Research Article

Table of Contents | Genet. Mol. Res. 2017 (4)

Displaying 1 - 15 of 50
Research Article

Chinese chive (Allium tuberosum Rottler ex Spr.) is an important vegetable crop. However, genetic and breeding studies of the species have been restricted by the lack of simple sequence repeat markers (SSRs). In the present study, a total of 2553 Chinese chive SSRs were developed from the species’ transcriptome, with 626, 643, and 536 of the makers located in coding sequences, 5' untranslated regions and 3' untranslated region, respectively. The annotation of SSR-containing expressed sequence tags revealed that the transcripts were enriched for several Gene Ontology (GO) categories, including ‘protein binding’, ‘regulation of transcription’, and ‘integral to membrane’. Among the 2,553 SSRs, di- and tri-nucleotide repeat motifs were the most abundant (52.3 and 45.6%, respectively), and AC/GT and GAA/TTC were the most frequent di- and tri-nucleotide motifs, respectively. PCR amplification, using 100 SSR primer pairs, revealed that 94% of the markers were of good quality and that 83-88 of the makers could be amplified in six other Allium species. This suggests that the markers had high cross-species transferability. The substantial number of SSRs developed will provide a valuable resource for future genetic and breeding studies in Chinese chive

Genet. Mol. Res. 16(4): gmr16039861
DOI: 10.4238/gmr16039861
Research Article

The yellow-throated marten (Martes flavigula Boddaert 1785) is a medium-sized carnivore and a top predator in South Korea that is distributed throughout Western and Southeast Asia and Siberia in a wide range of habitats. In this study, we developed a panel of polymorphic microsatellite markers for M. flavigula by Illumina next-generation sequencing for investigation of population genetics. A total of 887 candidate microsatellite markers were identified and characterized from genomic sequences. By testing the markers in three individuals, we found 73 satisfactory microsatellite loci consisting of tri- or tetranucleotide repeats. We designed four multiplex panels of 33 microsatellite loci and applied them to 35 individuals from South Korea. The number of alleles and polymorphism information content per locus varied from 2 to 9 and from 0.164 to 0.841, respectively. The observed and expected heterozygosity per locus ranged from 0.143 (MF233) to 0.800 (MF339) and from 0.183 (MF233) to 0.871 (MF327) respectively. Nine of the 33 loci deviated significantly from Hardy-Weinberg equilibrium. We also found that at least 10 of the loci were transferrable to two other species of Mustelidae (Meles and Mustela sibirica). These markers can be applied to studies of genetic variation and population structure and can be useful for ex situ conservation and ecological monitoring by non-invasive sampling of M. flavigula populations.

Genet. Mol. Res. 16(4): gmr16039854
DOI: 10.4238/gmr16039854
Research Article
Authors:

It was considered processes transmutation of genome mechanism from the point of view of thermodynamics, biophysics, and biochemistry. Just it was explained mechanisms maintenance stability Internal Energy of Stationary State an able-bodied organism according first law of thermodynamics. Besides it was considered some negative influences on an organism of solar radiation causing germination viruses. Hence it was described mechanisms normal development of an organism reflecting activity of cellular genomes via generating cellular divisions. The links between genomic mechanisms and mechanisms maintenance stability Internal Energy of an organism and cells of an organism exert activity stem cells which induce cells types division in healthy tissues. The local violation these links due to viral affection causes local tissue transitions normal genomic cycle into genomic cycle of benign neoplasm, i.e., the transition of genomic link due to viral affection of cellular genomic link leading to forming benign neoplasm. The mechanism of these transformations in cellular genome was described from point of views of thermodynamics, biophysics, and biochemistry. Also, it was elucidated the cause that genomic mechanism of benign neoplasm don’t break Stationary State of an organism. Furthermore, it was described the viral affecting genomic link of cells in benign neoplasm causing mechanism transmutation benign neoplasm into cancer with forming Warburg effect mechanism. The forming cancer metabolism creates Quasi-Stationary State of cancer disease organism

Genet. Mol. Res. 16(4): gmr16039860
DOI: 10.4238/gmr16039860
Research Article

Clinical mastitis cows normally produce clotted milk, thus the much higher somatic cells in milk are unable to be counted by routine FOSS machine. The proteins coded by CD4 and LAG-3 genes can bind to MHC class II molecules and play important roles in in-flammatory diseases. The present study was designed to investigate the effects of single nucleotide polymorphisms (SNPs) in bovine CD4 and LAG-3 genes on the somatic cell counts (SCCs) of clinical mastitis Holstein cows. For the first time, we detected SCCs in the clinical mastitis cows’ milk by Newman’s staining combined with microscope assays. Our association results showed that two novel SNPs (T104010752C and C104028410T) identified in bovine CD4 and LAG-3 genes respectively were significantly associated with SCCs of clinical mastitis cows (P<0.05). In addition, the combined genotypic effect of both the SNPs was also significant on SCCs (P<0.05). The results imply that the novel SNPs in CD4 and LAG-3 genes could be significant candidate markers against Clinical mastitis in Holstein cattle.

Genet. Mol. Res. 16(4): gmr16039859
DOI: 10.4238/gmr16039859
Research Article
Authors:

In this study, we detected the morphological variation of
91 Perilla accessions from Northern and Southern China by the
measurement of 7 quantitative and 10 qualitative characters. The
accessions of cultivated var. frutescens were significantly different from
accessions of weedy var. frutescens and cultivated and weedy types of
var. crispa in 7 quantitative traits such as plant height (QN1), internodes
(QN2), the number of branches (QN3 and QN4), length of the largest
inflorescence (QN5), the number of florets (QN6) and flowering time
(QN7) etc. In addition, significant differences were found between
accessions of cultivated var. frutescens from northern and southern areas
of China for 7 quantitative traits. However, there were no significant
differences between accessions of cultivated and weedy types of var.
crispa. In principal components analysis (PCAs), 5 quantitative traits and
4 qualitative characters contributed in the positive direction on the first
axis. 2 quantitative and 6 qualitative characters contributed in the
negative direction on the first axis. The accessions of cultivated and
weedy types of var. crispa were clearly separated from accessions of
cultivated and weedy types of var. frutescens in the PCAs. In addition,
most accessions of cultivated var. frutescens from Northern China were
discriminated from accessions of cultivated and weedy types of var.
frutescens from Southern China. These findings in this study will assist
to better understand the morphological variation for two cultivated types
of Perilla crop and their weedy types according to the geographical
distribution in northern and southern areas of China. 

Genet. Mol. Res. 16(4): gmr16039853
DOI: 10.4238/gmr16039853
Research Article

Anopheles darlingi is the most anthropophilic mosquito related to Plasmodium infection
of malaria, causing significant morbidity and mortality in South America. Pyrethroid chemical has been
used to control mosquitos. We analyzed the expression of trypsin-3 and phosrestin II genes implicated
to feeding and resistance to insecticides, immune response and sensory antenna mechanisms,
respectively, of larvae and adult of A. darlingi, through quantitative reverse transcription polymerase
chain reaction (qRT-PCR). We aimed to validate the similarity in nucleotide sequences of A. darlingi
RNA sequencing libraries by in silico, and qRT- PCR, owing to their possible effects on the ability to
spread disease. The expression of trypsin-3 and phosrestin II was higher in the first and second instar
larvae as compared with that in adults. These differentially expressed trypsin-3 and phosrestin II genes
do not provide us evidence that both genes participate in pyrethroid resistance. The signaling pathway
involving both genes requires further study. Preliminary phylogenetic relationships and the
accumulation of mutations analysis in both genes were also compared with trypsin and phosrestin
sequences of 15 and 17 other anopheline species, respectively, to obtain a mutational rate of 0.02 on
phylogenetic trees. Trypsin gene of A. darlingi and A. albimanus clustered into the same group and was
distinct from the species of A. gambiae complex and other anopheline. For phosrestin II, A. darlingi 
was separated from the remaining species from Africa, Asia, and Europe. Although the groups showed
low to moderate support, it is possible to infer that both genes may belong to two evolutionary groups:
one presents in the anopheline species of New World and other in the anopheline species of Old World,
and be useful for future studies.

Genet. Mol. Res. 16(4): gmr16039852
DOI: 10.4238/gmr16039852
Research Article

The hemoglobinopathies are a group of hereditary alterations prevalent in
many parts of the world, but significantly affect the Brazilian population for its abundant
miscegenation. These alterations in structural genes that cause the formation of hemoglobin
variants, and/or regulatory genes, causing thalassemias. Currently, the number of identified
abnormal hemoglobin has increased due to improvement in methods of analysis, however,
many routine laboratories are not prepared for the correct identification of these changes. In
the present study aimed to assess the prevalence of hemoglobinopathies by classical
methods and perform the molecular characterization of mutations S, C, beta thalassemia
IVS-110, IVS-1, IVS-6 and CD-39 by gene amplification using the PCR technique – AE.
The molecular study used specific primers that bind promptly at the position of the mutated
allele in position and the normal allele, and thus can perform gene allele specific
amplification. We collected 200 samples of peripheral blood of patients in clinical
laboratories at PUC-Goiás from July/2012 to December 2012. We observed two patients
(1%) AC one (0.5%) AS, two (1%) with IVS-6 mutation and one (0.5%) IVS-6. The codon
39 and IVS-110 were not detected in any of the investigated patients. We concluded that our
molecular methodology in the characterization of hemoglobin mutations is useful and it can
be used to identify hemoglobinopathies. 

Genet. Mol. Res. 16(4): gmr16039851
DOI: 10.4238/gmr16039851
Research Article

Tunisia is one of the most important olive growing
countries in the Mediterranean basin and it is classified in fourth rank on
world scale in terms of olive oil production. Since the emergence of the
modern oliviculture, the identification, the evaluation and conservation
of the local genetic resources have been considered as a priority in
countries like Tunisia. Molecular studies for genetic characterization
allowed to enhance knowledge about the autochtonous olive germplasm,
but currently it lacks a systematic and extensive work to compare and
validate Tunisian olive varieties. This work focused on the molecular
characterization and identification of 21 olive accessions grown mainly
in the South East of Tunisia using a set of 16 microsatellite molecular
markers. An extent of authentication process was also carried out by
comparison with molecular profiles from Tunisian cultivars already
characterized from official collections obtained from a set of 12
commonly shared macrosatellite markers by different authors.
Population structure analysis of the Tunisian olive germplasm was also
conducted using structure software. The results highlighted that no
correlation between geographical and genetic origin occurred. New
alleles were individuated, and two new genotypes were characterized
contributing to enhance the Tunisian germplasm biodiversity. This work
allowed individuating a few olive accessions that should be considered
as reference cultivar in the authentication process and contributed to
clarify the genetic pattern of the Tunisian germplasm. 

Genet. Mol. Res. 16(4): gmr16039850
DOI: 10.4238/gmr16039850
Research Article

X-Fragile Syndrome (FXS) is the most common cause of inherited
intellectual disability and the second of genetic origin, with an estimated prevalence of
1/4000 men and 1/6000 women. The etiology is associated with a trinucleotide expansion of
CGG sequences and hypermethylation of the promoter region of the FMR1 (Fragile-X
Mental Retardation-1) gene, located in the Xq27.3 region. Symptoms occur due to lack of
Fragile X Mental Retardation Protein (FMRP), essential for dendrites growth and synaptic
function. This syndrome is commonly underdiagnosed in children and adolescents due to
the high phenotypic variability of patients and the need for a complex and high cost
laboratory diagnosis. This research aims to evaluate individuals referred by the public health
system of Goiás presenting intellectual deficiency suggestive of FXS and submitted to
molecular diagnosis by PCR. Thirty-one patients, ranging in age from 4 to 41 years, were
analyzed. It was possible to detect molecular alterations in the FMR1 gene in 6 patients with
complete mutations, consistent with the observed phenotypes. The use of molecular
techniques associated with capillary electrophoresis in an automatic genetic analyser
demonstrated rapid and efficient investigation of CGG repeats in the FMR1 gene. Its
inclusion in the public health service, in addition to universalizing access to genetic tests in
Brazil, bridging the gap between effective diagnosis and the technologies available until
now, has supported families in clarifying the etiology and assessing the risk of recurrence
through genetic counselling. 

Genet. Mol. Res. 16(4): gmr16039848
DOI: 10.4238/gmr16039848
Research Article

The aim of this study was to analyze the effects of high temperatures on ear fertility, yield components and protein content of wheat cultivars. Therefore, 96 genotypes were subjected to two environments in a greenhouse: control and heat stress. Each environment had two replicates, totalling 192 plots. The evaluations were: number of ear per plant, number of ear per pot, ear weight, number of grains per ear, number of sterile spikelet’s, number of viable grains, grain weight and protein content. Principal component analysis (PCA) and genetic and phenotypic correlations were performed. The results showed a significant drop in productivity of the genotypes subjected to heat stress as well as significant increase in the number of sterile spikelet’s. The PCA allowed the selection of nine promising genotypes for cultivation in environments with high temperatures with basis on these traits, especially the cultivars CD 104, CD 122 and TBIO Itaipu.

Genet. Mol. Res. 16(4): gmr16039847
DOI: 10.4238/gmr16039847
Research Article

MicroRNAs (miRNAs) are non-coding small RNA molecules that regulate the differential expression of genes. The expression of miRNAs is dysregulated in various types of cancers,
including Gastric Cancer (GC), and has both prognostic and diagnostic potential. To interpret the role of miRNA expression in GC, we evaluated the expression profile using high-throughput miRNA array followed by in-depth systems biological analyses. Total RNA was isolated from 34 GC patients and 15 normal controls and hybridised and differentially expressed miRNAs in GC compared to normal controls were analysed. A total of 250 miRNAs were found to be differentially expressed in GC with a fold change ranging from + 2.5984 to – 3.5271 compared to normal gastric tissues. The differentially expressed miRNAs were further subjected to Ingenuity Pathway Analysis to understand the modulation of cellular and molecular functions and associated physiological system development and functions in GC. The Oncomirs such as miR-155-5p, miR-17-5p, miR-21-5p, miR-23a-3p, miR-24-3p, and miR-320b were significantly (P<0.05) upregulated and all the other miRNAs, mostly tumor suppressors, were significantly downregulated (P<0.05) leading to the reduction in cell death and the induction of gastric cancer, cellular growth and proliferation, cellular movement, cellular assembly and organization, DNA replication, recombination and repair, organismal injury and abnormalities and metastasis of tumor in GC compared to normal tissues. The high-throughput miRNA microarray coupled with systems biological analyses showed that miRNAs are  ysregulated in GC, causing the initiation, progression, and metastasis of GC. In conclusion, the novel GC-inducing miRNA signatures decrypted in our study can further be exploited for precision medicine in clinics.

Genet. Mol. Res. 16(4): gmr16039845
DOI: 10.4238/gmr16039845
Research Article

When a low activity of acid α-glucosidase (GAA) is
found, particularly in newborn screening programs, to differentiate α-
glucosidase pseudo deficiency from true Pompe disease is important and
urgent, as the result generates parental stress and also because this
differentiation drives decisions related to the management of the case.
Here, we report a case of GAA pseudo deficiency detected in a newborn
screening performed by a private laboratory in Brazil. The confirmatory
laboratory investigation performed at our service showed reduction of
GAA activity on the dried blood spot, with inconclusive results when
GAA activity was assayed in leukocytes. Genotyping of the GAA gene
with next-generation sequencing revealed the common pathogenic
mutation c.-32-13T>G and the “pseudo deficiency allele” p.
[Gly576Ser; Glu689Lys], each one in heterozygous state and in trans.
This report illustrates the need of newborn screening programs to have
the adequate support to perform a comprehensive investigation
whenever an abnormality is found in the initial screening test.

Genet. Mol. Res. 16(4): gmr16039844
DOI: 10.4238/gmr16039844
Research Article

The objective of the current study was to evaluate single
nucleotide polymorphisms (SNP) for potential growth and carcass trait
associations located in two previously described quantitative trait loci
(QTL) regions associated with bovine respiratory disease. A population
of 323 crossbred steers sired by five purebred sire breeds between 2010-
2013 (Angus, Braford, Braunvieh, Charolais, and Simmental) were
evaluated from birth until harvest. Eighty-two SNP were evaluated in
the current study for potential significant associations with growth and
carcass traits (58 on BTA6 and 24 on BTA20). A total of nine unique
SNP (rs41595713, rs42403565, rs42571566, rs42900130, rs41931108,
rs42480445, rs43451134, rs42524450, rs41626155) were significantly
associated (P < 0.05) with specific growth traits such as birth weight,
weaning weight and hip height. Six of these significant SNP were
located on BTA6 and three were located on BTA20. When evaluating
the carcass traits hot carcass weight (HCW), yield grade (YG), marbling
score (MARB), and rib eye area (REA) a total of nine unique SNP
(rs42900130, rs42961882, rs43446022, rs41931108, rs41595713,
rs41653357, rs43036576, rs42823614, rs42512588) were significantly
associated (P < 0.05) with carcass traits. For both of these regions,
animals inheriting differing genotypes from the previously described
SNP, had significantly different levels of performance for specific 
 
growth and carcass traits. Although multiple SNP were identified as
significant with growth and carcass traits, these SNP identified herein
must be validated in a larger more diverse population prior to
implementation into marker assisted selection programs.

Genet. Mol. Res. 16(4): gmr16039843
DOI: 10.4238/gmr16039843
Research Article

Oral cancer incidence is higher in individuals between
the fifth and seventh decades of life, but some studies indicate a
decreasing age trend. From the epidemiological point of view,
alcohol consumption is associated with the emergence of oral cancer
by interfering with mechanisms of DNA synthesis and repair. From
a genetic standpoint, variant alleles in genes encoding the enzymes
of alcohol (CYP2E1 and ADH) and acetaldehyde (ALDH2)
metabolism may play an important role in the genesis of oral cancer.
This study aimed to assess the relation of polymorphisms ADH1B
(rs1229984 and rs2066702), ADH1C (rs698), ALDH2 (rs671) and
CYP2E1 96bp insertion and the risk of squamous cell carcinoma of
the mouth floor, as well as its clinicopathological and prognostic
characteristics in relation to alcohol consumption. Our sample group
was made of 301 patients, with 159 controls without a previous
history of cancer and 142 patients with oral cancer. Genomic DNA
was extracted from peripheral blood samples and genotypes were
determined by PCR-RFLP. Our results suggest that the presence of
ALDH2 Lys504 allele and 96bp insertion CYP2E1 were
significantly associated with oral cancer risk. ADH1C gene Ile350
allele was associated with the presence of positive lymph nodes, and
lymphatic invasion was related to the presence of polymorphic
alleles ADH1B*1, ADH1C Ile350 and ALDH2 Lys504. In
conclusion, these results reveal potential markers of oral cancer risk
and behavior. 

Genet. Mol. Res. 16(4): gmr16039829
DOI: 10.4238/gmr16039829
Research Article

A targeted next generation sequencing (NGS) approach analysing contemporaneously 20 different genes mainly involved in craniosynostosis was adopted to molecularly diagnose the family of a 2-years old girl affected by Saethre–Chotzen syndrome, a syndromic form of craniosynostosis. The identified pathogenic variant in the TWIST1 gene lies in a conserved residue (Arg118) that shifts from a positively charged amino acid to a non-polar amino acid and segregates in all the examined affected familial members, although with variable phenotypic expression. An accurate molecular diagnosis is of obvious value for the clinical management of individuals with isolated or syndromic craniosynostosis to define their medical needs, the recurrence risk and allow the identification of available therapeutic opportunity. Given the high number of associated genes, an NGS approach is the election choice to increase the yield of genetic diagnosis, leading to an expansion of the genotypic and phenotypic spectrum of these rare syndromes

Genet. Mol. Res. 16(4): gmr16039828
DOI: 10.4238/gmr16039828

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