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Table of contents: 2018

Research Article

Rheumatoid arthritis (RA) is an autoimmune disease with increasing activity of T lymphocytes and abnormal production of inflammatory cytokines. Interleukin-27 (IL-27), a multifunction cytokine with contradictory inflammatory effect. Polymorphism of IL-27 was reported to be predisposed to many inflammatory diseases and autoimmune diseases. We aimed to assess the role of IL-27 polymorphism in the predisposition of RA in Egyptian population. A case control study included 100 patients with RA and 100 healthy subjects represented the control group. The IL-27−924A/G gene polymorphism was investigated by RFLP-PCR. The serum level of IL-27was estimated by enzyme-linked immunosorbent assay. The AA genotype was significantly higher in patients with rheumatoid arthritis as compared with the control group (P=0.02, OR (95% CI)=0.4 (0.1-1.2). In addition, we observed significant elevation in the level of serum IL-27 in the patients group in comparison with the healthy subjects. We found that patients with AA genotype or A allele had significant higher level of serum IL-27. There was positive relationship between the serum level of IL-27 and severity of the disease. It was concluded that AA genotype of IL-27 gene might be a risk factor for the incidence of RA in Egyptian population. Patient with significantly higher blood levels of IL-27 were at risk for increasing disease activity.

Genet. Mol. Res. 17(2): gmr16039915
DOI: 10.4238/gmr16039915
Research Article

Twenty-three polymorphic microsatellite loci were developed from the black rockfish, Sebastes schlegelii, with an enriched partial genomic library by magnetic beads and polymorphism of these loci was assessed in 32 individuals from a wild population. The loci yielded 2-19 alleles per locus, the observed, expected heterozygosity and polymorphic information content ranged from 0.063 to 1.000, 0.091 to 0.945 and 0.085 to 0.926, respectively. Twenty loci confirmed to Hardy-Weinberg equilibrium and only one pairs of loci show significant linkage disequilibrium after Bonferroni’s correction. The availability of these markers will facilitate studies of the conservation genetics of S. schlegelii.

Genet. Mol. Res. 17(2): gmr16039912
DOI: 10.4238/gmr16039912
Research Article

The purpose of this research was to select the development of superior genotypes of snap beans adapted to edaphoclimatic conditions of the North and Northwest of Rio de Janeiro State, Brazil, applying the mixed model methodology. The test was installed and carried out in the experimental area of the Instituto Federal Fluminense (IFF), located in the municipality of Bom Jesus do Itabapoana, Rio de Janeiro State, Brazil, using the modified SSD (Single Seed Descent) method. The experiment was of randomized block design with three replications. We evaluated weight of pod per plant and number of pod per plant in ten progenies from the snap bean breeding program of the Universidade Estadual do Norte Fluminense (UENF); individual plants were assessed in each plot and in each replication (block). All progenies had mean productivity superior to 1 kg of pod per plant and 144 pods per plant. The 7 and 2 progenies, which came from the crossings between (UENF 7-5-1) L6 × L20 (UENF 14-3-3) and (UENF 7-5-1) L6 × L13 (UENF 7-20-1), stood out from the others, as they led to a higher predicted additive gain for the two evaluated traits. We concluded that the selection for production of snap beans and grains applying BLUP enabled the prediction and achievement of significant genetic gains for breeding snap beans for subsequent generations

Genet. Mol. Res. 17(2): gmr16039914
DOI: 10.4238/gmr16039914
Research Article

Scientometrics is a quantitative evaluation of scientific and technological activities. The main objective is to point the number of methodologies used in scientific studies or even the structure of several research centers. This type of metric study belongs to the area of sociology of scientific knowledge. It covers quantitative analyzes of scientific activities through the use of mathematical and statistical techniques for the development of the study. A literature review was conducted using the Genetics and Molecular Research (GMR) database. GMR is a fully electronic journal available at no cost to readers through the Internet at http://www.geneticsmr.org. We performed a quantitative analysis regarding genetic polymorphisms on the GMR scientific production between 2009 and 2013. We used the keywords polymorphism AND genetics OR molecular marker in order to conduct the literature survey. We found 423 articles related to genetic polymorphism and 87% were original articles. Six countries account for about 89% of publications and China is responsible for 56% of all publications. Moreover, the number of papers grew each year, from 3.8% in 2009 up to 35.5% in 2013. The organisms most studied in those articles were humans (61.2%). Techniques such as sequencing, RFLP (Restriction Fragment Length Polymorphism), SSCP (single-strand conformational polymorphism), RAPD (random amplified polymorfic DNA) and Multiplex were used, and these methods and their validation are efficient in the study of gene polymorphisms. Moreover, polymerase chain reaction (PCR) is the technique most used in the field of genetic polymorphisms (74%).

Genet. Mol. Res. 17(2): gmr16039913
DOI: 10.4238/gmr16039913
Research Article

Sesame (Sesamum indicum L.), a member of the Pedaliaceae family, is one of the oldest oilseed crops. For its high oil content, it is known as the “queen of oilseeds”. MicroRNAs (miRNAs) represent a class of endogenous non-coding small RNAs that play important roles in multiple biological processes by degrading targeted mRNAs or repressing mRNA translation. Thousands of miRNAs have been identified in many plant species by computational methods, whereas there is no report of miRNAs in S. indicum till date. In present study, previously known plant miRNAs were BLASTed against the Expressed Sequence Tag (EST) database of Sesame genes. The aligned miRNA hits were further aligned to protein database and BLASTX was carried out to remove protein coding primary miRNAs. The non-coding precursor miRNAs were subjected to online MFold server in order to predict their secondary structures. After applying the filtering criteria, a total of 12 potential miRNAs belonging to 6 miRNAs families were detected. 203 unique miRNAs: target pairs were predicted online by psRNATarget web server. Most of the targets were found to encode transcription factors or enzymes that participate in the regulation of development, growth, metabolism, and other physiological processes and stress response.

Genet. Mol. Res. 17(2): gmr16039911
DOI: 10.4238/gmr16039911
Research Article

Marine sponges harbor diverse bacterial communities. Sponge associated bacteria produce potential secondary metabolites of medical use. Little is known about sponge associated diversity from red sea therefore, we have collected two sponge samples i.e., Pione vastifica and Siphonochalinna siphonella collected from north of red sea in Obhur region, Jeddah Saudi Arabia. By using culture dependent method, we have isolated 95 different bacterial species from two marine sponge samples. These marine bacteria were screened for their antagonistic potential against fungal pathogens (Phytophthora capsici and Pythium ultimum) and human pathogenic bacteria (E. coli, Methicillin-resistant Staphylococcus aureus, E. faecalis, and P. aeroginosa). Among all 37 (39%) marine bacteria showed inhibition against oomycetes, only 27 (28.4%) exhibited antibacterial activity while 19 (20%) exhibited both antifungal and antibacterial activities. These bacterial strains were further screened for enzyme production (cellulase, protease, lipase, and amylase). Most of the strains were positive for production of lipase enzyme. These antimicrobial activities and enzyme production suggest their role in marine sponge as protecting against different marine pathogens. Taxonomic and phylogenetic analyses on the basis of 16S rRNA gene sequences showed that dominant phylum was γ-Proteobacteria. Our results highlighted that marine sponges are potential source of marine bacteria producing antimicrobial metabolites and enzymes of pharmaceutical and industrial significance.

Genet. Mol. Res. 17(2): gmr16039910
DOI: 10.4238/gmr16039910
Research Article

Honey bees (Apis mellifera) are exposed to sublethal doses of insecticides, but little is known about insecticide effects on their survivorship associated to health-related gene expression. To test the effect of sublethal doses of clothianidin, imidacloprid and carbaryl on the lifespan and health of honey bees, workers were orally and topically exposed to LD5 doses of these insecticides. The survivorship of treated bees was monitored and the expression of three immune-related genes, hymenoptaecin (AmHym), basket (AmBask) and lysozyme (AmLyso2) was analyzed at 24 and 72 hours post treatment (hpt), as well as that of the antioxidant-related gene vitellogenin (AmVit2), the poly-U binding factor (AmPuf68), and the detoxification gene cytochrome P450 (AmCYP9Q3). The three insecticides significantly reduced the length of life of bees but the mode of application did not affect survivorship. AmHym, AmBask and AmVit2 expression was significantly down-regulated at 72 hpt in bees treated with clothianidin and imidacloprid, indicating immunosuppression. However, AmLyso2, AmCYP9Q3 and AmPuf68 were significantly up-regulated. The down-regulation of AmVit2 could have caused decreased resistance to oxidative stress. AmPuf68 expression could be associated with increased protection against xenobionts. AmCYP9Q3 was up-regulated at 24 and 72 hpt in oral exposures, but only until 72 hpt in topical exposures, indicating faster sensitivity towards detoxification mechanisms in oral treatments. This study demonstrated detrimental effects of sublethal doses of clothianidin, imidacloprid and carbaryl on honey bee survivorship, immunity and antioxidant mechanisms, and an induction of defense and detoxification responses that could be physiologically costly to the bees.

Genet. Mol. Res. 17(2): gmr16039908
DOI: 10.4238/gmr16039908
Research Article

Bacillus licheniformis M2-7 is a heat-resistant bacterium able to biotransform polycyclic aromatic hydrocarbons. It can transform a wide range of these compounds as naphthalene, phenanthrene, pyrene and benzo[a]pyrene. Benzo[a]pyrene is a polycyclic aromatic hydrocarbon of high molecular weight considered as potentially toxic and carcinogenic for humans. Aiming to discover the genes involved in the biotransformation of benzo[a]pyrene, we made a B. licheniformis M2-7 genomic library in E. coli. We isolated two E. coli strains that were able to grow in minimal salt medium supplemented with benzo[a]pyrene. From the analysis of the DNA fragments in the clones H23 and H38, we identified open reading frames coding for 5 possible genes, among them pobA and fabHB, which products are the enzymes 4-hydroxybenzoate 3-monooxygenase and the ketoacyl-ACP synthase III, respectively. To evaluate the role of these genes in the metabolism of benzo[a]pyrene in B. licheniformis M2-7, we estimated their relative expression through reverse transcription quantitative PCR. Finally, we observed that the genes pobA and fabHB were overexpressed after 3 h under induction with benzo[a]pyrene, suggesting that this strain could use these genes during the metabolism of this PAH, plus it does it in a faster time than that reported for other bacterial genera

Genet. Mol. Res. 17(2): gmr16039916
DOI: 10.4238/gmr16039916
Research Article

Genome wide association studies are performed to narrow down or, better still, pinpoint the region or genes involved in the regulation of a known phenotype. The data concerning litter size usually comes from a restrict number of individuals due to the laborious and costly nature of the phenotyping by lambing data of several breeding seasons. Genome-wide association was performed in a population in which segregates a major gene determinant of prolificacy in sheep. This is the allele of the GDF9 SNP called Vacaria: c943C> T, detected in Ile de France flocks in Southern Brazil. The Vacaria genotype and phenotype data did agree with the GDF9 sheep chromosome 5 regions from genomic analyses. OAR5_45481559, a marker located within the GDF9 gene (chr5: 41,841,919 bp), had nominal p-value significance but did not reach Bonferroni-corrected significance levels. However, other chromosome 5 SNP markers (s17197, s48166, s25202, and OAR5_47774570), located at chr5: 43,415,384 - 43,708,878 bp, did show nominal and Bonferroni p-value significances. These first three markers showed to be in linkage disequilibrium with OAR5_45481559, thus confirming Plink and Emmax (Genome-Wide Association Studies (GWAS) packages) abilities of locating the correct genomic region associated to phenotypes. These results are indicative that GWAS is a useful method for searching candidate genes in prolific animals, since the linkage disequilibrium is verified in a range of 2 Mbp

Genet. Mol. Res. 17(2): gmr16039909
DOI: 10.4238/gmr16039909
Research Article

The Helicoverpa armigera (Hübner) is a recent pest in Brazil, causing losses in tomato production in the Espírito Santo and Goiás states, in Brazil. A promising alternative to control this insect pest is the development of resistent tomato varieties. The breeding programs have aimed to introduce alleles of resistance present in the wild tomato accessions in the cultivated tomato. Thus, the objective of this study was to identify resistance to in tomato genotypes with high zingiberene leaf contents in the segregating population (F2) from the first backcross to Solanum lycopersicum 'Redenção' from S. habrochaites var. hirsutum accession 'PI-127826'. For this, the glandular trichomes present in the leaves of the selected genotypes were quantified and submitted to two antixenosis and one antibiosis test of resistance to H. armigera. The genotypes 'RVTZ-2011-pl#117', 'RVTZ-2011-pl#185', 'RVTZ-2011-pl#335', and 'RVTZ-2011-pl#503' showed a high density of type IV and type VI glandular trichomes. These genotypes showed higher resistance levels to H. armigera by antixenosis and antibiosis than the Redenção variety. The indirect selection for high zingiberene content and high density of type IV and type VI trichomes was effective to obtain tomato genotypes with higher levels of resistance to H. armigera

Genet. Mol. Res. 17(2): gmr16039907
DOI: 10.4238/gmr16039907
Research Article

Purpose: To investigate the effect of resuscitation with acetated Ringer's solution during hemorrhagic shock (HS) on inflammatory factors and nuclear factor κB (NF-κB) signaling pathway in liver tissue. Methods: In this study, a rat HS model was established. HS rats received acetated Ringer's solution, lactated Ringer's solution and saline for fluid resuscitation. Inflammatory factors (TNF-α, IL-4 and IL-10) for the evaluation of three kinds of resuscitation mfluid anti-inflammatory effect. Expression of proteins in NF-κB pathway was evaluated to elucidate the mechanism of acetated Ringer's solution in preventing HS-induced liver injury. Results: Although HS upregulated inflammatory response in liver tissue, acetated Ringer's solution t-treatment can inhibit the inflammation and improve liver injury. We also found that acetated ringer’s solution treatment attenuated HS-induced liver injury in NF-κB pathway. Conclusion: Acetated Ringer's solution may improve HS-induced liver injury. The mechanism of its action may be by inhibiting the NF-κB pathway.

Genet. Mol. Res. 17(2): gmr16039906
DOI: 10.4238/gmr16039906
Research Article

Expression of lipid metabolism and myosin heavy chain genes was evaluated in skeletal muscle of pig’s genotypes submitted to different dietary digestible lysine contents. Fifty-two barrows and fifty gilts from three genotypes (G: Piau, Duroc and Pietrain crossbreds) were assigned to three dietary digestible lysine contents (DL: Low, Medium and High). Ten genes were evaluated, being six involved with lipid metabolism: Fatty acid synthase (FAS), Stearoyl-CoA desaturase (SCD), Protein kinase AMP-activated γ1 subunit (PRKAG1), Protein kinase AMP-activated γ3 subunit (PRKAG3), Hormone sensitive lipase (HSL), Heart fatty acid-binding protein (H-FABP), and four in Myosin heavy chain: MyHC I, MyHC IIa, MyHC IIb and MyHC IIx. There were no G × DL interactions. The expression levels for FAS, SCD, PRKAG1, HFABP, MyHC IIb and MyHC IIa were affected by G (P<0.05). A higher expression were observed for FAS in Pietrain barrows and gilts (P<0.05); for SCD in Duroc barrows, and in Duroc and Pietrain gilts (P<0.05); for PRKAG1 in Piau barrows and gilts (P<0.05); for H-FABP and MyHC IIb in Duroc and Pietrain barrows (P<0.05); and for MyHC IIa in Duroc and Pietrain gilts (P<0.05). The expression levels for MyHC IIb, PRKAG3 and MyHC IIa were affected by DL (P<0.05). A higher ex’pression were observed for MyHC IIb in barrows fed High and Medium DL, and in gilts fed High DL (P<0.05); for PRKAG3 in barrows fed Low DL (P<0.05); and for MyHC IIa in gilts fed High DL (P<0.05). Our results indicate that genotype and dietary lysine appear to affect the expression of lipid metabolism and myosin heavy chain genes of barrows and gilts in different ways.

Genet. Mol. Res. 17(2): gmr16039904
DOI: 10.4238/gmr16039904
Research Article

To develop a method to identify Clematidis radix et Rhizoma using sequence similarity and sequence-specific genetic polymorphisms based on the ITS sequences. DNA was extracted from leaves of Clematis mandshurica Rupr and C. hexapetala using a DNA extraction kit. ITS sequences were amplified by PCR, and analyzed in Contig Express, DNAman, and MEGA 5.0. The core haplotype was determined, and similarities between the core and other haplotypes were calculated. In total, 138 ITS sequences of C. mandshurica were obtained with a length of 611 bp. The similarity threshold between C. mandshurica and counterfeit species was 99%. Using specific mutation sites, we could identify C. chinensis, C. hexapetala, and C. mandshurica rapidly and accurately. A new DNA-based method has been established to rapidly and accurately identify Clematidis radix et Rhizoma.

Genet. Mol. Res. 17(2): gmr16039905
DOI: 10.4238/gmr16039905
Research Article

The butterflies are one of the insect groups which undergo typical complete metamorphosis in their life history. However, up to now, little is known about the genomic mechanism that regulates the butterfly metamorphosis. In this study, using a swallowtail butterfly P. polytes as a model organism, a high-throughput sequencing platform was employed to perform the transcriptome and gene expression analyses in order to explore the P. polytes transcriptome features during different developmental stages. The results showed that approximately 398 million useful (Q20) reads were assembled into groups of 14698 (L1), 14264 (L2), 15084 (L3), 15520 (P1), 15052 (P2), 15720 (P3) and 15709 (A1), 14668 (A2), 16152 (A3) genes, respectively, with 58.19% to 67.11% of the data successfully mapped to the reference genome; the transcriptome change analysis via the DEGs Package revealed that dramatic gene expression differences were presented among the different developmental stages, that is, totally, 1162, 891 and 1723 genes were differentially expressed between adult and pupal, adult and larval, larval and pupal stages, respectively, with a number of these differentially expressed genes associated with the functions of digestion, cuticularization, chemoreception, wing formation, and so on. These differentially expressed genes and potential candidate genes required for butterfly metamorphosis by comparative transcriptomics may shed some new insights on molecular mechanisms underlying complete metamorphosis.

Genet. Mol. Res. 17(2): gmr16039902
DOI: 10.4238/gmr16039902
Research Article

Sheeppox virus (SPPV) is one of the listed and notifiable disease affect sheep production with major effect on the trade of new breed of sheep. This study was conducted to identify sheep pox by using cell culture, electron microscope (EM) and open reading frame (ORF) 103 gene during an outbreak of local breed of sheep occurred in Sharkia Governorate, Egypt in April 2017. Affected adult sheep showed typical skin pox lesion on face, the inner side of lips, inner aspect of the thigh and under the tail. The incidence rate of infection was 23.5% and the mortality rate in young lambs aged 3 to 6 months old was 8.2%. Forty-three scabs and tissue samples from clinically diseased adult sheep and dead lambs were collected and subjected to culture on Vero cell. The cytopathic effect (CPE) was observed within 3 to 7 days in 40 samples. A typical Poxvirus was a brick-like shape with round ends by negative staining of EM and ovoid like structure with dumb-bell shaped DNA core with concave bodies sides by positive staining of EM. By conventional PCR utilizing ORF103 gene and obtained bands of about 570 bp referred to SPPV. The sequence amplicon was analyzed by NCBI-BLAST and register in GeneBank under accession N. MG873537 and phylogentic tree was designed which revealed that the isolated strain of SPPV was resembled with other strains of SPPV isolated in Egypt, India, China, and USA. Finally, both EM and PCR are considered as sensitives, rapids, and powerful methods to identify SPPV from tissue and scab’s samples without the need of further culture in addition to the useful and easily use of ORF103 gene to differentiate SPPV from other Capripoxvirus.

Genet. Mol. Res. 17(2): gmr16039901
DOI: 10.4238/gmr16039901

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