Search results for: suppressor genes

Authors: Gousilin Leandra Rocha Da Silva, Stéfani T. A. Dantas, Bruna F. Rossi, Erika R. Bonsaglia, Ivana G. Castilho, Terue Sadatsune, Ary Fernandes Júnior, Vera l. M. Rall

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Kidney failure causes decreased diuresis and accumulation of nitrogenous substances in the body. To increase patient survival, hemodialysis is used as a partial substitute for renal function. However, contamination of the water used in this treatment, causing bacteremia in patients, is a worldwide concern. The Burkholderia cepacia complex (Bcc), a group of bacteria with more than 20 species, is frequently isolated from hemodialysis water samples and comprises opportunistic bacteria, affecting immunosuppressed patients, due to its wide variety of virulence factors, in addition to innate resistance to several antimicrobial agents, contributing to the permanence in the hospital environment and to the pathogenesis in the host. The objective of the present work was to characterize molecularly and phenotypically Bcc isolates collected from the water and dialysate of the Hemodialysis Unit and from the blood of patients at a Public Hospital in Botucatu, São Paulo, Brazil, between 2019 and 2021. We used 33 Bcc isolates, previously obtained from blood cultures from patients with bacteremia undergoing hemodialysis treatment (2019-2021) and 24 isolates obtained from water and dialysate samples in a Hemodialysis Unit (same period). The recA gene was sequenced to identify the specific species among the Bcc group. All isolates were tested for the presence of some genes that encode virulence factors such as cblA, esmR, zmpA and zmpB. Considering the epidemiology of the outbreak, the Bcc isolates were molecularly characterized by Multi Locus Sequence Type (MLST) and by pulsed-field gel electrophoresis (PFGE). The verification and quantification of biofilm in a polystyrene microplate were performed by submitting the isolates to different incubation temperatures (20°C, average water temperature and 35°C, optimal temperature for group growth). The antibiogram was performed with disc diffusion tests on agar, using discs impregnated with cefepime (30µg), ceftazidime (30µg), ciprofloxacin (5µg), gentamicin (10µg), imipenem (10µg), amikacin 30µg), sulfametazol/trimethoprim (23.75/1.25µg) and ampicillin/sulbactam (10/10µg). The presence of ZmpB was identified in all isolates, while ZmpA was observed in 96.5% of the isolates, while none of them presented the cblA and esmR genes. The antibiogram of the 33 human isolates indicated that all were resistant to gentamicin, colistin, ampicillin/sulbactam and imipenem. 16 (48.5%) isolates were resistant to amikacin and lower rates of resistance were observed for meropenem, ceftazidime, cefepime, ciprofloxacin and piperacycline/tazobactam (6.1%). All isolates were sensitive to sulfametazol/trimethoprim, levofloxacin and tigecycline. As for the water isolates, resistance was observed only to gentamicin (34.8%) and imipenem (17.4%). According to PFGE results, all isolates obtained from humans and water belonged to the same pulsotype (1), which was identified by recA sequencing as B. cepacia¸, belonging to sequence type ST-767. By observing a single pulse type over three years, one can observe the persistence of this isolate in the pipeline, contaminating patients undergoing hemodialysis, despite the routine disinfection of water with peracetic acid. This persistence is probably due to the production of biofilm, which protects bacteria from disinfectants and, making this scenario more critical, several isolates proved to be multidrug-resistant (resistance to at least three groups of antimicrobials), turning the patient care even more difficult.

Keywords: hemodialysis, burkholderia cepacia, PFGE, MLST, multi drug resistance

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Authors: Ireneusz Majsterek, Karolina Przybylowska, Lukasz Dziki, Adam Dziki, Jacek Kabzinski

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Colorectal cancer (CRC) is one of the deadliest cancers. Every year we see an increase in the number of cases, and in spite of intensive research etiology of the disease remains unknown. For many years, researchers are seeking to associate genetic factors with an increased risk of CRC, so far it has proved to be a compelling link between the MMR system of DNA repair and hereditary nonpolyposis colorectal cancers (HNPCC). Currently, research is focused on finding the relationship between the remaining DNA repair systems and an increased risk of developing colorectal cancer. The aim of the study was to determine the relationship between gene polymorphisms Ser835Ser of XPF gene and Gly23Ala of XPA gene–elements of NER DNA repair system, and modulation of the risk of colorectal cancer in the Polish population. Determination of the molecular basis of carcinogenesis process and predicting increased risk will allow qualifying patients to increased risk group and including them in preventive program. We used blood collected from 110 patients diagnosed with colorectal cancer. The control group consisted of equal number of healthy people. Genotyping was performed by TaqMan method. The obtained results indicate that the genotype 23Gly/Ala of XPA gene is associated with an increased risk of colorectal cancer, while 23Ala/Ala as well as TCT allele of Ser835Ser of XPF gene may reduce the risk of CRC.

Keywords: NER, colorectal cancer, XPA, XPF, polymorphisms

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Authors: Niousha Bagheri Khulenjani, Mohammad Saniee Abadeh

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Learning from very big datasets is a significant problem for most present data mining and machine learning algorithms. MicroRNA (miRNA) is one of the important big genomic and non-coding datasets presenting the genome sequences. In this paper, a hybrid method for the classification of the miRNA data is proposed. Due to the variety of cancers and high number of genes, analyzing the miRNA dataset has been a challenging problem for researchers. The number of features corresponding to the number of samples is high and the data suffer from being imbalanced. The feature selection method has been used to select features having more ability to distinguish classes and eliminating obscures features. Afterward, a Convolutional Neural Network (CNN) classifier for classification of cancer types is utilized, which employs a Genetic Algorithm to highlight optimized hyper-parameters of CNN. In order to make the process of classification by CNN faster, Graphics Processing Unit (GPU) is recommended for calculating the mathematic equation in a parallel way. The proposed method is tested on a real-world dataset with 8,129 patients, 29 different types of tumors, and 1,046 miRNA biomarkers, taken from The Cancer Genome Atlas (TCGA) database.

Keywords: cancer classification, feature selection, deep learning, genetic algorithm

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Authors: H. Necef, A. Benayad

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Fungi are becoming more and more important in our life. Therefore, as a start for the symposium on filamentous fungi in biotechnology a short survey of the role of fungi in biotechnology. Salin soils occupy about 7% of land area; they are characterized by unsuitable physical conditions for the growth of living organisms. However, researches showed that some microorganisms especially fungi are able to grow and adapt to such extreme conditions; it is due to their ability to develop different physiological mechanisms in their adaptation. This is the first study on the physiological and biological characteristics of El-Beida marsh. Nine soil samples were taken at different points in two steps, the first was in winter (low temperature), and the second was in summer (high temperature). The physicochemical analyses of the soil were conducted, then the isolation process was applied using two methods, direct method and dilution method (10-1, 10-2, 10-3, 10-4). Different species of fungi were identified belong to 21 genera in addition to 3 yeast species, Aspergillus showed the highest proportion by 43%, then Penicillium by 20% then Alternaria by 7%, in addition to various genera in different proportions. As for the sampling periods, it was observed that the spread of fungi in winter was higher than in summer with the proportion 75.47% and 24.53% respectively. Some halotolerant fungi have a biotechnological importance especially if the salinity of the medium is necessary for the fermentation, and if the halotolerance genes of the fungus will define, this will open the research to study and improve this property for the industrial important micro-organisms.

Keywords: salinity, identification, aspergillus oryzae, halotolerance, fungi

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Authors: S. Taghavi Kalajahi, A. Koerdt, T. Lund Skovhus

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Cathodic protection (CP) is an electrochemical method to control and manage corrosion in different industries and environments. CP which is widely used, especially in buried and sub-merged environments, which both environments are susceptible to microbiologically influenced corrosion (MIC). Most of the standards recommend performing CP using -800 mV, however, if MIC threats are high or sulfate reducing bacteria (SRB) is present, the recommendation is to use more negative potentials for adequate protection of the metal. Due to the lack of knowledge and research on the effectiveness of CP on MIC, to the author’s best knowledge, there is no information about what MIC threat is and how much more negative potentials should be used enabling adequate protection and not overprotection (due to hydrogen embrittlement risk). Recently, the development and cheaper price of molecular microbial methods (MMMs) open the door for more effective investigations on the corrosion in the presence of microorganisms, along with other electrochemical methods and surface analysis. In this work, using MMMs, the gene expression of SRB biofilm under different potentials of CP will be investigated. The specific genes, such as pH buffering, metal oxidizing, etc., will be compared at different potentials, enabling to determine the precise potential that protect the metal effectively from SRB. This work is the initial step to be able to standardize the recommended potential under MIC condition, resulting better protection for the infrastructures.

Keywords: cathodic protection, microbiologically influenced corrosion, molecular microbial methods, sulfate reducing bacteria

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Authors: L. K. Davis

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The effects of the evolution force are observable in nature at all structural levels ranging from small molecular systems to conversely enormous biospheric systems. However, the evolution force and work associated with formation of biological structures has yet to be described mathematically or theoretically. In addressing the conundrum, we consider evolution from a unique perspective and in doing so we introduce the “Fundamental Theory of the Evolution Force: FTEF”. We utilized synthetic evolution artificial intelligence (SYN-AI) to identify genomic building blocks and to engineer 14-3-3 ζ docking proteins by transforming gene sequences into time-based DNA codes derived from protein hierarchical structural levels. The aforementioned served as templates for random DNA hybridizations and genetic assembly. The application of hierarchical DNA codes allowed us to fast forward evolution, while dampening the effect of point mutations. Natural selection was performed at each hierarchical structural level and mutations screened using Blosum 80 mutation frequency-based algorithms. Notably, SYN-AI engineered a set of three architecturally conserved docking proteins that retained motion and vibrational dynamics of native Bos taurus 14-3-3 ζ.

Keywords: 14-3-3 docking genes, synthetic protein design, time-based DNA codes, writing DNA code from scratch

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Authors: Maryam Saeidi, Ehsan Motamedian, Seyed Abbas Shojaosadati

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Zymomonas mobilis is known as an example of the uncoupled growth phenomenon. This microorganism also has a unique metabolism that degrades glucose by the Entner–Doudoroff (ED) pathway. In this paper, a genome-scale metabolic model including 434 genes, 757 reactions and 691 metabolites was reconstructed to simulate uncoupled growth and study its effect on flux distribution in the central metabolism. The model properly predicted that ATPase was activated in experimental growth yields of Z. mobilis. Flux distribution obtained from model indicates that the major carbon flux passed through ED pathway that resulted in the production of ethanol. Small amounts of carbon source were entered into pentose phosphate pathway and TCA cycle to produce biomass precursors. Predicted flux distribution was in good agreement with experimental data. The model results also indicated that Z. mobilis metabolism is able to produce biomass with maximum growth yield of 123.7 g (mol glucose)-1 if ATP synthase is coupled with growth and produces 82 mmol ATP gDCW-1h-1. Coupling the growth and energy reduced ethanol secretion and changed the flux distribution to produce biomass precursors.

Keywords: genome-scale metabolic model, Zymomonas mobilis, uncoupled growth, flux distribution, ATP dissipation

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Authors: Man-Ho Oh

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Membrane localized Leucine-Rich-Repeat Receptor-Like Kinases (LRR-RLKs) play crucial roles in plant growth and abiotic/biotic stress responses in higher plants including Arabidopsis and Brassica species. Among several Receptor-Like Kinases (RLKs), Leucine-Rich-Repeat Receptor-Like-Kinases (LRR-RLKs) are the major group of genes that play crucial roles related to growth, development and stress conditions in plant system. Since it is involved in several functional roles, it seems to be very important to investigate their roles in higher plants. We are particularly interested in brassinosteroid (BR) signaling, which is mediated by the BRASSINOSTEROID INSENSITIVE 1 (BRI1) receptor kinase and its co-receptor, BRI1-ASSOCIATED KINASE 1 (BAK1). Autophosphorylation of receptor kinases is recognized to be an important process in activation of signaling in higher plants. Although the plant receptors are generally classified as Ser/Thr protein kinases, many other receptor kinases including BRI1 and BAK1 are shown to autophosphorylate on Tyr residues in addition to Ser/Thr. As an interesting result, we determined that several 14-3-3 regulatory proteins bind to BRI1-CD and are phosphorylated by several receptor kinases in vitro, suggesting that BRI1 is critical for diverse signaling.

Keywords: autophosphorylation, brassinosteroid, BRASSINOSTEROID INSENSITIVE 1, BRI1-ASSOCIATED KINASE 1, Leucine-Rich-Repeat Receptor-Like Kinases (LRR-RLKs)

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Authors: Alexandra-Monica Toma

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As the internet became a ruling force of society, computer-mediated communication has enriched its methods to convey meaning by combining linguistic means to visual means of expressivity. One of the elements of cyberspace is what we call a meme, a succinct, visually engaging tool used to communicate ideas or emotions, usually in a funny or ironic manner. Coined by Richard Dawkings in the late 1970s to refer to cultural genes, this term now denominates a special type of vernacular language used to share content on the internet. This research aims to analyse the basic mechanism that stands at the basis of meme creation as a blend of innovation and imitation and will approach some of the most widely used image macros remixed to generate new content while also pointing out success strategies. Moreover, this paper discusses whether memes can transcend the light-hearted and playful mood they mirror and become biting and sharp cultural comments. The study also uses the concept of multimodality and stresses how the text interacts with image, discussing three types of relations between the two: symmetry, amplification, and contradiction. We will furthermore show that memes are cultural artifacts and virtual tropes highly dependent on context and societal issues by using a corpus of memes created related to the COVID-19 pandemic.

Keywords: context, computer-mediated communication, memes, multimodality

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Authors: M. Lizzy Madiwani, Ignatious Ncube, Evelyn Madoroba

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This study was designed to determine the distribution of pathogenic bacteria in household raised chickens and study their virulence and antibiotic profiles. For this purpose, 40 chickens were purchased from families in the Capricorn district and sacrificed for sampling. Tissues were cultured on different bacteriological media followed by biotyping using Matrix-assisted Laser Desorption Ionization-time of Flight (MALDI-TOF). Disk diffusion test was performed to determine the antibiotic susceptibility profiles of these bacteria. Out of a total of 160 tissue samples evaluated, E. coli and Salmonella were detected in these tissues. Furthermore, determination of the pathogenic E. coli and Salmonella strains at species level using primer sets that target selected genes of interest in the polymerase chain reaction (PCR) assay was employed. The invA gene, a confirmatory gene of Salmonella was detected in all the Salmonella isolates. The study revealed that there is a high distribution of Salmonella and pathogenic E. coli in these chickens. Therefore, further studies on identification at the species level are highly recommended to provide management and sanitation practices to lower this prevalence. The antimicrobial susceptibly data generated from this study can be a valuable reference to veterinarians for treating bacterial diseases in poultry.

Keywords: antimicrobial, Escherichia coli, pathogens, Salmonella

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Authors: Reem Al-Shidhani, Isabelle S. R. Storer, Michael J. Bromley, Lydia Tabernero

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Invasive fungal diseases are an increasing global health concern that contributes to the high mortality rates in immunocompromised patients. The rising of antifungal resistance severely lowers the efficacy of the limited antifungal agents available. New antifungal drugs that target new mechanisms are necessary to tackle the current shortfalls. Amongst post- modifications, phosphorylation is a predominant and an outstanding protein alteration in all eukaryotes. In fungi, protein phosphorylation plays a vital role in many signal transduction pathways, including cell cycle, cell growth, metabolism, transcription, differentiation, proliferation, and virulence. The investigation of Aspergillus fumigatus phosphatases revealed seven genes essential for viability. Inhibiting one of these phosphatases is a new interesting route to develop novel antifungal drugs. In this study, we carried out an early drug discovery process targeting oneessential phosphatase, GlcA. Here, we report the identification of new GlcA inhibitors that show antifungal activity. These important finding open a new avenue to the development of novel antifungals to expand the current narrow arsenal of clinical candidates.

Keywords: invasive fungal diseases, phosphatases, GlcA, competitive inhibitors

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Authors: Abdelaziz Messis, Azzeddine Bettache, Nawel Boucherba, Said Benallaoua, Mouloud Kecha

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Actinobacteria are of special biotechnological interest since they are known to produce chemically diverse compounds with a wide range of biological activity. This distinct clade of Gram-positve bacteria include some of the key antibiotic producers and are also sources of several bioactive compounds, established commercially a newly filamentous bacteria was recovered from Tikjda forest soil (Algeria) for its high antifungal activity against various pathogenic and phytopathogenic fungi. The nucleotide sequence of the 16S rRNA gene (1454 pb) of Streptomyces sp. TKJ2 exhibited close similarity (99 %) with other Streptomyces16S rRNA genes. Antifungal metabolite production of Streptomyces sp TKJ2 was evaluated using six different fermentation media. The extracellular products contained potent antifungal agents. Antifungal protein produced by Streptomyces sp. TKJ2 on PCA medium has been purified by ammonium sulfate precipitation, SPE column chromatography and high-performance liquid chromatography in a reverse-phase column. The UV chromatograms of the active fractions obtained at 214 nm by NanoLC-ESI-MS/MS have different molecular weights. The F20 Peptidic fraction obtained from culture filtrat of Streptomyces sp. TKJ2 precipitated at 30% of ammonium sulfate was selected for analysis by infusion ESI-MS which yielded a singly charged ion mass of 437.17 Da.

Keywords: actinobacteria, antifungal protein, chromatography, Streptomyces

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Authors: Sonam Kumari

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Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, possesses a remarkable feature of entering into and emerging from a persistent state. The mechanism by which Mtb switches from the dormant state to the replicative form is still poorly characterized. Proteome studies have given us an insight into the role of certain proteins in giving stupendous virulence to Mtb, but numerous dotsremain unconnected and unaccounted. The WhiB family of proteins is one such protein that is associated with developmental processes in actinomycetes.Mtb has seven such proteins (WhiB1 to WhiB7).WhiB proteins are transcriptional regulators; their conserved C-terminal HTH motif is involved in DNA binding. They regulate various essential genes of Mtbby binding to their promoter DNA. Biophysical Analysis of the effect of DNA binding on WhiB proteins has not yet been appropriately characterized. Interaction with DNA induces conformational changes in the WhiB proteins, confirmed by steady-state fluorescence and circular dichroism spectroscopy. ITC has deduced thermodynamic parameters and the binding affinity of the interaction. Since these transcription factors are highly unstable in vitro, their stability and solubility were enhanced by the co-expression of molecular chaperones. The present study findings help determine the conditions under which the WhiB proteins interact with their interacting partner and the factors that influence their binding affinity. This is crucial in understanding their role in regulating gene expression in Mtbandin targeting WhiB proteins as a drug target to cure TB.

Keywords: tuberculosis, WhiB proteins, mycobacterium tuberculosis, nucleic acid binding

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Authors: Mohammadjavad Sotoudeheian, Navid Farahmandian

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Cardiac hypertrophy arises in response to persistent increases in hemodynamic loads. In comparison, diabetic cardiomyopathy is defined by an abnormal myocardial changes without other cardiac-related risk factors. Pathological cardiac hypertrophy and myocardial remodeling are hallmarks of cardiovascular diseases and are risk factors for heart failure. The transcription factor forkhead box class O (FOXOs) can protect heart tissue by hostile oxidative stress and stimulating apoptosis and autophagy. FOXO proteins, as sensitive elements and mediators in response to environmental changes, have been revealed to prevent and inverse cardiac hypertrophy. FOXOs are inhibited by insulin and are critical mediators of insulin action. Insulin deficiency and uncontrolled diabetes lead to a catabolic state. FOXO1 acts downstream of the insulin-dependent pathways, which are dysregulated in diabetes. It regulates cardiomyocyte hypertrophy downstream of IGF1R/PI3K/Akt activation, which are critical regulators of cardiac hypertrophy. The complex network of signaling pathways comprising insulin/IGF-1 signaling, AMPK, JNK, and Sirtuins regulate the development of cardiovascular dysfunction by modulating the activity of FOXOs. Insulin receptors and IGF1R act via the PI3k/Akt and the MAPK/ERK pathways. Activation of Akt in response to insulin or IGF-1 induces phosphorylation of FOXOs. Increased protein synthesis induced by activation of the IGF-I/Akt/mTOR signaling pathway leads to hypertrophy. This pathway and the myostatin/Smad pathway are potent negative muscle development regulators. In cardiac muscle, insulin receptor substrates (IRS)-1 or IRS-2 activates the Akt signaling pathway and inactivate FOXO1. Under metabolic stress, p38 MAPK promotes degradation of IRS-1 and IRS-2 in cardiac myocytes and activates FOXO1, leading to cardiomyopathy. Sirt1 and FOXO1 interaction play an essential role in starvation-induced autophagy in cardiac metabolism. Inhibition of Angiotensin-II induced cardiomyocyte hypertrophy is associated with reduced FOXO1 acetylation and activation of Sirt1. The NF-κB, ERK, and FOXOs are de-acetylated by SIRT1. De-acetylation of FOXO1 induces the expression of genes involved in autophagy and stimulates autophagy flux. Therefore, under metabolic stress, FOXO1 can cause diabetic cardiomyopathy. The overexpression of FOXO1 leads to decreased cardiomyocyte size and suppresses cardiac hypertrophy through inhibition of the calcineurin–NFAT pathway. Diabetes mellitus is associated with elevation of O-GlcNAcylation. Some of its binding partners regulate the substrate selectivity of O-GlcNAc transferase (OGT). O-GlcNAcylation of essential contractile proteins may inhibit protein-protein interactions, reduce calcium sensitivity, and modulate contractile function. Uridine diphosphate (UDP)-GlcNAc is the obligatory substrate of OGT, which catalyzes a reversible post-translational protein modification. The increase of O-GlcNAcylation is accompanied by impaired cardiac hypertrophy in diabetic hearts. Inhibition of O-GlcNAcylation blocks activation of ERK1/2 and hypertrophic growth. O-GlcNAc modification on NFAT is required for its translocation from the cytosol to the nucleus, where NFAT stimulates the transcription of various hypertrophic genes. Inhibition of O-GlcNAcylation dampens NFAT-induced cardiac hypertrophic growth. Transcriptional activity of FOXO1 is enriched by improved O-GlcNAcylation upon high glucose stimulation or OGT overexpression. In diabetic conditions, the modification of FOXO1 by O-GlcNAc is promoted in cardiac troponin I and myosin light chain 2. Therefore targeting O-GlcNAcylation represents a potential therapeutic option to prevent hypertrophy in the diabetic heart.

Keywords: diabetes, cardiac hypertrophy, O-GlcNAcylation, FOXO1, Akt, PI3K, AMPK, insulin

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Authors: Lamis Naddaf, Yuval Tabach

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In this research, we identified the missense genetic variants that have the potential to enhance resistance against cancer. Such field has not been widely explored, as researchers tend to investigate mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution, and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and can have significant implications on improved risk estimation, diagnostics, prognosis and even for personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and picked up the alleles that showed a correlation with the species’ cancer resistance. We predicted 250 protecting variants (PVs) with a 0.01 false discovery rate and more than 20 thousand PVs with a 0.25 false discovery rate. Cancer resistance in Mammals and reptiles was significantly predicted by the number of PVs a species has. Moreover, Genes enriched with the protecting variants are enriched in pathways relevant to tumor suppression like pathways of Hedgehog signaling and silencing, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are more abundant in healthy people compared to cancer patients within different human races.

Keywords: comparative genomics, machine learning, cancer resistance, cancer-protecting alleles

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Authors: Caroline Kim

Abstract:

The designation autism spectrum disorder (ASD) groups complex disorders in the development of the brain. Autism is defined essentially as a condition in which an individual lacks a theory of mind. The theory of mind, in this sense, explains the ability of an individual to attribute feelings, emotions, or thoughts to another person. An autistic patient is characteristically unable to determine what an interlocutor is feeling, or to understand the beliefs of others. However, it is possible that autism cannot plausibly characterized as the lack of theory of mind in an individual. Genes, the bran, and its interplay with environmental factors may also cause autism. A mutation in a gene may be hereditary, or instigated by diseases such as mumps. Though an autistic patient may experience abnormalities in the cerebellum and the cortical regions, these are in fact only possible theories as to a biochemical explanation behind the disability. The prevailing theory identifying autism with lacking the theory of mind is supported by behavioral observation, but this form of observation is itself determined by socially constructed standards, limiting the possibility for empirical verification. The theory of mind infers that the beliefs and emotions of people are causally based on their behavior. This paper demonstrates the fallacy of this inference, critiquing its basis in socially constructed values, and arguing instead for a biochemical approach free from the conceptual apparatus of language and social expectation.

Keywords: autism spectrum disorder, sociology of psychology, social construction, the theory of mind

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Authors: Ergun Sakalar, Kubra Bilgic

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Faster detection and characterization of pathogens are the basis of the evoid from foodborne pathogens. Salmonella spp., Shigella spp. and Listeria monocytogenes are common foodborne bacteria that are among the most life-threatining. It is important to rapid and accurate detection of these pathogens to prevent food poisoning and outbreaks or to manage food chains. The present work promise to develop a sensitive, species specific and reliable PCR based detection system for simultaneous detection of Salmonella spp., Shigella spp. and Listeria monocytogenes. For this purpose, three genes were picked out, ompC for Salmonella spp., ipaH for Shigella spp. and hlyA for L. monocytogenes. After short pre-enrichment of milk was passed through a vacuum filter and bacterial DNA was exracted using commercially available kit GIDAGEN®(Turkey, İstanbul). Detection of amplicons was verified by examination of the melting temperature (Tm) that are 72° C, 78° C, 82° C for Salmonella spp., Shigella spp. and L. monocytogenes, respectively. The method specificity was checked against a group of bacteria strains, and also carried out sensitivity test resulting in under 10² CFU mL⁻¹ of milk for each bacteria strain. Our results show that the flourescence based triplex qPCR method can be used routinely to detect Salmonella spp., Shigella spp. and L. monocytogenes during the milk processing procedures in order to reduce cost, time of analysis and the risk of foodborne disease outbreaks.

Keywords: evagreen, food-born bacteria, pathogen detection, real-time pcr

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Authors: Lamis Naddaf, Yuval Tabach

Abstract:

We identified missense genetic variants with the potential to enhance resistance against cancer. Such a field has not been widely explored as researchers tend to investigate the mutations that cause diseases, in response to the suffering of patients, rather than those mutations that protect from them. In conjunction with the genomic revolution and the advances in genetic engineering and synthetic biology, identifying the protective variants will increase the power of genotype-phenotype predictions and have significant implications for improved risk estimation, diagnostics, prognosis, and even personalized therapy and drug discovery. To approach our goal, we systematically investigated the sites of the coding genomes and selected the alleles that showed a correlation with the species’ cancer resistance. Interestingly, we found several amino acids that are more generally preferred (like the Proline) or avoided (like the Cysteine) by the resistant species. Furthermore, Cancer resistance in mammals and reptiles is significantly predicted by the number of the predicted protecting variants (PVs) a species has. Moreover, PVs-enriched-genes are enriched in pathways relevant to tumor suppression. For example, they are enriched in the Hedgehog signaling and silencing pathways, which its improper activation is associated with the most common form of cancer malignancy. We also showed that the PVs are mostly more abundant in healthy people compared to cancer patients within different human races.

Keywords: cancer resistance, protecting variant, naked mole rat, comparative genomics

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Authors: F. M. El-Domyati, A. Atef, S. Edris, N. O. Gadalla, M. A. Al-Kordy, A. M. Ramadan, Y. M. Saad, H. S. Al-Zahrani, A. Bahieldin

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Transcriptome retrieved from SRA database of different tissues and treatments of C. roseus was assembled in order to detect tissue-specific transcription factors (TFs) and TFs possibly related to terpenoid indole alkaloids (TIA) pathway. A number of 290 TF-like transcripts along with 12 transcripts related to TIA biosynthetic pathway were divided in terms of co-expression in the different tissues, treatments and genotypes. Three transcripts encoding peroxidases 1 and 12 were downregulated in hairy root, while upregulated in mature leaf. Eight different transcripts of the TIA pathway co-expressed with TFs either functioning downstream tryptophan biosynthesis, e.g., tdc, str1 and sgd, or upstream vindoline biosynthesis, e.g., t16h, omt, nmt, d4h and dat. The results showed no differential expression of TF transcripts in hairy roots knocked down for tdc gene (TDCi) as compared to their wild type controls. There were several evidences of tissue-specific expression of TF transcripts in flower, mature leaf, root/hairy root, stem, seedling, hairy root and immature/mature leaves. Regulation included transcription factor families, e.g., bHLH, MYB and WRKY mostly induced by ABA and/or JA (or MeJA) and regulated during abiotic or biotic stress. The information of tissue-specific regulation and co-expression of TFs and genes in the TIA pathway can be utilized in manipulating alkaloid biosynthesis in C. roseus.

Keywords: SRA database, bHLH, MYB, WRKY, co-expression

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Authors: Chenyu Huang, Minrong Cui, Hua Fang, Luqing Zhang, Yunlong Yu

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The emergence and spread of antibiotic resistance genes (ARGs) have become a pressing issue in global agricultural production. However, understanding how these ARGs spread across different spatial scales, especially when exposed to both pesticides and antibiotics, has remained a challenge. Here, metagenomic assembly and binning methodologies were used to determine the mechanism of ARG propagation within soil-lettuce systems exposed to both fungicides and antibiotics. The results of our study showed that the presence of fungicide and antibiotic stresses had a significant impact on certain bacterial communities. Notably, we observed that ARGs were primarily transferred from the soil to the plant through plasmids. The selective pressure exerted by fungicides and antibiotics contributed to an increase in unique ARGs present on lettuce leaves. Moreover, ARGs located on chromosomes and plasmids followed different transmission patterns. The presence of diverse selective pressures, a result of compound treatments involving antibiotics and fungicides, amplifies this phenomenon. Consequently, there is a higher probability of bacteria developing multi-antibiotic resistance under the combined pressure of fungicides and antibiotics. In summary, our findings highlight that combined fungicide and antibiotic treatments are more likely to drive the acquisition of ARGs within the soil-plant system and may increase the risk of human ingestion.

Keywords: soil-lettuce system, fungicide, antibiotic, ARG, transmission

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Authors: Hieu Van Dong, Giang Thi Huong Tran, Giap Van Nguyen, Tung Duy Dao, Vuong Nghia Bui, Le Thi My Huynh, Yohei Takeda, Haruko Ogawa, Kunitoshi Imai

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Chicken anemia virus (CAV) has a ubiquitous and worldwide distribution in chicken production. Our group previously reported high seroprevalence of CAV in chickens in northern Vietnam. In the present study, 330 tissue samples collected from commercial and breeder chicken farms in eleven provinces in northern Vietnam were tested for the CAV infection. We found that 157 out of 330 (47.58%) chickens were positive with CAV genes by real-time PCR method. Nine CAV strains obtained from the different location and time were forwarded to the full-length sequence of CAV VP1 gene. Phylogenetic analysis of the Vietnamese CAV vp1 gene indicated that the CAVs circulating in northern Vietnam were divided into three distinct genotypes, II, III, and V, but not clustered with the vaccine strains. Among the three genotypes, genotype III was the major one widely spread in Vietnam, and that included three sub-genotypes, IIIa, IIIb, and IIIc. The Vietnamese CAV strains were closely related to the Chinese, Taiwanese, and USA strains. All the CAV isolates had glutamine at amino acid position 394 in the VP1 gene, suggesting that they might be highly pathogenic strains. One strain was defined to be genotype V, which had not been reported for Vietnamese CAVs. Additional studies are required to further evaluate the pathogenicity of CAV strains circulating in Vietnam.

Keywords: chicken anemia virus, genotype, genetic characteristics, Vietnam

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Authors: Oktira Roka Aji, Maelita R. Moeis, Ihsanawati, Ernawati A. Giri-Rachman

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Globally, tuberculosis (TB) remains a leading cause of death. The emergence of multidrug-resistant strains and extensively drug-resistant strains have become a major public concern. One of the potential candidates for drug target is the cytoplasmic domain of PhoR Histidine Kinase, a part of the Two Component System (TCS) PhoR-PhoP in Mycobacterium tuberculosis (Mtb). TCS PhoR-PhoP relay extracellular signal to control the expression of 114 virulent associated genes in Mtb. The 3D structure of PhoR cytoplasmic domain is needed to screen novel drugs using structure based drug discovery. The PhoR cytoplasmic domain from Mtb H37Rv was overexpressed in E. coli BL21(DE3), then purified using IMAC Ni-NTA Agarose his-tag affinity column and DEAE-ion exchange column chromatography. The molecular weight of the purified protein was estimated to be 37 kDa after SDS-PAGE analysis. This sample was used for pre-crystallization screening by applying sitting drop vapor diffusion method using Natrix (HR2-116) 48 solutions crystal screen kit at 25ºC. Needle-like crystals were observed after the seventh day of incubation in test solution No.47 (0.1 M KCl, 0.01 M MgCl2.6H2O, 0.05 M Tris-Cl pH 8.5, 30% v/v PEG 4000). Further testing is required for confirming the crystal.

Keywords: tuberculosis, two component system, histidine kinase, needle-like crystals

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Authors: Youn Young Shim, Ji Hye Kim, Jae Youl Cho, Martin J. T. Reaney

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Flaxseed (Linum usitatissimum L.) is gaining popularity in the food industry as a superfood due to its health-promoting properties. The flax plant synthesizes an array of biologically active cyclic peptides or linusorbs (LOs, a.k.a. cyclolinopeptides) from three or more ribosome-derived precursors. [1–9-NαC]-linusorb B3 and [1–9-NαC]-linusorb B2, suppress immunity, induce apoptosis in human epithelial cancer cell line (Calu-3) cells, and inhibit T-cell proliferation, but the mechanism of LOs action is unknown. Using gene expression analysis in nematode cultures and human cancer cell lines, we have observed that LOs exert their activity, in part, through induction of apoptosis. Specific LOs’ properties include: 1) distribution throughout the body after flaxseed consumption; 2) induce heat shock protein (HSP) 70A production as an indicator of stress and address the issue in Caenorhabditis elegans (exposure of nematode cultures to [1–9-NαC]-linusorb B3 induced a 30% increase in production of the HSP 70A protein); 3) induce apoptosis in Calu-3 cells; and 4) modulate regulatory genes in microarray analysis. These diverse activities indicate that LOs might induce apoptosis in cancer cells or act as versatile platforms to deliver a variety of biologically active molecules for cancer therapy.

Keywords: flaxseed, linusorb, cyclic peptide, orbitides, heat shock protein, apoptosis, anti-cancer

Procedia PDF Downloads 117

Authors: Rabia Faridi, Rizwana Maqbool, Umara Sahar Rana, Zaheer Ahmad

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Climate change impacts agriculture, notably in Germany, where spring faba beans predominate. However, improved winter hardiness aligns with milder winters, enabling autumn-sown varieties. Genetic resistance to Ascochyta blight is vital for crop integration. Traditional breeding faces challenges due to complex inheritance. This study assessed 224 homozygous faba bean lines for Ascochyta resistance traits. To achieve h²>70%, 12 replicates were required (realized h²=87%). Genetic variation and strong trait correlations were observed. Five lines outperformed 29H, while three were highly susceptible. A genome-wide association study (GWAS) with 188 inbred lines and 2058 markers, including 17 guide SNP markers, identified 12 markers associated with resistance traits, potentially indicating new resistance genes. One guide marker (Vf-Mt1g014230-001) on chromosome III validated a known QTL. The guided marker approach complemented GWAS, facilitating marker-assisted selection for Ascochyta resistance. The Göttingen Winter Bean Population offers promise for resistance breeding.

Keywords: genome wide association studies, marker assisted breeding, faba bean, ascochyta blight

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Authors: Ashish Kumar Pathak, Ritika Sharma, Vishal Nath, Sudhir Pratap Singh, Rakesh Tuli

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Litchi is a sub-tropical fruit crop with genotypes bearing delicious juicy fruits with variable seed size (bold to rudimentary size). Small seed size is a desirable trait in litchi, as it increases consumer acceptance and fruit processing. The biochemical activities in mid- stage ovules (e.g. 16, 20, 24 and 28 days after anthesis) determine the fate of seed and fruit development in litchi. Comprehensive ovule-specific transcriptome analysis was performed in two litchi genotypes with contrasting seed size to gain molecular insight on determinants of seed fates in litchi fruits. The transcriptomic data was de-novo assembled in 1,39,608 trinity transcripts, out of which 6,325 trinity transcripts were differentially expressed between the two contrasting genotypes. Differential transcriptional pattern was found among ovule development stages in contrasting litchi genotypes. The putative genes for salicylic acid, jasmonic acid and brassinosteroid pathway were down-regulated in ovules of small-seeded litchi. Embryogenesis, cell expansion, seed size and stress related trinity transcripts exhibited altered expression in small-seeded genotype. The putative regulators of seed maturation and seed storage were down-regulated in small-seed genotype.

Keywords: Litchi, seed, transcriptome, defence

Procedia PDF Downloads 220

Authors: Yessengali Ussenbekov, Valery Terletskiy, Orik Zhanserkenova, Shynar Kasymbekova, Indira Beyshova, Aitkali Imanbayev, Almas Serikov

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Currently, there are 46 hereditary diseases afflicting cattle with known molecular genetic diagnostic methods developed for them. Genetic anomalies frequently occur in the Holstein cattle breeds from American and Canadian bloodlines. The data on the incidence of BLAD, CVM, DUMPS and BC autosomal recessive lethal mutations in pedigree animals are discordant, the detrimental allele incidence rates are high for the Holstein cattle breed, whereas the incidence rates of these mutations are low in some breeds or they are completely absent. Data were obtained on the basis of frozen semen of stud bulls. DNA was extracted from the semen with the DNA-Sorb-B extraction kit. The lethal mutation in the genes CD18, SLC35A3, UMP and ASS of Alatau stud bulls (N=124) was detected by polymerase chain reaction and RFLP analysis. It was established that stud bulls of the local Alatau breed were not carriers of the BLAD, CVM, DUMPS, and BC detrimental mutations. However, with a view to preventing the dissemination of hereditary diseases it is recommended to monitor the pedigree stock using molecular genetic methods.

Keywords: PCR, autosomal recessive point mutation, BLAD, CVM, DUMPS, BC, stud bulls

Procedia PDF Downloads 421

Authors: Abdul Musaweer Habib, Habibul Hasan Mazumder, Saiful Islam, Sohel Sikder, Omar Faruk Sikder

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The plethora of genome sequence information of bacteria in recent times has ushered in many novel strategies for antibacterial drug discovery and facilitated medical science to take up the challenge of the increasing resistance of pathogenic bacteria to current antibiotics. In this study, we adopted subtractive genomics approach to analyze the whole genome sequence of the Fusobacterium nucleatum, a human oral pathogen having association with colorectal cancer. Our study divulged 1499 proteins of Fusobacterium nucleatum, which has no homolog in human genome. These proteins were subjected to screening further by using the Database of Essential Genes (DEG) that resulted in the identification of 32 vitally important proteins for the bacterium. Subsequent analysis of the identified pivotal proteins, using the KEGG Automated Annotation Server (KAAS) resulted in sorting 3 key enzymes of F. nucleatum that may be good candidates as potential drug targets, since they are unique for the bacterium and absent in humans. In addition, we have demonstrated the 3-D structure of these three proteins. Finally, determination of ligand binding sites of the key proteins as well as screening for functional inhibitors that best fitted with the ligands sites were conducted to discover effective novel therapeutic compounds against Fusobacterium nucleatum.

Keywords: colorectal cancer, drug target, Fusobacterium nucleatum, homology modeling, ligands

Procedia PDF Downloads 362

Authors: Abdullah Mohammad, Abdullah Alshemali, Esmaeil Alsaleh

Abstract:

The chemical composition of desalinated water is modified to make it more acceptable to the end-user. Sometimes, this modification is approached by mixing with brackish water that is known to contain a variety of minerals. Expectedly, besides minerals, brackish water indigenous bacterial communities access the final mixture hence reaching the end consumer. The current project examined the safety of using brackish water as an ingredient in potable water. Pseudomonas aeruginosa strains were detected in potable and brackish water samples collected from storage facilities in residential areas as well as from main water distribution and storage tanks. The application of molecular and biochemical fingerprinting methods, including phylogeny, RFLP (restriction fragment length polymorphism), MLST (multilocus sequence typing) and substrate specificity testing, suggested that the potable water P. aeruginosa strains were most probably originated from brackish water. Additionally, all the sixty-four isolates showed multi-drug resistance (MDR) phenotype and harboured the three genes responsible for biofilm formation. These virulence factors represent serious health hazards compelling the scientific community to revise the WHO (World Health Organization) and USEP (US Environmental Protection Agency) A potable water quality guidelines, particularly those related to the types of bacterial genera that evade the current water quality guidelines.

Keywords: potable water, brackish water, pseudomonas aeroginosa, multidrug resistance

Procedia PDF Downloads 99

Authors: Yogesh Dalvi, Ruby Varghese, Nibu Varghese, C. K. Krishnan Nair

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Introduction: The Genus Phellinus, locally known as Phansomba is a well-known traditional folk medicine. Especially, in Western Ghats of India, many tribes use several species of Phellinus for various ailments related to teeth, throat, tongue, stomach and even wound healing. It is one of the few mushrooms which play a pivotal role in Ayurvedic Dravyaguna. Aim: The present study focuses on to investigate phytochemical analysis, antioxidant, and antitumor (in vitro and in vivo) potential of Phellinus robinae from South India, Kerala Material and Methods: The present study explores the following: 1. Phellinus samples were collected from Ranni, Pathanamthitta district of Kerala state, India from Artocarpus heterophyllus Lam. and species were identified using rDNA region. 2. The fruiting body was shadow dried, powdered and extracted with 50% alcohol using water bath at 60°C which was further condensed by rotary evaporator and lyophilized at minus 40°C temperature. 3. Secondary metabolites were analyzed by using various phytochemical screening assay (Hager’s Test, Wagner’s Test, Sodium hydroxide Test, Lead acetate Test, Ferric chloride Test, Folin-ciocalteu Test, Foaming Test, Benedict’s test, Fehling’s Test and Lowry’s Test). 4. Antioxidant and free radical scavenging activity were analyzed by DPPH, FRAP and Iron chelating assay. 5. The antitumor potential of Water alcohol extract of Phellinus (PAWE) is evaluated through In vitro condition by Trypan blue dye exclusion method in DLA cell line and In vivo by murine model. Result and Discussion: Preliminary phytochemical screening by various biochemical tests revealed presence of a variety of active secondary molecules like alkaloids, flavanoids, saponins, carbohydrate, protein and phenol. In DPPH and FRAP assay PAWE showed significantly higher antioxidant activity as compared to standard Ascorbic acid. While, in Iron chelating assay, PAWE exhibits similar antioxidant activity that of Butylated Hydroxytoluene (BHT) as standard. Further, in the in vitro study, PAWE showed significant inhibition on DLA cell proliferation in dose dependent manner and showed no toxicity on mice splenocytes, when compared to standard chemotherapy drug doxorubicin. In vivo study, oral administration of PAWE showed dose dependent tumor regression in mice and also raised the immunogenicity by restoring levels of antioxidant enzymes in liver and kidney tissue. In both in vitro and in vivo gene expression studies PAWE up-regulates pro-apoptotic genes (Bax, Caspases 3, 8 and 9) and down- regulates anti-apoptotic genes (Bcl2). PAWE also down regulates inflammatory gene (Cox-2) and angiogenic gene (VEGF). Conclusion: Preliminary phytochemical screening revealed that PAWE contains various secondary metabolites which contribute to its antioxidant and free radical scavenging property as evaluated by DPPH, FRAP and Iron chelating assay. PAWE exhibits anti-proliferative activity by the induction of apoptosis through a signaling cascade of death receptor-mediated extrinsic (Caspase8 and Tnf-α), as well as mitochondria-mediated intrinsic (caspase9) and caspase pathways (Caspase3, 8 and 9) and also by regressing angiogenic factor (VEGF) without any inflammation or adverse side effects. Hence, PAWE serve as a potential antioxidant and antitumor agent.

Keywords: antioxidant, antitumor, Dalton lymphoma ascites (DLA), fungi, Phellinus robinae

Procedia PDF Downloads 285

Authors: Gizem Buldum, Alexander Bismarck, Athanasios Mantalaris

Abstract:

Cellulose is the most abundant biopolymer on earth and it is currently being utilised in a multitude of industrial applications. Over the last 30 years, attention has been paid to the bacterial cellulose (BC), since BC exhibits unique physical, chemical and mechanical properties when compared to plant-based cellulose, including high purity and biocompatibility. Although Acetobacter xylinum is the most efficient producer of BC, it’s long doubling time results in insufficient yields of the cellulose production. This limits widespread and continued use of BC. In this study, E. coli BL21 (DE3) or E. coli HMS cells are selected as host organisms for the expression of bacterial cellulose synthase operon (bcs) of A.xylinum. The expression system is created based on pET-Duet1 and pCDF plasmid vectors, which carry bcs operon. The results showed that all bcs genes were successfully transferred and expressed in E.coli strains. The expressions of bcs proteins were shown by SDS and Native page analyses. The functionality of the bcs operon was proved by congo red binding assay. The effect of culturing temperature and the inducer concentration (IPTG) on cell growth and plasmid stability were monitored. The percentage of plasmid harboring cells induced with 0.025 mM IPTG was obtained as 85% at 22˚C in the end of 10-hr culturing period. It was confirmed that the high output cellulose production machinery of A.xylinum can be transferred into other organisms.

Keywords: bacterial cellulose, biopolymer, recombinant expression system, production

Procedia PDF Downloads 372