Stem Cells Authors: Wiśniowiecka-Kowalnik B, Nowakowska BA Tags: J Appl Genet Source Type: research

Diversity and mycotoxin production by Fusarium temperatum and Fusarium subglutinans as causal agents of pre-harvest Fusarium maize ear rot in Poland.
Abstract Maize ear rot is a common disease found worldwide, caused by several toxigenic Fusarium species. Maize ears and kernels infected by Fusarium subglutinans contained significant amounts of beauvericin, fusaproliferin, moniliformin, and enniatins. In 2011, F. subglutinans sensu lato has been divided into two species: Fusarium temperatum sp. nov. and F. subglutinans sensu stricto, showing different phylogeny and beauvericin production within the populations of maize pathogens in Belgium. Isolates of the new species-F. temperatum-were also identified and characterized in Spain, Argentina, Poland, France, and C...
Source: J Appl Genet - November 15, 2018 Category: Genetics & Stem Cells Authors: Stępień Ł, Gromadzka K, Chełkowski J, Basińska-Barczak A, Lalak-Kańczugowska J Tags: J Appl Genet Source Type: research

The ftsA gene as a molecular marker for phylogenetic studies in Bradyrhizobium and identification of Bradyrhizobium japonicum.
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. The ftsA gene sequences of all bradyrhizobial strains with completely or partially sequenced genomes, available in the GenBank database, were also included into the analysis. The phylogeny of the ftsA gene was compared to the phylogenies of other chromosomal genes commonly used in the studies of Bradyrhizob...
Source: J Appl Genet - November 11, 2018 Category: Genetics & Stem Cells Authors: Kalita M, Małek W Tags: J Appl Genet Source Type: research

Mapping of QTL associated with seed longevity in durum wheat (Triticum durum Desf.).
This study confirms the results of previous investigations in bread wheat and provides a baseline for further research in durum wheat. PMID: 30414053 [PubMed - as supplied by publisher] (Source: J Appl Genet)
Source: J Appl Genet - November 9, 2018 Category: Genetics & Stem Cells Authors: Arif MAR, Börner A Tags: J Appl Genet Source Type: research

Genome-wide regulatory gene-derived SSRs reveal genetic differentiation and population structure in fiber flax genotypes.
Abstract 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. The panel included 33 accessions from India, including ...
Source: J Appl Genet - October 27, 2018 Category: Genetics & Stem Cells Authors: Saha D, Rana RS, Das S, Datta S, Mitra J, Cloutier SJ, You FM Tags: J Appl Genet Source Type: research

Karyotype analysis of eight cultivated Allium species.
Abstract 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 tetrapl...
Source: J Appl Genet - October 23, 2018 Category: Genetics & Stem Cells Authors: Maragheh FP, Janus D, Senderowicz M, Haliloglu K, Kolano B Tags: J Appl Genet Source Type: research

Genetic diversity, linkage disequilibrium, and population structure in a panel of Brazilian rice accessions.
aro C Abstract 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 intro...
Source: J Appl Genet - October 23, 2018 Category: Genetics & Stem Cells Authors: Venske E, Stafen CF, de Oliveira VF, da Maia LC, de Magalhães Junior AM, McNally KL, Costa de Oliveira A, Pegoraro C Tags: J Appl Genet Source Type: research

5'-flanking variants of equine casein genes (CSN1S1, CSN1S2, CSN2, CSN3) and their relationship with gene expression and milk composition.
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. Statistical analysis revealed that some are putatively associated with gene expression or milk composition - for example, the c.-2047_-2048in...
Source: J Appl Genet - October 16, 2018 Category: Genetics & Stem Cells Authors: Cieslak J, Wodas L, Borowska A, Pawlak P, Czyzak-Runowska G, Wojtowski J, Puppel K, Kuczynska B, Mackowski M Tags: J Appl Genet Source Type: research

Homozygous 2p11.2 deletion supports the implication of ELMOD3 in hearing loss and reveals the potential association of CAPG with ASD/ID etiology.
hak S Abstract 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 2p11.2 reg...
Source: J Appl Genet - October 4, 2018 Category: Genetics & Stem Cells Authors: Lahbib S, Leblond CS, Hamza M, Regnault B, Lemée L, Mathieu A, Jaouadi H, Mkaouar R, Youssef-Turki IB, Belhadj A, Kraoua I, Bourgeron T, Abdelhak S Tags: J Appl Genet Source Type: research

Structural and copy number chromosome abnormalities in canine cutaneous mast cell tumours.
s J Abstract 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. No centric fusions were detected. The in...
Source: J Appl Genet - October 4, 2018 Category: Genetics & Stem Cells Authors: Vozdova M, Kubickova S, Cernohorska H, Fröhlich J, Fictum P, Rubes J Tags: J Appl Genet Source Type: research

The molecular and phenotypic characterization of fructophilic lactic acid bacteria isolated from the guts of Apis mellifera L. derived from a Polish apiary.
Abstract 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. The ...
Source: J Appl Genet - September 29, 2018 Category: Genetics & Stem Cells Authors: Pachla A, Wicha M, Ptaszyńska AA, Borsuk G, -Trokenheim ŁŁ, Małek W Tags: J Appl Genet Source Type: research

Efficient construction of Streptococcus anginosus mutants in strains of clinical origin.
Abstract 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 ...
Source: J Appl Genet - September 26, 2018 Category: Genetics & Stem Cells Authors: Obszańska K, Kern-Zdanowicz I, Sitkiewicz I Tags: J Appl Genet Source Type: research

Breaking bad news in genetic counseling-problems and communication tools.
Abstract 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. PMID: 30255485 [PubMed -...
Source: J Appl Genet - September 25, 2018 Category: Genetics & Stem Cells Authors: Witt MM, Jankowska KA Tags: J Appl Genet Source Type: research

Genomic prediction ability for beef fatty acid profile in Nelore cattle using different pseudo-phenotypes.
Abstract 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 (0.58), another with low heritability (0.13). Ten replicates were performed for each trait...
Source: J Appl Genet - September 24, 2018 Category: Genetics & Stem Cells Authors: Chiaia HLJ, Peripolli E, de Oliveira Silva RM, Feitosa FLB, de Lemos MVA, Berton MP, Olivieri BF, Espigolan R, Tonussi RL, Gordo DGM, de Albuquerque LG, de Oliveira HN, Ferrinho AM, Mueller LF, Kluska S, Tonhati H, Pereira ASC, Aguilar I, Baldi F Tags: J Appl Genet Source Type: research

Identification novel LQT syndrome-associated variants in Polish population and genotype-phenotype correlations in eight families.
We report three novel variants (KCNQ1 p.46, KCNH2 p.D803Y, SCN5A p.G1391R) which have never been reported for this AA location in LQTS; the phenotype-genotype correlation suggests their pathogenicity. PMID: 30244407 [PubMed - as supplied by publisher] (Source: J Appl Genet)
Source: J Appl Genet - September 22, 2018 Category: Genetics & Stem Cells Authors: Szperl M, Kozicka U, Kosiec A, Kukla P, Roszczynko M, Biernacka EK Tags: J Appl Genet Source Type: research

Reference gene validation for normalization of RT-qPCR assay associated with germination and survival of rice under hypoxic condition.
Abstract 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 r...
Source: J Appl Genet - September 20, 2018 Category: Genetics & Stem Cells Authors: Kumar D, Das PK, Sarmah BK Tags: J Appl Genet Source Type: research

Do GWAS and studies of heterozygotes for NPC1 and/or NPC2 explain why NPC disease cases are so rare?
Abstract 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. PMID: 30209687 [PubMed - as supplied by publisher] (Source: J Appl Genet)
Source: J Appl Genet - September 13, 2018 Category: Genetics & Stem Cells Authors: Erickson RP Tags: J Appl Genet Source Type: research

Myofibrillar myopathy in the genomic context.
Abstract 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 identifica...
Source: J Appl Genet - September 10, 2018 Category: Genetics & Stem Cells Authors: Fichna JP, Maruszak A, Żekanowski C Tags: J Appl Genet Source Type: research

The influence of Al3+ on DNA methylation and sequence changes in the triticale ( × Triticosecale Wittmack) genome.
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. The direction of methylation change was dependent on phenotype and organ. Al treatment increased the level of global DNA methylation in roots of T lines by approximately 0.6%, whereas dem...
Source: J Appl Genet - August 30, 2018 Category: Genetics & Stem Cells Authors: Agnieszka N Tags: J Appl Genet Source Type: research

Elevated expression of p53 in early colon polyps in a pig model of human familial adenomatous polyposis.
Abstract 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. We analysed groups of pigs carrying a truncating mutation in APC (APC1...
Source: J Appl Genet - August 25, 2018 Category: Genetics & Stem Cells Authors: Sikorska A, Flisikowska T, Stachowiak M, Kind A, Schnieke A, Flisikowski K, Switonski M Tags: J Appl Genet Source Type: research

Correction to: Novel 1q22-q23.1 duplication in a patient with lambdoid and metopic craniosynostosis, muscular hypotonia, and psychomotor retardation.
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 " PMID: 30145696 [PubMed - as supplied by publisher] (Source: J Appl Genet)
Source: J Appl Genet - August 25, 2018 Category: Genetics & Stem Cells Authors: Sowińska-Seidler A, Olech EM, Socha M, Larysz D, Jamsheer A Tags: J Appl Genet Source Type: research

hTERT promoter methylation status in peripheral blood leukocytes as a molecular marker of head and neck cancer progression.
Abstract 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. The aim of this study was to analyze the hTERT gene pr...
Source: J Appl Genet - August 7, 2018 Category: Genetics & Stem Cells Authors: Sobecka A, Blaszczak W, Barczak W, Golusinski P, Rubis B, Masternak MM, Suchorska WM, Golusinski W Tags: J Appl Genet Source Type: research

Disease not genetic but infectious: multiple tuberculomas and fibrinous pericarditis as symptoms pathognomonic for tuberculosis of Frederic Chopin.
Abstract 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 int...
Source: J Appl Genet - July 25, 2018 Category: Genetics & Stem Cells Authors: Witt M, Szklener A, Marchwica W, Dobosz T Tags: J Appl Genet Source Type: research

Identification and expression of genes in response to cassava bacterial blight infection.
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. Among all identified QTL, CBB14_10dai_1, CBB14_10dai_2, and CBB14_12dai showed the most significant (P 
Source: J Appl Genet - July 23, 2018 Category: Genetics & Stem Cells Authors: Tappiban P, Sraphet S, Srisawad N, Smith DR, Triwitayakorn K Tags: J Appl Genet Source Type: research

An EMS-induced new sequence variant, TEMS5032, in the coding region of SRS3 gene leads to shorter grain length in rice (Oryza sativa L.).
Abstract 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. Further, the mutation was found to affect 1...
Source: J Appl Genet - July 17, 2018 Category: Genetics & Stem Cells Authors: Ngangkham U, Nath M, Dokku P, Amitha Mithra SV, Ramamurthy S, Singh NK, Sharma RP, Mohapatra T Tags: J Appl Genet Source Type: research

Transcriptome analysis reveals candidate genes involved in splay leg syndrome in piglets.
Abstract 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. A total of 555 diff...
Source: J Appl Genet - July 6, 2018 Category: Genetics & Stem Cells Authors: Wu T, Zhang X, Tian M, Tao Q, Zhang L, Ding Y, Zhang X, Yin Z Tags: J Appl Genet Source Type: research

Population analysis of Magnaporthe oryzae by using endogenous repetitive DNA sequences and mating-type alleles in different districts of Karnataka, India.
Abstract 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. Among 72 isolates, 44 isolates belonged to MAT1 type (male...
Source: J Appl Genet - July 3, 2018 Category: Genetics & Stem Cells Authors: Jagadeesh D, Prasanna Kumar MK, Devaki NS Tags: J Appl Genet Source Type: research