Search results for: gene and chromosome issue

Authors: Antonela Matana, Dubravka Brdar, Vesela Torlak, Marijana Popovic, Ivana Gunjaca, Ozren Polasek, Vesna Boraska Perica, Maja Barbalic, Ante Punda, Caroline Hayward, Tatijana Zemunik

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Parathyroid hormone (PTH) plays a critical role in the regulation of bone mineral metabolism and calcium homeostasis. Higher PTH levels are associated with heart failure, hypertension, coronary artery disease, cardiovascular mortality and poorer bone health. A twin study estimated that 60% of the variation in PTH concentrations is genetically determined. Only one GWAS of PTH concentration has been reported to date. Identified loci explained 4.5% of the variance in circulating PTH, suggesting that additional genetic variants remain undiscovered. Therefore, the aim of this study was to identify novel genetic variants associated with PTH levels in a general population. We have performed a GWAS meta-analysis on 2596 individuals originating from three Croatian cohorts: City of Split and the Islands of Korčula and Vis, within a large-scale project of “10,001 Dalmatians”. A total of 7 411 206 variants, imputed using the 1000 Genomes reference panel, with minor allele frequency ≥ 1% and Rsq ≥ 0.5 were analyzed for the association. GWAS within each data set was performed under an additive model, controlling for age, gender and relatedness. Meta-analysis was conducted using the inverse-variance fixed-effects method. Furthermore, to identify sex-specific effects, we have conducted GWAS meta-analyses analyzing males and females separately. In addition, we have performed biological pathway analysis. Four SNPs, representing one locus, reached genome-wide significance. The most significant SNP was rs11099476 on chromosome 4 (P=1.15x10-8), which explained 1.14 % of the variance in PTH. The SNP is located near the protein-coding gene RASGEF1B. Additionally, we detected suggestive association with SNPs, rs77178854 located on chromosome 2 in the DPP10 gene (P=2.46x10-7) and rs481121 located on chromosome 1 (P=3.58x10-7) near the GRIK1 gene. One of the top hits detected in the main meta-analysis, intron variant rs77178854 located within DPP10 gene, reached genome-wide significance in females (P=2.21x10-9). No single locus was identified in the meta-analysis in males. Fifteen biological pathways were functionally enriched at a P<0.01, including muscle contraction, ion homeostasis and cardiac conduction as the most significant pathways. RASGEF1B is the guanine nucleotide exchange factor, known to be associated with height, bone density, and hip. DPP10 encodes a membrane protein that is a member of the serine proteases family, which binds specific voltage-gated potassium channels and alters their expression and biophysical properties. In conclusion, we identified 2 novel loci associated with PTH levels in a general population, providing us with further insights into the genetics of this complex trait.

Keywords: general population, genome-wide association analysis, parathyroid hormone, single nucleotide polymorphisms.

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Authors: Mona Heydari, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Prediction of perturbations after genetic manipulation (especially gene knockout) is one of the important challenges in systems biology. In this paper, a new algorithm is introduced that integrates microarray data into the metabolic model. The algorithm was used to study the change in the cell phenotype after knockout of Gss gene in Escherichia coli BW25113. Algorithm implementation indicated that gene deletion resulted in more activation of the metabolic network. Growth yield was more and less regulating gene were identified for mutant in comparison with the wild-type strain.

Keywords: metabolic network, gene knockout, flux balance analysis, microarray data, integration

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Authors: Garima Chaudhary

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The gender of an individual in forensic DNA analysis is normally accessed by using the STR multiplexes with the incorporated gender based marker amelogenin or in other words by presence or absence of Y-Chromosome, but it may not be true in all the cases. We hereby report an interesting case of a phenotypic female carrying a male karyotype (46XY). In the alleged murder case, the deceased female with XY genotype was noticed. The expression of 18 Y-linked genes was studied to measure the extent of expression. Expression at 4 loci was observed that might have caused the misinterpretation in forensic casework. This clinical situation of the deceased in this case was diagnosed as testicular feminization syndrome, which characterize a female phenotype with a male karyotype (46, XY). Most of these cases have SRY (testis determining factor). The genetic explanation of this phenomenon is not very clear. Here, we are discussing the impact of such situations of genetic discrepancy in forensic interpretation of results. In the presented murder case of a phenotypic female, sexual assault was also suspected. For confirmation vaginal swabs and micro slides were also sent to us for DNA examination. After DNA analysis using STR markers, Y-chromosome was detected in the samples which supporting the suspicion of sexual assault before murder. When the reference blood sample of the deceased was analyzed, it was found to be case of testicular feminization syndrome. Interesting inferences were made from the results obtained.

Keywords: DNA profiling, forensic case study, Y chromosome, females

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Authors: Abdullah M. Alzahrani

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The karyotypes of Khalas (KH), Sukkary (SK), Sheeshi (SS), Shibeebi (SB) and Sillije (SJ) date palm cultivars were investigated. Data showed no variation in chromosome number, 2n = 36, 34 autosomes in addition to XX in females and XY in males. Mean autosomes length ranged from 3.85-9.93 μm and 3.71-2.73 μm for X and Y chromosomes, respectively. The formula of female date palm karyotype was 8m + 4sm +2st + 4t, and submedian Y chromosome. Relative chromosome length ranged from 3.3- 9.38 μm. SS cultivar showed high asymmetry levels by scoring low values of Syi (45.51), TF (42.8) and high values for A1 (0.53), A (0.41) and AI (0.29). Syi developed an inverse relation with A1 and A while A exhibited a direct correlation with A1. Cultivars SK, SB and SJ score medium values of Syi, A1, AI and A. KH cultivar exhibited high symmetry by scoring highest values of Syi (53.68), TF (51.81) and lowest values of A1 (0.44), A (0.34) and AI (0.18). Higher DI value was obtained in SB cultivar (1.34) followed by SJ (1.15) and low DI scores of 0.99, 0.86 and 0.71 were detected in KH, SS and SK, respectively. Stebbins classification assorted SS as 3B and the other cultivars as 2B, insuring the evolution and asymmetry of SS compared to the other karyotypes. Scatter diagram of Syi-A1 couple has the advantage of revealing high degree of sensitivity to present karyotype interrelationships, followed by AI-A and CVCL-CVCI couples.

Keywords: Karyotype, date palm, Khalas, Sukkary, Sheeshi

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Authors: Irina S. Kolesnikova, Alexander A. Dolskiy, Natalya A. Lemskaya, Yulia V. Maksimova, Asia R. Shorina, Alena S. Telepova, Alexander S. Graphodatsky, Dmitry V. Yudkin

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A cytogenetic and molecular genetic study of the family with a male child who had mental retardation and autistic features revealed an abnormal chromosome 13 bearing an enlarged p-arm with amplified ribosomal DNA (rDNA) in a boy and his father. Cytogenetic analysis using standard G-banding and FISH with labeled rDNA probes revealed an abnormal chromosome 13 with an enlarged p-arms due to rDNA amplification in a male child, who had clinically confirmed mental retardation and an autistic behavior. This chromosome is evidently inherited from the father, who has morphologically the same chromosome, but is healthy. The karyotype of the mother was normal. Ag-NOR staining showed brightly stained large whole-p-arm nucleolus organizer regions (NORs) in a child and normal-sized NORs in his father with 13p+-NOR-amount mosaicism. qRT-PCR with specific primers showed highly increased levels of 18S, 28S and 5,8 S ribosomal RNA (rRNA) in the patient’s blood samples compared to a normal healthy control donor. Both patient’s father and mother had no elevated levels of rRNAs expression. Thus, in this case, rRNA level seems to correlate with mental retardation in familial individuals with 13p+. Our findings of rRNA overexpression in a patient with mental retardation and his parents may show a possible link between the karyotype (p-arm enlargement due to rDNA amplification), rDNA functionality (rRNA overexpression), functional changes in the brain and mental retardation. The study is supported by Russian Science Foundation Grant 15-15-10001.

Keywords: mental retardation, ribosomal DNA–rDNA, ribosomal RNA–rRNA, nucleolus organizer region–NOR, chromosome 13

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Authors: Nicolae Bold, Daniel Nijloveanu

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The idea of cropping-system is a method used by farmers. It is an environmentally-friendly method, protecting the natural resources (soil, water, air, nutritive substances) and increase the production at the same time, taking into account some crop particularities. The combination of this powerful method with the concepts of genetic algorithms results into a possibility of generating sequences of crops in order to form a rotation. The usage of this type of algorithms has been efficient in solving problems related to optimization and their polynomial complexity allows them to be used at solving more difficult and various problems. In our case, the optimization consists in finding the most profitable rotation of cultures. One of the expected results is to optimize the usage of the resources, in order to minimize the costs and maximize the profit. In order to achieve these goals, a genetic algorithm was designed. This algorithm ensures the finding of several optimized solutions of cropping-systems possibilities which have the highest profit and, thus, which minimize the costs. The algorithm uses genetic-based methods (mutation, crossover) and structures (genes, chromosomes). A cropping-system possibility will be considered a chromosome and a crop within the rotation is a gene within a chromosome. Results about the efficiency of this method will be presented in a special section. The implementation of this method would bring benefits into the activity of the farmers by giving them hints and helping them to use the resources efficiently.

Keywords: chromosomes, cropping, genetic algorithm, genes

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Authors: Alhadi Bustaman, Soeganda Formalidin, Titin Siswantining

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DNA microarray technology is used to analyze thousand gene expression data simultaneously and a very important task for drug development and test, function annotation, and cancer diagnosis. Various clustering methods have been used for analyzing gene expression data. However, when analyzing very large and heterogeneous collections of gene expression data, conventional clustering methods often cannot produce a satisfactory solution. Biclustering algorithm has been used as an alternative approach to identifying structures from gene expression data. In this paper, we introduce a transform technique based on singular value decomposition to identify normalized matrix of gene expression data followed by Mixed-Clustering algorithm and the Lift algorithm, inspired in the node-deletion and node-addition phases proposed by Cheng and Church based on Agglomerative Hierarchical Clustering (AHC). Experimental study on standard datasets demonstrated the effectiveness of the algorithm in gene expression data.

Keywords: agglomerative hierarchical clustering (AHC), biclustering, gene expression data, lymphoma, singular value decomposition (SVD)

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Authors: Hazha Hidayat, Shayma Ibrahim

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Folate metabolism plays a crucial role in the normal development of the neonatal central nervous system. It is regulated by MTHFR gene polymorphism. Any factors, which will affect this metabolism either by hereditary or gene mutation will lead to many mental disorders. The purpose of this study was to investigate whether MTHFR gene mutation contributes to the development of mental retardation and CP combined with mental retardation in Erbil city. DNA was isolated from the peripheral blood samples of 40 cases suffering from mental retardation (MR) and CP combined with MR were recruited, sequence the 4, 6, 7, 8 exons of the MTHFR gene were done to identify the variants. Exons were amplified by PCR technique and then sequenced according to Sanger method to show the differences with MTHFR reference sequences. We observed (14) mutations in 4, 6, 7, 8 exons in the MTHFR gene associated with Cerebral Palsy combined with mental retardation included deletion, insertion, Substitution. The current study provides additional evidence that multiple variations in the MTHFR gene are associated with mental retardation and Cerebral Palsy.

Keywords: methylenetetrahydrofolate reductase (MTHFR) gene, SNPs, homocysteine, sequencing

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Authors: Somyung Oh, Jeonghyeon Ha, Kyungwon Lee, Sejong Oh

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Microarray is a general scheme to find differentially expressed genes for target concept. The output is expressed by heat map, and biologists analyze related terms of gene ontology to find some characteristics of differentially expressed genes. In this paper, we propose integrated visualization tool for heat map and gene ontology graph. Previous two methods are used by static manner and separated way. Proposed visualization tool integrates them and users can interactively manage it. Users may easily find and confirm related terms of gene ontology for given differentially expressed genes. Proposed tool also visualize connections between genes on heat map and gene ontology graph. We expect biologists to find new meaningful topics by proposed tool.

Keywords: heat map, gene ontology, microarray, differentially expressed gene

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Authors: K. Rawojć, J. Miszczyk, A. Możdżeń, A. Panek, J. Swakoń, M. Rydygier

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Due to the mitotic delay, poor mitotic index and disappearance of lymphocytes from peripheral blood circulation, assessing the DNA damage after high dose exposure is less effective. Conventional chromosome aberration analysis or cytokinesis-blocked micronucleus assay do not provide an accurate dose estimation or radiosensitivity prediction in doses higher than 6.0 Gy. For this reason, there is a need to establish reliable methods allowing analysis of biological effects after exposure in high dose range i.e., during particle radiotherapy. Lately, Premature Chromosome Condensation (PCC) has become an important method in high dose biodosimetry and a promising treatment modality to cancer patients. The aim of the study was to evaluate the usefulness of drug-induced PCC scoring procedure in an experimental mode, where 100 G2/M cells were analyzed in different dose ranges. To test the consistency of obtained results, scoring was performed by 3 independent persons in the same mode and following identical scoring criteria. Whole-body exposure was simulated in an in vitro experiment by irradiating whole blood collected from healthy donors with 60 MeV protons and 250 keV X-rays, in the range of 4.0 – 20.0 Gy. Drug-induced PCC assay was performed on human peripheral blood lymphocytes (HPBL) isolated after in vitro exposure. Cells were cultured for 48 hours with PHA. Then to achieve premature condensation, calyculin A was added. After Giemsa staining, chromosome spreads were photographed and manually analyzed by scorers. The dose-effect curves were derived by counting the excess chromosome fragments. The results indicated adequate dose estimates for the whole-body exposure scenario in the high dose range for both studied types of radiation. Moreover, compared results revealed no significant differences between scores, which has an important meaning in reducing the analysis time. These investigations were conducted as a part of an extended examination of 60 MeV protons from AIC-144 isochronous cyclotron, at the Institute of Nuclear Physics in Kraków, Poland (IFJ PAN) by cytogenetic and molecular methods and were partially supported by grant DEC-2013/09/D/NZ7/00324 from the National Science Centre, Poland.

Keywords: cell response to radiation exposure, drug induced premature chromosome condensation, premature chromosome condensation procedure, proton therapy

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Authors: Yamunah Devi Apalasamy, Sanjay Rampal, Tin Tin Su, Foong Ming Moy, Hazreen Abdul Majid, Awang Bulgiba, Zahurin Mohamed

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Obesity is a growing global health issue. Obesity results from a combination of environmental and genetics factors. Brain-derived neurotrophic factor (BDNF), a gene encodes the BDNF protein and the BDNF gene have been linked to regulation of body weight and appetite. Genome-wide association studies have identified the BDNF variants to be related to obesity among Caucasians, East Asians, and Filipinos. However, the role of BDNF in other ethnic groups remains inconclusive. This case control study aims to investigate the associations of BDNF gene polymorphisms with obesity and metabolic parameters in Malaysian Malays. BDNF rs4074134, BDNF rs10501087 and BDNF rs6265 were genotyped using Sequenom MassARRAY. Anthropometric, body fat, fasting lipids and glucose levels were measured. A total of 663 subjects (194 obese and 469 non-obese) were included in this study. There were no significant associations association between BDNF SNPs and obesity. The allelic and genotype frequencies of the BDNF SNPs were similar in the obese and non-obese groups. After adjustment for age and sex, the BDNF variants were not associated with obesity, body fat, fasting lipids and glucose levels. Haplotypes at the BDNF gene region, were not significantly associated with obesity. The BDNF rs4074134 was in strong LD with BDNF rs10501087 (D'=0.98) and BDNF rs6265 (D'=0.87). The BDNF rs10501087 was also in strong LD with BDNF rs6265 (D'=0.91). Our findings suggest that the BDNF variants and the haplotypes of BDNF gene were not associated with obesity and metabolic traits in this study population. Further research is needed to explore other BDNF variants with a larger sample size with gene-environment interactions in multi ethnic Malaysian population.

Keywords: genomics of obesity, SNP, BMI, haplotypes

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Authors: Shohei Maruyama, Yasuo Matsuyama, Sachiyo Aburatani

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The development of the method to annotate unknown gene functions is an important task in bioinformatics. One of the approaches for the annotation is The identification of the metabolic pathway that genes are involved in. Gene expression data have been utilized for the identification, since gene expression data reflect various intracellular phenomena. However, it has been difficult to estimate the gene function with high accuracy. It is considered that the low accuracy of the estimation is caused by the difficulty of accurately measuring a gene expression. Even though they are measured under the same condition, the gene expressions will vary usually. In this study, we proposed a feature extraction method focusing on the variability of gene expressions to estimate the genes' metabolic pathway accurately. First, we estimated the distribution of each gene expression from replicate data. Next, we calculated the similarity between all gene pairs by KL divergence, which is a method for calculating the similarity between distributions. Finally, we utilized the similarity vectors as feature vectors and trained the multiclass SVM for identifying the genes' metabolic pathway. To evaluate our developed method, we applied the method to budding yeast and trained the multiclass SVM for identifying the seven metabolic pathways. As a result, the accuracy that calculated by our developed method was higher than the one that calculated from the raw gene expression data. Thus, our developed method combined with KL divergence is useful for identifying the genes' metabolic pathway.

Keywords: metabolic pathways, gene expression data, microarray, Kullback–Leibler divergence, KL divergence, support vector machines, SVM, machine learning

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Authors: Amir Bastani

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The result of the research in the field of human behavioural genetics demonstrates a genetic contribution of behavioural differences in aggression, violence, drug and substance abuse, antisocial personality disorder and other related traits. As the field of human behavioural genetics progresses and achieves credibility, the criminal accused continue to use its types of evidence into the criminal law. One of the most important genetic factors which controls certain neurotransmitters like dopamine and serotonin is the Monoamine Oxidase Acid A (MAOA) gene, known as the 'warrior gene'. The high-profile study by Caspi and colleagues in 2002 showed that the combination between one type of variation of the MAOA gene and childhood maltreatment noticeably predisposes a person to antisocial behaviour. Moreover, further scientific research shows that individuals with the MAOA gene have to some degree difficulties in controlling their impulses. Based on the evidence of MAOA, some criminal accused claimed difficulties in self-control. In the first case – the famous case of Mobley – the court rejected the MAOA evidence on the ground of the lack of scientific support. In contrast, in other cases after the Mobley trial, courts accepted the evidence of MAOA. In this paper, the issue of lack of impulse control produced by the MAOA gene and cases which relied on the MAOA evidence and successfully being accepted will be reviewed in detail. Finally, the anticipation of the paper for the future use of the MAOA evidence in criminal cases will be presented.

Keywords: genetic defence, criminal responsibility, MAOA, self-control

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Authors: Rachel Matar, Maxime Merheb

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Chemical drugs have been used for many centuries as the only way to cure diseases until the novel gene therapy has been created in 1960. Gene therapy is based on the insertion, correction, or inactivation of genes to treat people with genetic illness (1). Gene therapy has made wonders in Parkison’s, Alzheimer and multiple sclerosis. In addition to great promises in the healing of deadly diseases like many types of cancer and autoimmune diseases (2). This method implies the use of recombinant DNA technology with the help of different viral and non-viral vectors (3). It is nowadays used in somatic cells as well as embryos and gametes. Beside all the benefits of gene therapy, this technique is deemed by some opponents as an ethically unacceptable treatment as it implies playing with the genes of living organisms.

Keywords: gene therapy, genetic disease, cancer, multiple sclerosis

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Authors: Daina Jonkus, Liga Paura, Tatjana Sjakste, Kristina Dokane

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The aim of this study was to analyse PRKAG3 and RYR1 gene and genotypes frequencies in Latvian White pigs’ breed. Genotypes of RYR1 gene two loci (rs196953058 and rs323041392) in 89 exon and PRKAG3 gene two loci (rs196958025 and rs344045190) in gene promoter were detected in 103 individuals of Latvian white pigs’ breed. Analysis of RYR1 gene loci rs196953058 shows all individuals are homozygous by T allele and all animals are with genotypes TT, its mean - in 2769 position is Phenylalanine. Analysis of RYR1 gene loci rs323041392 shows all individuals are homozygous by G allele and all animals are with genotypes GG, its mean - in 4119 positions is Asparagine. In loci rs196953058 and rs323041392, there were no gene polymorphisms. All analysed individuals by two loci rs196953058-rs323041392 have TT-GG genotypes or Phe-Asp amino acids. In PRKAG3 gene loci rs196958025 and rs344045190 there was gene polymorphisms. In both loci frequencies for A allele was higher: 84.6% for rs196958025 and 73.0% for rs344045190. Analysis of PRKAG3 gene loci rs196958025 shows 74% of individuals are homozygous by An allele and animals are with genotypes AA. Only 4% of individuals are homozygous by G allele and animals are with genotypes GG, which is associated with pale meat colour and higher drip loss. Analysis of PRKAG3 gene loci rs344045190 shows 46% of individuals are homozygous with genotypes AA and 54% of individuals are heterozygous with genotypes AG. There are no individuals with GG genotypes. According to the results, in Latvian white pigs population there are no rs344435545 (RYR1 gene) CT heterozygous or TT recessive homozygous genotypes, which is related to the meat quality and pigs’ stress syndrome; and there are 4% rs196958025 (PRKAG3 gene) GG recessive homozygote genotypes, which is related to the meat quality. Acknowledgment: the investigation is supported by VPP 2014-2017 AgroBioRes Project No. 3 LIVESTOCK.

Keywords: genotype frequencies, pig, PRKAG3, RYR1

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Authors: Hamid Mustafa, Adeela Ajmal, Kim EuiSoo, Noor-ul-Ain

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World wild, buffalo production is considered as most important component of food industry. Efficient buffalo production is related with reproductive performance of this species. Lack of knowledge of reproductive efficiency and its related genes in buffalo species is a major constraint for sustainable buffalo production. In this study, we performed some bioinformatics analysis on Follicle Stimulating Hormone Receptor (FSHR) gene and explored the possible relationship of this gene among different buffalo breeds and with other farm animals. We also found the evolution pattern for this gene among these species. We investigate CDS lengths, Stop codon variation, homology search, signal peptide, isoelectic point, tertiary structure, motifs and phylogenetic tree. The results of this study indicate 4 different motif in this gene, which are Activin-recp, GS motif, STYKc Protein kinase and transmembrane. The results also indicate that this gene has very close relationship with cattle, bison, sheep and goat. Multiple alignment (MA) showed high conservation of motif which indicates constancy of this gene during evolution. The results of this study can be used and applied for better understanding of this gene for better characterization of Follicle Stimulating Hormone Receptor (FSHR) gene structure in different farm animals, which would be helpful for efficient breeding plans for animal’s production.

Keywords: buffalo, FSHR gene, bioinformatics, production

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Authors: Micheal Olaolu Arowolo, Muhammad Azam, Fei He, Mihail Popescu, Dong Xu

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As the quantity of biological articles rises, so does the number of biological route figures. Each route figure shows gene names and relationships. Annotating pathway diagrams manually is time-consuming. Advanced image understanding models could speed up curation, but they must be more precise. There is rich information in biological pathway figures. The first step to performing image understanding of these figures is to recognize gene names automatically. Classical optical character recognition methods have been employed for gene name recognition, but they are not optimized for literature mining data. This study devised a method to recognize an image bounding box of gene name as a photo using deep Siamese neural network models to outperform the existing methods using ResNet, DenseNet and Inception architectures, the results obtained about 84% accuracy.

Keywords: biological pathway, gene identification, object detection, Siamese network

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Authors: Sanaa Rashed Abdallah, Yasser F. Hassan

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The paper will introduce an approach where a rough sets, gene expression programming and rough neural networks are used cooperatively for learning and classification support. The Objective of gene expression programming rough neural networks (GEP-RNN) approach is to obtain new classified data with minimum error in training and testing process. Starting point of gene expression programming rough neural networks (GEP-RNN) approach is an information system and the output from this approach is a structure of rough neural networks which is including the weights and thresholds with minimum classification error.

Keywords: rough sets, gene expression programming, rough neural networks, classification

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Authors: Bryony Davies

Abstract:

Many cell and tissue culture practices ignore the effects of gravity on cell biology, and little is known about how cell components may move in response to gravitational forces. Starfish oocytes provide an excellent model for interrogating the movement of cell components due to their unusually large size, ease of handling, and high transparency. Chromosomes from starfish oocytes can be visualised by microinjection of the histone-H2B-mCherry plasmid into the oocytes. The movement of the chromosomes can then be tracked by live-cell fluorescence microscopy. The results from experiments using these methods suggest that there is a replicable downward movement of centrally located chromosomes at a median velocity of 0.39 μm/min. Chromosomes nearer the nuclear boundary showed more restricted movement. Chromosome density and shape could also be altered by microinjection of restriction enzymes, primarily Alu1, before imaging. This was found to alter the speed of chromosome movement, with chromosomes from Alu1-injected nuclei showing a median downward velocity of 0.60 μm/min. Overall, these results suggest that there is a non-negligible movement of chromosomes in response to gravitational forces and that this movement can be altered by enzyme activity. Future directions based on these results could interrogate if this observed downward movement extends to other cell components and to other cell types. Additionally, it may be important to understand whether gravitational orientation and vertical positioning of cell components alter cell behaviour. The findings here may have implications for current cell culture practices, which do not replicate cell orientations or external forces experienced in vivo. It is possible that a failure to account for gravitational forces in 2D cell culture alters experimental results and the accuracy of conclusions drawn from them. Understanding possible behavioural changes in cells due to the effects of gravity would therefore be beneficial.

Keywords: starfish, oocytes, live-cell imaging, microinjection, chromosome dynamics

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Authors: Yudi Zhao, Ziyun Zhou, Yueting Yao, Shuying Dai, Zhiling Yan, Longyu Yang, Chuanyin Li, Li Shi, Yufeng Yao

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HPV16 E4 gene plays an important role in viral genome amplification and release. Therefore, a variation of the E4 gene nucleic acid sequence may affect the carcinogenicity of HPV16. In order to understand the relationship between the variation of HPV16 E4 gene and cervical cancer, this study was to amplify and sequence the DNA sequences of E4 genes in 118 HPV16-positive cervical cancer patients and 151 HPV16-positive asymptomatic individuals. After obtaining E4 gene sequences, the phylogenetic trees were constructed by the Neighbor-joining method for gene variation analysis. The results showed that: 1) The distribution of HPV16 variants between the case group and the control group differed greatly (P = 0.015)，and the Asian-American（AA）variant was likely to relate to the occurrence of cervical cancer. 2) DNA sequence analysis showed that there were significant differences in the distribution of 8 variants between the case group and the control group (P < 0.05). And 3) In European (EUR) variant, two variations, C3384T (L18L) and A3449G (P39P), were associated with the initiation and development of cervical cancer. The results suggested that the variation of HPV16 E4 gene may be a contributor affecting the occurrence as well as the development of cervical cancer, and different HPV16 variants may have different carcinogenic capability.

Keywords: cervical cancer, HPV16, E4 gene, variations

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Authors: Wisam H. Benamer, Ehab A. Elfallah, Mohamed A. Elshaari, Farag A. Elshaari

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A challenge for laboratories is to provide bacterial identification and antibiotic sensitivity results within a short time. Hence, advancement in the required technology is desirable to improve timing, accuracy and quality. Even with the current advances in methods used for both phenotypic and genotypic identification of bacteria the need is there to develop method(s) that enhance the outcome of bacteriology laboratories in accuracy and time. The hypothesis introduced here is based on the assumption that the chromosome of any bacteria contains unique sequences that can be used for its identification and typing. The outcome of a pilot study designed to test this hypothesis is reported in this manuscript. Methods: The complete chromosome sequences of several bacterial species were downloaded to use as search targets for unique sequences. Visual basic and SQL server (2014) were used to generate a complete set of 18-base long primers, a process started with reverse translation of randomly chosen 6 amino acids to limit the number of the generated primers. In addition, the software used to scan the downloaded chromosomes using the generated primers for similarities was designed, and the resulting hits were classified according to the number of similar chromosomal sequences, i.e., unique or otherwise. Results: All primers that had identical/similar sequences in the selected genome sequence(s) were classified according to the number of hits in the chromosomes search. Those that were identical to a single site on a single bacterial chromosome were referred to as unique. On the other hand, most generated primers sequences were identical to multiple sites on a single or multiple chromosomes. Following scanning, the generated primers were classified based on ability to differentiate between medically important bacterial and the initial results looks promising. Conclusion: A simple strategy that started by generating primers was introduced; the primers were used to screen bacterial genomes for match. Primer(s) that were uniquely identical to specific DNA sequence on a specific bacterial chromosome were selected. The identified unique sequence can be used in different molecular diagnostic techniques, possibly to identify bacteria. In addition, a single primer that can identify multiple sites in a single chromosome can be exploited for region or genome identification. Although genomes sequences draft of isolates of organism DNA enable high throughput primer design using alignment strategy, and this enhances diagnostic performance in comparison to traditional molecular assays. In this method the generated primers can be used to identify an organism before the draft sequence is completed. In addition, the generated primers can be used to build a bank for easy access of the primers that can be used to identify bacteria.

Keywords: bacteria chromosome, bacterial identification, sequence, primer generation

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Authors: I. Boroňová, J. Bernasovská, J. Kľoc, Z. Tomková, E. Petrejčíková, S. Mačeková, J. Poráčová, M. M. Blaščáková

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Osteoporosis is a common multifactorial disease with a strong genetic component characterized by reduced bone mass and increased risk of fractures. Genetic factors play an important role in the pathogenesis of osteoporosis. The aim of our study was to identify the genotype and allele distribution of T245G polymorphism in OPG gene in Slovak postmenopausal women. A total of 200 unrelated Slovak postmenopausal women with diagnosed osteoporosis and 200 normal controls were genotyped for T245G (rs3134069) polymorphism of OPG gene. Genotyping was performed using the Custom Taqman®SNP Genotyping assays. Genotypes and alleles frequencies showed no significant differences (p=0.5551; p=0.6022). The results of the present study confirm the importance of T245G polymorphism in OPG gene in the pathogenesis of osteoporosis.

Keywords: OPG gene, T245G polymorphism, osteoporosis, T245G polymorphism, real-time PCR

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Authors: Tiancheng Lan

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E10A is a kind of replication-defective adenovirus which carries the human endostatin gene to inhibit the growth of tumors. Kringle 5(K5) has almost the same function as angiostatin to also inhibit the growth of tumors since they are all the byproduct of the proteolytic cleavage of plasminogen. Tumor size increasing can be suppressed because both of the endostatin and K5 can restrain the angiogenesis process. Therefore, in order to improve the treatment effect on tumor, 2A peptide is used to construct a fusion gene carrying both E10A and K5. Using 2A peptide is an ideal strategy when a fusion gene is expressed because it can avoid many problems during the expression of more than one kind of protein. The overlap extension PCR is also used to connect 2A peptide with E10A and K5. The final construction of fusion gene E10A-2A-K5 can provide a possible new method of the anti-angiogenesis treatment with a better expression performance.

Keywords: E10A, Kringle 5, 2A peptide, overlap extension PCR

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Authors: Mhaned Oubounyt, Jan Baumbach

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Differences in co-expression networks between two or multiple cells (sub)types across conditions is a pressing problem in single-cell RNA sequencing (scRNA-seq). A key challenge is to define those co-variations that differ between or among cell types and/or conditions and phenotypes to examine small regulatory networks that can explain mechanistic differences. To this end, we developed SCANet, an all-in-one Python package that uses state-of-the-art algorithms to facilitate the workflow of a combined single-cell GCN (Gene Correlation Network) and GRN (Gene Regulatory Networks) pipeline, including inference of gene co-expression modules from scRNA-seq, followed by trait and cell type associations, hub gene detection, co-regulatory networks, and drug-gene interactions. In an example case, we illustrate how SCANet can be applied to identify regulatory drivers behind a cytokine storm associated with mortality in patients with acute respiratory illness. SCANet is available as a free, open-source, and user-friendly Python package that can be easily integrated into systems biology pipelines.

Keywords: single-cell, co-expression networks, drug-gene interactions, co-regulatory networks

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Authors: Sanjeev Kumar Shukla, Govind Singh, Prabhat Pant Shahzad Ahmad

Abstract:

Background: Graves’ disease is an autoimmune disorder with a genetic predisposition, and CD40 plays a pathogenic role in various autoimmune diseases. A single nucleotide polymorphism at position –1 of the Kozak sequence of the 5 untranslated regions of the CD40 gene of exon 1 has been reported to be associated with the development of Graves’ Disease. Objective: The aim of the present study was to investigate whether CD40 gene polymorphism confers susceptibility to Graves’ disease in the Kumaon region. CD40 gene polymorphisms were studied in Graves’ Disease patients (n=50) and healthy control subjects without anti-thyroid autoantibodies or a family history of autoimmune disorders (n=50). Material and Method: CD40 gene polymorphisms were studied in fifty Graves’ Disease patients and fifty healthy control subjects. All samples were collected from STG Hospital, Haldwani, Nainital. A C/T polymorphism at position –1 of the CD40 gene was measured using the polymerase chain reaction-restriction fragment length polymorphism. Results: There was no significant difference in allele or genotype frequency of the CD40 SNP between Graves’ Disease and control subjects. There was a significant decrease in the TT genotype frequency in the Graves’ Disease patients who developed Graves’ Disease after 40 years old than those under 40 years of age. These data suggest that the SNP of the CD40 gene is associated with susceptibility to the later onset of Graves’ Disease. Conclusion: The CD40 gene was a different susceptibility gene for Graves’ Disease within certain families because it was both linked and associated with Graves’ Disease.

Keywords: autoimmune diseases, pathogenesis, diagnosis, therapy

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Authors: Ki-Yeo Kim

Abstract:

Trends in genetics are transforming in order to identify differential coexpressions of correlated gene expression rather than the significant individual gene. Moreover, it is known that a combined biomarker pattern improves the discrimination of a specific cancer. The identification of the combined biomarker is also necessary for the early detection of invasive oral squamous cell carcinoma (OSCC). To identify the combined biomarker that could improve the discrimination of OSCC, we explored an appropriate number of genes in a combined gene set in order to attain the highest level of accuracy. After detecting a significant gene set, including the pre-defined number of genes, a combined expression was identified using the weights of genes in a gene set. We used the Principal Component Analysis (PCA) for the weight calculation. In this process, we used three public microarray datasets. One dataset was used for identifying the combined biomarker, and the other two datasets were used for validation. The discrimination accuracy was measured by the out-of-bag (OOB) error. There was no relation between the significance and the discrimination accuracy in each individual gene. The identified gene set included both significant and insignificant genes. One of the most significant gene sets in the classification of normal and OSCC included MMP1, SOCS3 and ACOX1. Furthermore, in the case of oral dysplasia and OSCC discrimination, two combined biomarkers were identified. The combined genomic expression achieved better performance in the discrimination of different conditions than in a single significant gene. Therefore, it could be expected that accurate diagnosis for cancer could be possible with a combined biomarker.

Keywords: oral squamous cell carcinoma, combined biomarker, microarray dataset, correlated genes

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Authors: Umme Shahera, Saifullah Munshi, Munira Jahan, Afzalun Nessa, Shahinul Alam, Shahina Tabassum

Abstract:

The development of HCC is a multi-stage process. Several extrinsic factors, such as aflatoxin, HBV, nutrition, alcohol, and trace elements are thought to initiate or/and promote the hepatocarcinogenesis. Alteration of p53 status is an important intrinsic factor in this process as p53 is essential for preventing inappropriate cell proliferation and maintaining genome integrity following genotoxic stress. This study was designed to assess the correlation of p53 gene expression with HBV-DNA and serum Alanine transaminase (ALT) in patients with cirrhosis and HCC. The study was conducted among 60 patients. The study population were divided into four groups (15 in each groups)-HBV positive cirrhosis, HBV negative cirrhosis, HBV positive HCC and HBV negative HCC. Expression of p53 gene was observed using real time PCR. P53 gene expressions in the above mentioned groups were correlated with serum ALT level and HBV viral load. p53 gene was significantly higher in HBV-positive patients with HCC than HBV-positive cirrhosis. Similarly, the expression of p53 was significantly higher in HBV-positive HCC than HBV-negative HCC patients. However, the expression of p53 was reduced in HBV-positive cirrhosis in comparison with HBV-negative cirrhosis. P53 gene expression in liver was not correlated with the serum levels of ALT in any of the study groups. HBV- DNA load also did not correlated with p53 gene expression in HBV positive HCC and HBV positive cirrhosis patients. This study shows that there was no significant change with the expression of p53 gene in any of the study groups with ALT level or viral load, though differential expression of p53 gene were observed in cirrhosis and HCC patients.

Keywords: P53, ALT, HBV-DNA, liver cirrhosis, hepatocellular carcinoma

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Authors: Neda Menbari, Ramin Mehdiabadi

Abstract:

Background: breast cancer remains a critical global health issue, constituting a leading cause of cancer-related mortality in women. MicroRNAs (miRs) are natural RNA molecules that play an important role in cellular processes and regulate post-transcriptional gene expression. MiR-216b-5p is a miR that acts as a tumor suppressor. The expression levels of FoxM1 and miR-216b-5p in malignant and control cells have been evaluated by quantitative polymerase chain reaction (qPCR) technique and flow cytometry. Results: the results of this study revealed a significant downregulation of miR-216b-5p in cancerous cells compared to the control MCF-10A cells (P=0.0004). Interestingly, the expression of miR-216b-5p exhibited an inverse relationship with key clinical indicators such as tumor size, grade, and lymph node invasion. Conclusion: The study's findings showed the prognostic value of miR-216b-5p levels in breast cancer, and its reduced expression correlates with unfavorable tumor characteristics. This research recommends performing more studies on the role of FoxM1 and miR-216b-5p in breast cancer pathology which potentially paving the way for targeted therapeutic interventions.

Keywords: breast cancer, gene expression, FOXM1, microRNA

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Authors: Alieh Farshbaf, Tayyeb Bahrami

Abstract:

Introduction: Cc-chemokine receptor-5 (CCR5) is known as a main co-receptor in human immunodeficiency virus type-1 (HIV-1) infection. Many studies showed 32bp deletion (Δ32) in CCR5 gene, provide natural resistance to HIV-1 infection in homozygous individuals. Inducing the resistance mechanism by CCR5 in HIV-1 infected patients eliminated many problems of highly-active-anti retroviral therapy (HAART) drugs like as low safety, side-effects and virus rebounding from latent reservoirs. New treatments solved some restrictions that are based on gene modification and cell therapy. Literature review: The stories of the “Berlin and Boston patients” showed autologous hematopoietic stem cells transplantation (HSCT) could provide effective cure of HIV-1 infected patients. Furthermore, gene modification by zinc finger nuclease (ZFN) demonstrated another successful result again. Despite the other studies for gene therapy by ∆32 genotype, there is another mutation -CCR5 ∆32/m303- that provides HIV-1 resistant. It is a heterozygote genotype for ∆32 and T→A point mutation at nucleotide 303. These results approved the key role of CCR5 gene. Conclusion: Recent studies showed immune gene therapy and cell therapy could provide effective cure for refractory disease like as HIV. Eradication of HIV-1 from immune system was not observed by HAART, because of reloading virus genome from latent reservoirs after stopping them. It is showed that CCR5 could induce natural resistant to HIV-1 infection by the new approaches based on stem cell transplantation and gene modifying.

Keywords: CCR5, HIV-1, stem cell, immune gene therapy, gene modification

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Authors: Elly Usman, S. Dante, Diah Purnamasari

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Type 2 diabetes mellitus ( T2DM ) is a syndrome characterized by a state of increased blood sugar levels due to chronic disorders of insulin secretion by pancreatic beta cells and insulin action or a combination of both. The organic cation transporter 1, encoded by the SLC22A1 gene, responsible for the uptake of the antihyperglycemic drug, metformin, in the hepatocyte. We assessed whether a genetic variation in the SLC22A1 gene was associated with the glucose - lowering effect of metformin. Method case study research design. Samples are children with type 2 diabetes mellitus who meet the inclusion criteria. The results proportions SLC22A1 gene polymorphisms in children with diabetes mellitus type 2 amounted to 52.04 % at position 400T/C, there is one heterozygous and one at position 595T/C Conclusion The presence of SLC22A1 gene polymorphisms in children with diabetes mellitus type 2.

Keywords: diabetes Mellitus type 2, metformin, organic cation transporter 1, pharmacogenomics

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