Search results for: gene circuits

Authors: M. A. Grigoryev, A. N. Shishkov, D. A. Sychev

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The article defines the necessity of choosing the optimal power circuits scheme of the electric drive with field regulated reluctance machine. The specific weighting factors are calculation, the linear regression dependence of specific losses in semiconductor frequency converters are presented depending on the values of the rated current. It is revealed that with increase of the carrier frequency PWM improves the output current waveform, but increases the loss, so you will need depending on the task in a certain way to choose from the carrier frequency. For task of optimization by criterion of the minimum electrical losses regression dependence of the electrical losses in the frequency converter circuit at a frequency of a PWM signal of 0 Hz. The surface optimization criterion is presented depending on the rated output torque of the motor and number of phases. In electric drives with field regulated reluctance machine with at low output power optimization criterion appears to be the worst for multiphase circuits. With increasing output power this trend hold true, but becomes insignificantly different optimal solutions for three-phase and multiphase circuits. This is explained to the linearity of the dependence of the electrical losses from the current.

Keywords: field regulated reluctance machine, the electrical losses, multiphase power circuit, the surface optimization criterion

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Authors: Yuriy A. Knirel

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Enteric bacteria Escherichia coli is the predominant facultative anaerobe of the colonic flora, and some specific serotypes are associated with enteritis, hemorrhagic colitis, and hemolytic uremic syndrome. Shigella spp. are human pathogens that cause diarrhea and bacillary dysentery (shigellosis). They are in effect E. coli with a specific mode of pathogenicity. Strains of Salmonella enterica are responsible for a food-borne infection (salmonellosis), and specific serotypes cause typhoid fever and paratyphoid fever. All these bacteria are closely related in respect to structure and genetics of the lipopolysaccharide, including the O-polysaccharide part (O‑antigen). Being exposed to the bacterial cell surface, the O antigen is subject to intense selection by the host immune system and bacteriophages giving rise to diverse O‑antigen forms and providing the basis for typing of bacteria. The O-antigen forms of many bacteria are unique, but some are structurally and genetically related to others. The sequenced O-antigen gene clusters between conserved galF and gnd genes were analyzed taking into account the O-antigen structures established by us and others for all S. enterica and Shigella and most E. coli O-serogroups. Multiple genetic mechanisms of diversification of the O-antigen forms, such as lateral gene transfer and mutations, were elucidated and are summarized in the present paper. They include acquisition or inactivation of genes for sugar synthesis or transfer or recombination of O-antigen gene clusters or their parts. The data obtained contribute to our understanding of the origins of the O‑antigen diversity, shed light on molecular evolutionary relationships between the O-antigens of enteric bacteria, and open a way for studies of the role of gene polymorphism in pathogenicity.

Keywords: enteric bacteria, O-antigen gene cluster, polysaccharide biosynthesis, polysaccharide structure

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Authors: Kumaran Narayanan, Pei-Sheng Liew

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This paper adapts the bacteriophage N15 protelomerase enzyme to assemble linear chromosomes as vectors for gene expression in human cells. Phage N15 has the unique ability to replicate as a linear plasmid with telomeres in E. coli during its prophage stage of life-cycle. The virus-encoded protelomerase enzyme cuts its circular genome and caps its ends to form hairpin telomeres, resulting in a linear human-chromosome-like structure in E. coli. In mammalian cells, however, no enzyme with TelN-like activities has been found. In this work, we show for the first-time transfer of the protelomerase from phage into human and mouse cells and demonstrate recapitulation of its activity in these hosts. The function of this enzyme is assayed by demonstrating cleavage of its target DNA, followed by detecting telomere formation based on its resistance to recBCD enzyme digestion. We show protelomerase expression persists for at least 60 days, which indicates limited silencing of its expression. Next, we show that an intact human β-globin gene delivered on this linear chromosome accurately retains its expression in the human cellular environment for at least 60 hours, demonstrating its stability and potential as a vector. These results demonstrate that the N15 protelomerse is able to function in mammalian cells to cut and heal DNA to create telomeres, which provides a new tool for creating novel structures by DNA resolution in these hosts.

Keywords: chromosome, beta-globin, DNA, gene expression, linear vector

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Authors: Zohar Manber, Ran Elkon

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Accumulation of somatic mutations (SMs) in the genome is a major driving force of cancer development. Most SMs in the tumor's genome are functionally neutral; however, some cause damage to critical processes and provide the tumor with a selective growth advantage (termed cancer driver mutations). Current research on functional significance of SMs is mainly focused on finding alterations in protein coding sequences. However, the exome comprises only 3% of the human genome, and thus, SMs in the noncoding genome significantly outnumber those that map to protein-coding regions. Although our understanding of noncoding driver SMs is very rudimentary, it is likely that disruption of regulatory elements in the genome is an important, yet largely underexplored mechanism by which somatic mutations contribute to cancer development. The expression of most human genes is controlled by multiple enhancers, and therefore, it is conceivable that regulatory SMs are distributed across different enhancers of the same target gene. Yet, to date, most statistical searches for regulatory SMs have considered each regulatory element individually, which may reduce statistical power. The first challenge in considering the cumulative activity of all the enhancers of a gene as a single unit is to map enhancers to their target promoters. Such mapping defines for each gene its set of regulating enhancers (termed "set of regulatory elements" (SRE)). Considering multiple enhancers of each gene as one unit holds great promise for enhancing the identification of driver regulatory SMs. However, the success of this approach is greatly dependent on the availability of comprehensive and accurate enhancer-promoter (E-P) maps. To date, the discovery of driver regulatory SMs has been hindered by insufficient sample sizes and statistical analyses that often considered each regulatory element separately. In this study, we analyzed more than 2,500 whole-genome sequence (WGS) samples provided by The Cancer Genome Atlas (TCGA) and The International Cancer Genome Consortium (ICGC) in order to identify such driver regulatory SMs. Our analyses took into account the combinatorial aspect of gene regulation by considering all the enhancers that control the same target gene as one unit, based on E-P maps from three genomics resources. The identification of candidate driver noncoding SMs is based on their recurrence. We searched for SREs of genes that are "hotspots" for SMs (that is, they accumulate SMs at a significantly elevated rate). To test the statistical significance of recurrence of SMs within a gene's SRE, we used both global and local background mutation rates. Using this approach, we detected - in seven different cancer types - numerous "hotspots" for SMs. To support the functional significance of these recurrent noncoding SMs, we further examined their association with the expression level of their target gene (using gene expression data provided by the ICGC and TCGA for samples that were also analyzed by WGS).

Keywords: cancer genomics, enhancers, noncoding genome, regulatory elements

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Authors: P. Sindhumole, K. Soumya, R. Renjimol

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Rice (Oryza sativa L.) is the major staple food crop over the world. It is prone to a number of biotic and abiotic stresses, out of which Bacterial Leaf Blight (BLB), caused by Xanthomonas oryzae pv. oryzae, is the most rampant. Management of this disease through chemicals or any other means is very difficult. The best way to control BLB is by the development of Host Plant Resistance. BLB resistance is not an activity of a single gene but it involves a cluster of more than thirty genes reported. Among these, Xa5 and Xa13 genes are two important ones, which can be diagnosed through marker assisted selection using closely linked molecular markers. During 2014, the first phase of field screening using forty traditional rice genotypes was carried out and twenty resistant symptomless genotypes were identified. Molecular characterisation of these genotypes using RM 122 SSR marker revealed the presence of Xa5 gene in thirteen genotypes. Forty-two traditional rice genotypes were used for the second phase of field screening for BLB resistance. Among these, sixteen resistant genotypes were identified. These genotypes, along with two susceptible check genotypes, were subjected to marker assisted selection for Xa13 gene, using the linked STS marker RG-136. During this process, presence of Xa13 gene could be detected in ten resistant genotypes. In future, these selected genotypes can be directly utilised as donors in Marker assisted breeding programmes for BLB resistance in rice.

Keywords: oryza sativa, SSR, STS, marker, disease, breeding

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Authors: Yunfeng Shan, Xiaoliang Wang, Youjun Zhou

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Whole-genome data from two lungfish species, along with other species, present a valuable opportunity to re-investigate the longstanding debate regarding the evolutionary relationships among tetrapods, lungfishes, and coelacanths. However, the use of bootstrap support has become outdated for large-scale phylogenomic data. Without robust phylogenetic support, the phylogenetic trees become meaningless. Therefore, it is necessary to re-evaluate the phylogenies of tetrapods, lungfishes, and coelacanths using novel measures of phylogenetic support specifically designed for phylogenomic data, as the previous phylogenies were based on 100% bootstrap support. Our findings consistently provide strong evidence favoring lungfish as the closest living relative of tetrapods. This conclusion is based on high internode certainty, relative gene support, and high gene concordance factor. The evidence stems from five previous datasets derived from lungfish transcriptomes. These results yield fresh insights into the three hypotheses regarding the phylogenies of tetrapods, lungfishes, and coelacanths. Importantly, these hypotheses are not mere conjectures but are substantiated by a significant number of genes. Analyzing real biological data further demonstrates that the inclusion of additional taxa leads to more diverse tree topologies. Consequently, gene trees and species trees may not be identical even when whole-genome sequencing data is utilized. However, it is worth noting that many gene trees can accurately reflect the species tree if an appropriate number of taxa, typically ranging from six to ten, are sampled. Therefore, it is crucial to carefully select the number of taxa and an appropriate outgroup, such as slow-evolving species, while excluding fast-evolving taxa as outgroups to mitigate the adverse effects of long-branch attraction and achieve an accurate reconstruction of the species tree. This is particularly important as more whole-genome sequencing data becomes available.

Keywords: novel measures of phylogenetic support for phylogenomic data, gene concordance factor confidence, relative gene support, internode certainty, origin of tetrapods

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Authors: Kwan-Ho Kim, Jin-Hong Park

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The multi-valued logic (MVL) circuits, which can handle more than two logic states, are one of the promising solutions to overcome the bit density limitations of conventional binary logic systems. Recently, tunneling devices such as Esaki diode and resonant tunneling diode (RTD) have been extensively explored to construct the MVL circuits. These tunneling devices present a negative differential resistance (NDR) phenomenon in which a current decreases as a voltage increases in a specific applied voltage region. Due to this non-monotonic current behavior, the tunneling devices have more than two threshold voltages, consequently enabling construction of MVL circuits. Recently, the emergence of two dimensional (2D) van der Waals (vdW) crystals has opened up the possibility to fabricate such tunneling devices easily. Owing to the defect-free surface of the 2D crystals, a very abrupt junction interface could be formed through a simple stacking process, which subsequently allowed the implementation of a high-performance tunneling device. Here, we report a vdW heterostructure based tunneling device with multiple threshold voltages, which was fabricated with black phosphorus (BP) and hafnium diselenide (HfSe₂). First, we exfoliated BP on the SiO₂ substrate and then transferred HfSe₂ on BP using dry transfer method. The BP and HfSe₂ form type-Ⅲ heterojunction so that the highly doped n+/p+ interface can be easily implemented without additional electrical or chemical doping process. Owing to high natural doping at the junction, record high peak to valley ratio (PVCR) of 16 was observed to the best our knowledge in 2D materials based NDR device. Furthermore, based on this, we first demonstrate the feasibility of the ternary latch by connecting two multi-threshold voltage devices in series.

Keywords: two dimensional van der Waals crystal, multi-valued logic, negative differential resistnace, tunneling device

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Authors: Özlem Ateş Sönmezoğlu, Begüm Terzi, Ahmet Yıldırım, Leyla Gündüz

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Durum wheat quality is defined as its suitability for pasta processing, that is pasta making quality. Another factor that determines the quality of durum wheat is the nutritional value of wheat or its final products. Wheat is a basic source of calories, proteins and minerals for humans in many countries of the world. For this reason, improvement of wheat nutritional value is of great importance. In recent years, deficiencies in protein and micronutrients, particularly in iron and zinc, have seriously increased. Therefore, basic foods such as wheat must be improved for micronutrient content. The effects of some major genes for grain quality established. Gpc-B1 locus is one of the genes increased protein and micronutrients content, and used in improvement studies of durum wheat nutritional value. The aim of this study was to increase the protein content and the micronutrient (Fe, Zn ve Mn) contents of an advanced durum wheat line (TMB 1) that was previously improved for its protein quality. For this purpose, TMB1 advanced durum wheat line were used as the recurrent parent and also, UC1113-Gpc-B1 line containing the Gpc-B1 gene was used as the gene source. In all of the generations, backcrossed plants carrying the targeted gene region were selected by marker assisted selection (MAS). BC4F1 plants MAS method was employed in combination with embryo culture and rapid plant growth in a controlled greenhouse conditions in order to shorten the duration of the transition between generations in backcross breeding. The Gpc-B1 gene was selected specific molecular markers. Since Yr-36 gene associated with Gpc-B1 allele, it was also transferred to the Gpc-B1 transferred lines. Thus, the backcrossed plants selected by MAS are resistance to yellow rust disease. This research has been financially supported by TÜBİTAK (112T910).

Keywords: Durum wheat, Gpc-B1, MAS, Triticum durum, Yr-36

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Authors: M. Chukhryaeva, R. Skhalyakho, J. Kagazegeva, E. Pocheshkhova, L. Yepiskopossyan, O. Balanovsky, E. Balanovska

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The Middle East is crossroad of different populations at different times. The Kurds are of particular interest in this region. Historical sources suggested that the origin of the Kurds is associated with Medes. Therefore, it was especially interesting to compare gene pool of Kurds with other supposed descendants of Medes-Tats. Yezidis are ethno confessional group of Kurds. Yezidism as a confessional teaching was formed in the XI-XIII centuries in Iraq. Yezidism has caused reproductively isolation of Yezidis from neighboring populations for centuries. Also, isolation helps to retain Yezidian caste system. It is unknown how the history of Yezidis affected its genу pool because it has never been the object of researching. We have examined the Y-chromosome variation in Yezidis and Kurdish males to understand their gene pool. We collected DNA samples from 90 Yezidi males and 24 Kurdish males together with their pedigrees. We performed Y-STR analysis of 17 loci in the samples collected (Yfiler system from Applied Biosystems) and analysis of 42 Y-SNPs by real-time PCR. We compared our data with published data from other Kurdish groups and from European, Caucasian, and West Asian populations. We found that gene pool of Yezidis contains haplogroups common in the Middle East (J-M172(xM67,M12)- 24%, E-M35(xM78)- 9%) and in South Western Asia (R-M124- 8%) and variant with wide distribution area - R-M198(xM458- 9%). The gene pool of Kurdish has higher genetic diversity than Yezidis. Their dominants haplogroups are R-M198- 20,3 %, E-M35- 9%, J-M172- 9%. Multidimensional scaling also shows that the Kurds and Yezidis are part of the same frontier Asian cluster, which, in addition, included Armenians, Iranians, Turks, and Greeks. At the same time, the peoples of the Caucasus and Europe form isolated clusters that do not overlap with the Asian clusters. It is noteworthy that Kurds from our study gravitate towards Tats, which indicates that most likely these two populations are descendants of ancient Medes population. Multidimensional scaling also reveals similarity between gene pool of Yezidis, Kurds with Armenians and Iranians. The analysis of Yezidis pedigrees and their STR variability did not reveal a reliable connection between genetic diversity and caste system. This indicates that the Yezidis caste system is a social division and not a biological one. Thus, we showed that, despite many years of isolation, the gene pool of Yezidis retained a common layer with the gene pool of Kurds, these populations have common spectrum of haplogroups, but Yezidis have lower genetic diversity than Kurds. This study received primary support from the RSF grant No. 16-36-00122 to MC and grant No. 16-06-00364 to EP.

Keywords: gene pool, haplogroup, Kurds, SNP and STR markers, Yezidis

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Authors: Peter. M. Kusen, Georg Wandrey, Christopher Probst, Dietrich Kohlheyer, Jochen Buchs, Jorg Pietruszkau

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Light as a stimulus provides the capability to develop regulation techniques for customizable gene expression. A great advantage is the extremely flexible and accurate dosing that can be performed in a non invasive and sterile manner even for high throughput technologies. Therefore, light regulation in a multiwell microbioreactor system was realized providing the opportunity to control gene expression with outstanding complexity. A light-regulated gene expression system in Saccharomyces cerevisiae was designed applying the strategy of caged compounds. These compounds are photo-labile protected and therefore biologically inactive regulator molecules which can be reactivated by irradiation with certain light conditions. The “caging” of a repressor molecule which is consumed after deprotection was essential to create a flexible expression system. Thereby, gene expression could be temporally repressed by irradiation and subsequent release of the active repressor molecule. Afterwards, the repressor molecule is consumed by the yeast cells leading to reactivation of gene expression. A yeast strain harboring a construct with the corresponding repressible promoter in combination with a fluorescent marker protein was applied in a Photo-BioLector platform which allows individual irradiation as well as online fluorescence and growth detection. This device was used to precisely control the repression duration by adjusting the amount of released repressor via different irradiation times. With the presented screening platform the regulation of complex expression procedures was achieved by combination of several repression/derepression intervals. In particular, a stepwise increase of temporally-constant expression levels was demonstrated which could be used to study concentration dependent effects on cell functions. Also linear expression rates with variable slopes could be shown representing a possible solution for challenging protein productions, whereby excessive production rates lead to misfolding or intoxication. Finally, the very flexible regulation enabled accurate control over the expression induction, although we used a repressible promoter. Summing up, the continuous online regulation of gene expression has the potential to synchronize gene expression levels to optimize metabolic flux, artificial enzyme cascades, growth rates for co cultivations and many other applications addicted to complex expression regulation. The developed light-regulated expression platform represents an innovative screening approach to find optimization potential for production processes.

Keywords: caged-compounds, gene expression regulation, optogenetics, photo-labile protecting group

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Authors: Dedy Pratama, Akhmadu Muradi, Hilman Ibrahim, Raden Suhartono, Alexander Jayadi Utama, Patrianef Darwis, S. Dwi Anita, Luluk Yunaini, Kemas Dahlan

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Introduction: Vascular endothelial growth factor (VEGF) gene shows association with various angiogenesis conditions including Diabetic Foot Ulcer (DFU) disease. In this study, we performed this study to examine VEGF gene polymorphism associated with DFU. Methods: Case-control study of polymorphism of VEGF gene +405 C>G and -460 T>C, of diabetes mellitus (DM) type 2 with Diabetic Foot Ulcer (DFU) in Cipto Mangunkusumo National Hospital (RSCM) Jakarta from June to December 2016. Results: There were 203 patients, 102 patients with DFU and 101 patients without DFU. Forty-nine point 8 percent of total samples is male and 50,2% female with mean age 56,06 years. Distribution of the wild-type genotype VEGF +405 C>G wild type CC was found in 6,9% of respondents, the number of mutant heterozygote CG was 69,5% and mutant homozygote GG was 19,7%. Cumulatively, there were 6,9% wild-type and 85,2% mutant and 3,9% of total blood samples could not be detected on PCR-RFLP. Distribution of VEGF allele +405 C>G C alleles were 43% and G alleles were 57%. Distribution of genotype from VEGF gene -460 T>C is wild type TT 42,9%, mutant heterozygote TC 37,9% and mutant homozygote CC 13,3%. Cumulatively, there were 42,9% wild-type and 51% mutant type. Distribution of VEGF -460 T>C were 62% T allele and 38% C allele. Conclusion: In this study we found the distribution of alleles from VEGF +405 C>G is C 43% and G 57% and from VEGF -460 T>C; T 62% and C 38%. We propose that G allele in VEGF +405 C>G can act as a protective allele and on the other hands T allele in VEGF -460 T>C could be acted as a risk factor for DFU in diabetic patients.

Keywords: diabetic foot ulcer, diabetes mellitus, polymorphism, VEGF

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Authors: Natasha Petrovska, Mirjana Pavlovic, Maria M. Larrondo-Petrie

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Neural stem cells (NSCs) are multi-potent, self-renewing cells that generate new neurons. Three subtypes of NSCs can be separated regarding the stages of NSC lineage: quiescent neural stem cells (qNSCs), activated neural stem cells (aNSCs) and neural progenitor cells (NPCs), but their gene expression signatures are not utterly understood yet. Single-cell examinations have started to elucidate the complex structure of NSC populations. Nevertheless, there is a lack of thorough molecular interpretation of the NSC lineage heterogeneity and an increasing need for tools to analyze and improve the efficiency and correctness of single-cell sequencing data. Feature selection and ordering can identify and classify the gene expression signatures of these subtypes and can discover novel subpopulations during the NSCs activation and differentiation processes. The aim here is to review the implementation of the feature selection technique on NSC subtypes and the classification techniques that have been used for the identification of gene expression signatures.

Keywords: feature selection, feature similarity, neural stem cells, genes, feature selection methods

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Authors: Aleksandr Nagay, Gulnoz Khamidullayeva

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It is known that an unbalanced intake of salt (NaCI), lifestyle and genetic predisposition to pathology is a key component of the risk and the development of essential hypertension (EH). Purpose: To study the relationship between salt-sensitivity and blood pressure (BP) on systolic (SBP) and diastolic (DBP) blood pressure, depending on the C825T polymorphism of GNB3 in individuals of Uzbek nationality with EH. Method: studied 148 healthy and 148 patients with EH with I-II degree (WHO/ISH, 2003) with disease duration 6,5±1,3 years. Investigation of the gene GNB3 was produced by PCR-RFLP method. Determination of salt-sensitivity was performed by the method of R. Henkin. Results: For a comparative analysis of BP, the groups with carriage of CТ and TT genotypes were combined. The analysis showed that carriers of CC genotype and low salt-sensitivity were determined by higher levels of SBP compared with carriers of CT and TT genotypes, and low salt-sensitivity of SBP: 166,2±4,3 against 158,2±9,1 mm Hg (p=0,000). A similar analysis on the values of DBP also showed significantly higher values of blood pressure in carriers of CC genotype DBP: 105,8±10,6 vs. 100,5±7,2 mm Hg, respectively (p=0,001). The average values of SBP and DBP in groups with carriers of CC genotype at medium or high salt-sensitivity in comparison with carriers of CT or TT genotype did not differ statistically SBP: 165,0±0,1 vs. 160,0±8,6 mm Hg (p=0,275) and DBP: 100,1±0,1 vs. 101,6±7,6 mm Hg (p=0,687), respectively. Conclusion: It is revealed that in patients with EH CC genotype of the gene GNB3 given salt-sensitivity has a negative effect on blood pressure profile. Since patients with EH with the CC genotype of GNB3 gene with low-salt taste sensitivity is determined by a higher level of blood pressure, both on SBP and DBP.

Keywords: salt sensitivity, essential hypertension EH, blood pressure BP, genetic predisposition

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Authors: Bououden Soraya

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This paper aims to study the existence of the change of coordinates which permits to transform a class of nonlinear dynamical systems into the so-called nonlinear observer canonical form (NOCF). Moreover, an algorithm to construct such a change of coordinates is given. Based on this form, we can design an observer with a linear error dynamic. This enables us to estimate the state of a nonlinear dynamical system. A concrete example (biological model) is provided to illustrate the feasibility of the proposed results.

Keywords: nonlinear observer canonical form, observer, design, gene regulation, gene expression

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Authors: Shahid Hussain Abro, Siamak Zohari, Lena H. M. Renström, Désirée S. Jansson, Faruk Otman, Karin Ullman, Claudia Baule

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Infectious bronchitis is an acute, highly contagious respiratory, nephropathogenic and reproductive disease of poultry that is caused by infectious bronchitis virus (IBV). The present study used a large data set of structural gene sequences, including newly generated ones and sequences available in the GenBank database to further analyze the diversity and to identify selective pressures and recombination spots. There were some deletions or insertions in the analyzed regions in isolates of the Italy-02 and D274 genotypes. Whereas, there were no insertions or deletions observed in the isolates of the Massachusetts and 4/91 genotype. The hypervariable nucleotide sequence regions spanned positions 152–239, 554–582, 686–737 and 802–912 in the S1 sub-unit of the all analyzed genotypes. The nucleotide sequence data of the E gene showed that this gene was comparatively unstable and subjected to a high frequency of mutations. The M gene showed substitutions consistently distributed except for a region between nucleotide positions 250–680 that remained conserved. The lowest variation in the nucleotide sequences of ORF5a was observed in the isolates of the D274 genotype. While, ORF5b and N gene sequences showed highly conserved regions and were less subjected to variation. Genes ORF3a, ORF3b, M, ORF5a, ORF5b and N presented negative selective pressure among the analyzed isolates. However, some regions of the ORFs showed favorable selective pressure(s). The S1 and E proteins were subjected to a high rate of mutational substitutions and non-synonymous amino acids. Strong signals of recombination breakpoints and ending break point were observed in the S and N genes. Overall, the results of this study revealed that very likely the strong selective pressures in E, M and the high frequency of substitutions in the S gene can probably be considered the main determinants in the evolution of IBV.

Keywords: IBV, avian infectious bronchitis, structural genes, genotypes, genetic diversity

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Authors: Aisling De Paor

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Scientific and technological developments are driving genetics and genetic technologies into the public sphere. Scientists are making genetic discoveries as to the make up of the human body and the cause and effect of disease, diversity and disability amongst individuals. Technological innovation in the field of genetics is also advancing, with the development of genetic testing, and other emerging genetic technologies, including gene editing (which offers the potential for genetic modification). In addition to the benefits for medicine, health care and humanity, these genetic advances raise a range of ethical, legal and societal concerns. From an ethical perspective, such advances may, for example, change the concept of humans and what it means to be human. Science may take over in conceptualising human beings, which may push the boundaries of existing human rights. New genetic technologies, particularly gene editing techniques create the potential to stigmatise disability, by highlighting disability or genetic difference as something that should be eliminated or anticipated. From a disability perspective, use (and misuse) of genetic technologies raise concerns about discrimination and violations to the dignity and integrity of the individual. With an acknowledgement of the likely future orientation of genetic science, and in consideration of the intersection of genetics and disability, this paper highlights the main concerns raised as genetic science and technology advances (particularly with gene editing developments), and the consequences for disability and human rights. Through the use of traditional doctrinal legal methodologies, it investigates the use (and potential misuse) of gene editing as creating the potential for a unique form of discrimination and stigmatization to develop, as well as a potential gateway to a form of new, subtle eugenics. This article highlights the need to maintain caution as to the use, application and the consequences of genetic technologies. With a focus on the law and policy position in Europe, it examines the need to control and regulate these new technologies, particularly gene editing. In addition to considering the need for regulation, this paper highlights non-normative approaches to address this area, including awareness raising and education, public discussion and engagement with key stakeholders in the field and the development of a multifaceted genetics advisory network.

Keywords: disability, gene-editing, genetics, law, regulation

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Authors: Chao Sima, Shanaz Ghandhi, Sally A. Amundson, Michael L. Bittner, David J. Brenner

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In a large-scale radiologic emergency, potentially affected population need to be triaged efficiently using various biomarkers where personal dosimeters are not likely worn by the individuals. It has long been established that radiation injury can be estimated effectively using panels of genetic biomarkers. Furthermore, the rate of radiation, in addition to dose of radiation, plays a major role in determining biological responses. Therefore, a better and more accurate triage involves estimating both the dose level of the exposure and the length of time of that exposure. To that end, a large in vivo study was carried out on mice with internal emitter caesium-137 (¹³⁷Cs). Four different injection doses of ¹³⁷Cs were used: 157.5 μCi, 191 μCi, 214.5μCi, and 259 μCi. Cohorts of 6~7 mice from the control arm and each of the dose levels were sacrificed, and blood was collected 2, 3, 5, 7 and 14 days after injection for microarray RNA gene expression analysis. Using a generalized linear model with penalized maximum likelihood, a panel of 244 genes was established and both the doses of injection and the number of days after injection were accurately predicted for all 155 subjects using this panel. This has proven that microarray gene expression can be used effectively in radiation biodosimetry in predicting both the dose levels and the length of exposure time, which provides a more holistic view on radiation exposure and helps improving radiation damage assessment and treatment.

Keywords: caesium-137, gene expression microarray, multivariate responses prediction, radiation biodosimetry

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Authors: Jake Gonzalez, Tommy Dang

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This paper proposes a temporal graph approach to visualize and analyze the evolution of gene relationships and nomenclature over time. An interactive web-based tool implements this temporal graph, enabling researchers to traverse a timeline and observe coupled dynamics in network topology and naming conventions. Analysis of a real human genomic dataset reveals the emergence of densely interconnected functional modules over time, representing groups of genes involved in key biological processes. For example, the antimicrobial peptide DEFA1A3 shows increased connections to related alpha-defensins involved in infection response. Tracking degree and betweenness centrality shifts over timeline iterations also quantitatively highlight the reprioritization of certain genes’ topological importance as knowledge advances. Examination of the CNR1 gene encoding the cannabinoid receptor CB1 demonstrates changing synonymous relationships and consolidating naming patterns over time, reflecting its unique functional role discovery. The integrated framework interconnecting these topological and nomenclature dynamics provides richer contextual insights compared to isolated analysis methods. Overall, this temporal graph approach enables a more holistic study of knowledge evolution to elucidate complex biology.

Keywords: temporal graph, gene relationships, nomenclature evolution, interactive visualization, biological insights

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Authors: Catherine Felce, Lior Pachter

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Current methods for building phylogenetic trees from gene expression data consider mean expression levels. With single-cell technologies, we can leverage more information about cell dynamics by considering the entire distribution of gene expression across cells. Using biophysical modeling, we propose a method for constructing phylogenetic trees from scRNA-seq data, building on Felsenstein's method of continuous characters. This method can highlight genes whose level of expression may be unchanged between species, but whose rates of transcription/decay may have evolved over time.

Keywords: phylogenetics, single-cell, biophysical modeling, transcription

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Authors: Kumaran Narayanan, Andrew N. Osahor

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E. coli has been engineered by our group and by others as a vector to deliver DNA into cultured human and animal cells. However, so far conditions to improve gene delivery using this vector have not been investigated, resulting in a major gap in our understanding of the requirements for this vector to function optimally. Our group recently published novel data showing that simple addition of the DNA transfection reagent Lipofectamine increased the efficiency of the E. coli vector by almost 3-fold, providing the first strong evidence that further optimization of bactofection is possible. This presentation will discuss advances that demonstrate the effects of several intracellular strategies that improve the efficiency of this vector. Conditions that promote endosomal escape of internalized bacteria to evade lysosomal destruction after entry in the cell, a known obstacle limiting this vector, are elucidated. Further, treatments that increase bacterial lysis so that the vector can release its transgene into the mammalian environment for expression will be discussed. These experiments will provide valuable new insight to advance this E. coli system as an important class of vector technology for genetic correction of human disease models in cells and whole animals.

Keywords: DNA, E. coli, gene expression, vector

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Authors: Fuad M. Alkoot

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Different experimental technologies such as microarray sequencing have been proposed to generate high-resolution genetic data, in order to understand the complex dynamic interactions between complex diseases and the biological system components of genes and gene products. However, the generated samples have a very large dimension reaching thousands. Therefore, hindering all attempts to design a classifier system that can identify diseases based on such data. Additionally, the high overlap in the class distributions makes the task more difficult. The data we experiment with is generated for the identification of autism. It includes 142 samples, which is small compared to the large dimension of the data. The classifier systems trained on this data yield very low classification rates that are almost equivalent to a guess. We aim at reducing the data dimension and improve it for classification. Here, we experiment with applying a multistage PCA on the genetic data to reduce its dimensionality. Results show a significant improvement in the classification rates which increases the possibility of building an automated system for autism detection.

Keywords: PCA, gene expression, dimensionality reduction, classification, autism

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Authors: Jelena Slugan, Ivica Ružić

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We are witnessing the rapid development of technologies that change the world around us. However, curriculums and teaching processes are often slow to adapt to the change; it takes time, money and expertise to implement technology in the classroom. Therefore, the University of Split, Croatia, partnered with local school Marko Marulić High School and created the project "Modern competence in modern high schools" as part of which five different curriculums for STEM areas were developed. One of the curriculums involves combining information technology with physics. The main idea was to teach students how to use different circuits and microcomputers to explore nature and physical phenomena. As a result, using electrical circuits, students are able to recreate in the classroom the phenomena that they observe every day in their environment. So far, high school students had very little opportunity to perform experiments independently, and especially, those physics experiment did not involve ICT. Therefore, this project has a great importance, because the students will finally get a chance to develop themselves in accordance to modern technologies. This paper presents some new methods of teaching physics that will help students to develop experimental skills through the study of deterministic nature of physical laws. Students will learn how to formulate hypotheses, model physical problems using the electronic circuits and evaluate their results. While doing that, they will also acquire useful problem solving skills.

Keywords: ICT in physics, curriculum, laboratory activities, STEM (science, technology, engineering, mathematics)

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Authors: Mehdi Nasr-Esfahani, Leila Mohammad Bagheri, Ava Nasr-Esfahani

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Root and collar rot disease caused by Phytophthora capsici (Leonian) is one of the most serious diseases in pepper, Capsicum annuum L. In this study, a diverse collection of 37 commercial edible and ornamental pepper genotypes infected with P. capsici were investigated for biomass parameters and enzymatic activity of peroxidase or peroxide reductases (EC), superoxide dismutase (SOD), polyphenol oxidase (PPOs), catalase (CAT) and phenylalanine ammonia-lyase (PAL). Seven candidate DEG genes were also evaluated on resistant and susceptible pepper cultivars, through measuring product formation, using spectrophotometry and real-time polymerase chain reaction. All the five enzymes and seven defense-gene candidates were up-regulated in all inoculated pepper accessions to P. capsici. But, the enzymes and DEG genes were highly expressed in resistant cv. 19OrnP-PBI, 37ChillP-Paleo, and “23CherryP-Orsh". The expression level of enzymes were 1.5 to 5.6-fold higher in the resistant peppers, than the control non-inoculated genotypes. Also, the transcriptional levels of related candidate DEG genes were 3.16 to 5.90-fold higher in the resistant genotypes. There was a direct and high correlation coefficient between resistance, bio-mass parameters, enzymatic activity, and resistance gene expression. The related enzymes and candidate genes expressed herein will provide a basis for further gene cloning and functional verification studies, and also will aid in an understanding of the regulatory mechanism of pepper resistance to P. capsici.

Keywords: AP2/ERF, cDNA, enzymes, MIP gene, q-RTPCR, XLOC

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Authors: Priya Arora, Ashutosh Mishra

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Gene identification, towards the pursuit of mutated genes, leading to Parkinson’s disease, puts forward a challenge towards proactive cure of the disorder itself. Computational analysis is an effective technique for exploring genes in the form of protein sequences, as the theoretical and manual analysis is infeasible. The limitations and effectiveness of a particular computational method are entirely dependent on the previous data that is available for disease identification. The article presents a sequence-based classification method for the identification of genes responsible for Parkinson’s disease. During the initiation phase, the physicochemical properties of amino acids transform protein sequences into a feature vector. The second phase of the method employs Jaccard distances to select negative genes from the candidate population. The third phase involves artificial neural networks for making final predictions. The proposed approach is compared with the state of art methods on the basis of F-measure. The results confirm and estimate the efficiency of the method.

Keywords: disease gene identification, Parkinson’s disease, physicochemical properties of amino acid, protein sequences

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Authors: Swati Gautam, Amita Jain, Shyampyari Jaiswar

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Objective: To elucidate the role of (ApaI&TaqI) VDR gene polymorphism in the pathogenesis of female genital tuberculosis (FGTB) cases. Background: Female genital TB represents about 15-20% of total extra-pulmonary TB (EPTB). Female subjects with vitamin D deficiency have been shown to be at higher risk of pulmonary TB as well as FGTB. In same context few functional polymorphism in vitamin D receptor (VDR) gene has been considered as an important genetic risk factor that modulate the development of FGTB. Therefore we aimed, to elucidate the role of (ApaI&TaqI) VDR gene polymorphism in the pathogenesis of FGTB. Study design: Case-Control study. Sample size: Cases (60) and Controls (60). Study site: Department of Obstetrics & Gynecology & Department of Microbiology, K.G.M.U. Lucknow, (UP). Inclusion criteria: Cases: Women with age group 20-35 years, premenstrual endometrial aspiration collected and included in the study, those were positive with acid-fast bacilli (AFB)/ TB-PCR/ LJ culture/ liquid culture. Controls: Women with age group 20-35 years having no history of ATT and all test negative for TB recruited as control. Exclusion criteria: -Women with endometriosis, polycystic ovaries (PCOD), positive on Chlamydia & gonorrhea, already on anti-tubercular therapy (ATT) excluded. Materials and Methods: Blood samples were collected in EDTA tubes from cases and controls stored at -20ºC. Genomic DNA extraction was carried out by salting-out method. Genotyping of VDR gene (ApaI&TaqI) polymorphism was performed by using single amplification refractory mutation system (ARMS) PCR technique. PCR products were analyzed by electrophoresis on 2% agarose gel. Statistical analysis was done by SPSS16.3 software & computing odds ratio (OR) with 95% CI. Results: Increased risk of female genital tuberculosis was observed in AA genotype (OR =1.1419-6.212 95% CI, P*<0.036) and A allele (OR =1.255-3.518, 95% CI, P* < 0.006) in FGTB as compared to controls. Moreover A allele was found more frequent in FGTB patients. No significant difference was observed in TaqI gene polymorphism of VDR gene. Conclusion: The ApaI polymorphism is significantly associated with etiology of FGTB and plays an important role as a genetic risk factor in FGTB women.

Keywords: ARMS, ATT, EPTB, FGTB, VDR

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Authors: Abdullah Alaklabi, Ibrahim A. Arif, Sameera O. Bafeel, Ahmad H. Alfarhan, Anis Ahamed, Jacob Thomas, Mohammad A. Bakir

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Diospyros mespiliformis (Hochst. ex A.DC.; Ebenaceae) is a large deciduous medicinal plant. This plant species is currently listed as endangered in Saudi Arabia. Molecular identification of this plant species based on short sequence regions (571 and 664 bp) of plastid rbcL (ribulose-1, 5-biphosphate carboxylase) gene was investigated in this study. The endangered plant specimens were collected from Al-Baha, Saudi Arabia (GPS coordinate: 19.8543987, 41.3059349). Phylogenetic tree inferred from the rbcL gene sequences showed that this species is very closely related with D. brandisiana. The close relationship was also observed among D. bejaudii, D. Philippinensis and D. releyi (≥99.7% sequence homology). The partial rbcL gene sequence region (571 bp) that was amplified by rbcL primer-pair rbcLaF-rbcLaR failed to discriminate D. mespiliformis from the closely related plant species, D. brandisiana. In contrast, primer-pair rbcL1F-rbcL724R yielded longer amplicon, discriminated the species from D. brandisiana and demonstrated nucleotide variations in 3 different sites (645G>T; 663A>C; 710C>G). Although D. mespiliformis (EU980712) and D. brandisiana (EU980656) are very closely related species (99.4%); however, studied specimen showed 100% sequence homology with D. mespiliformis and 99.6% with D. brandisiana. The present findings showed that rbcL short sequence region (664 bp) of plastid rbcL gene, amplified by primer-pair rbcL1F-rbcL724R, can be used for authenticating samples of D. mespiliforformis and may provide help in authentic identification and management process of this medicinally valuable endangered plant species.

Keywords: Diospyros mespiliformis, endangered plant, identification partial rbcL

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Authors: Vishal Pareek, Shubham Gupta, Sushil Chandra Jain

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With increasing high-speed computation demand the power consumption, heat dissipation and chip size issues are posing challenges for logic design with conventional technologies. Recovery of bit loss and bit errors is other issues that require reversibility and fault tolerance in the computation. The reversible computing is emerging as an alternative to conventional technologies to overcome the above problems and helpful in a diverse area such as low-power design, nanotechnology, quantum computing. Bit loss issue can be solved through unique input-output mapping which require reversibility and bit error issue require the capability of fault tolerance in design. In order to incorporate reversibility a number of combinational reversible logic based circuits have been developed. However, very few sequential reversible circuits have been reported in the literature. To make the circuit fault tolerant, a number of fault model and test approaches have been proposed for reversible logic. In this paper, we have attempted to incorporate fault tolerance in sequential reversible building blocks such as D flip-flop, T flip-flop, JK flip-flop, R-S flip-flop, Master-Slave D flip-flop, and double edge triggered D flip-flop by making them parity preserving. The importance of this proposed work lies in the fact that it provides the design of reversible sequential circuits completely testable for any stuck-at fault and single bit fault. In our opinion our design of reversible building blocks is superior to existing designs in term of quantum cost, hardware complexity, constant input, garbage output, number of gates and design of online testable D flip-flop have been proposed for the first time. We hope our work can be extended for building complex reversible sequential circuits.

Keywords: parity preserving gate, quantum computing, fault tolerance, flip-flop, sequential reversible logic

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Authors: Waqas Shafqat Chattha, Muhammad Iqbal, Amir Shakeel

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Transcriptional factors are proteins that play a vital role in regulating the transcription of target genes in different biological processes and are being widely studied in different plant species. In the current era of genomics, plant genomes sequencing has directed to the genome-wide identification, analyses and categorization of diverse transcription factor families and hence provide key insights into their structural as well as functional diversity. The DNA-binding with One Finger (DOF) proteins belongs to C2-C2-type zinc finger protein family. DOF proteins are plant-specific transcription factors implicated in diverse functions including seed maturation and germination, phytohormone signalling, light-mediated gene regulation, cotton-fiber elongation and responses of the plant to biotic as well as abiotic stresses. In this context, a genome-wide in-silico analysis of DOF TF family in diploid cotton species i.e. Gossypium raimondii has enabled us to identify 55 non-redundant genes encoding DOF proteins renamed as GrDofs (Gossypium raimondii Dof). Gene distribution studies have shown that all of the GrDof genes are unevenly distributed across 12 out of 13 G. raimondii chromosomes. The gene structure analysis illustrated that 34 out of 55 GrDof genes are intron-less while remaining 21 genes have a single intron. Protein sequence-based phylogenetic analysis of putative 55 GrDOFs has divided these proteins into 5 major groups with various paralogous gene pairs. Molecular evolutionary studies aided with the conserved domain as well as gene structure analysis suggested that segmental duplications were the principal contributors for the expansion of Dof genes in G. raimondii.

Keywords: diploid cotton , G. raimondii, phylogenetic analysis, transcription factor

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Authors: John Saaka

Abstract:

The increasing world population poses a threat to food security. To meet current and future food demands, sweetpotato stand a good chance because of its recent food security roles. Concerted efforts are needed for both regional and local level varietal development. Heterosis exploiting breeding scheme (HEBS) is one of the options used to improve yield in some crop species and could be a good approach for sweetpotato improvement in Ghana by establishing heterotic gene pools within a population. To achieve this, 22 parental lines were collected from different sources and put in a full diallel arrangement. A total of 149 families, 20 individual cuttings per family, were taken to the field, including ‘checks’ and parental lines for experimentation in a 1m X 0.3m planting order according to the Westcott design. Results from this study led to the characterization of the selected parents into three main heterotic gene pools based on their suitability for use as male, female or both, respectively. This study serves as a baseline for further characterization of the rest of the germplasm in the Ghanaian sweetpotato breeding program.

Keywords: sweetpotato, heterosis, germplasm, food security

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Authors: M. Omer Faruk, A. M. A. M. Zonaed Siddiki, M. Fazal Karim, Md. Masuduzzaman, S. Chowdhury, Md. Shafiqul Islam, M. Alamgir Hossain

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The dog tapeworms Echinococcus granulosus develop hydatid cysts in various organs in human and domestic animals worldwide including Bangladesh. The aim of this study was to identify and characterize the genotype of E. granulosus isolated from cattle using 12S rRNA and Cytochrome oxidase 1 (COX 1) genes. A total of 43 hydatid cyst samples were collected from 390 examined cattle samples derived from slaughterhouses. Among them, three cysts were fertile. Genomic DNA was extracted from germinal membrane and/or protoscoleces followed by PCR amplification of mitochondrial 12S rRNA and Cytochrome oxidase 1 gene fragments. The sequence data revealed existence of G1 (64.28%) and possible G3 (21.43%) genotypes for the first time in Bangladesh. The study indicates that common sheep strain G1 is the dominant subtype of E. granulosus in Chittagong region of Bangladesh. This will increase our understanding of the epidemiology of hydatidosis in the southern part of the country and will be useful to plan suitable control measures in the long run.

Keywords: Echinococcus granulosus, Cox1, 12S rRNA, molecular characterization, Bangladesh

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