Search results for: gene annotation

Authors: Sonia Bedhiaf-Romdhani

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The sheep (Ovis aries) was domesticated, approximately 11,000 years ago (YBP), in the Fertile Crescent from Asian Mouflon (Ovis Orientalis). The Northern African (NA) sheep is 7,000 years old, represents a remarkable diversity of sheep populations reared under traditional and low input farming systems (LIFS) over millennia. The majority of small ruminants in developing countries are encountered in low input production systems and the resilience of local communities in rural areas is often linked to the wellbeing of small ruminants. Regardless of the rich biodiversity encountered in sheep ecotypes there are four main sheep breeds in the country with 61,6 and 35.4 percents of Barbarine (fat tail breed) and Queue Fine de l’Ouest (thin tail breed), respectively. Phoenicians introduced the Barbarine sheep from the steppes of Central Asia in the Carthaginian period, 3000 years ago. The Queue Fine de l’Ouest is a thin-tailed meat breed heavily concentrated in the Western and the central semi-arid regions. The Noire de Thibar breed, involving mutton-fine wool producing animals, has been on the verge of extinction, it’s a composite black coated sheep breed found in the northern sub-humid region because of its higher nutritional requirements and non-tolerance of the prevailing harsher condition. The D'Man breed, originated from Morocco, is mainly located in the southern oases of the extreme arid ecosystem. A genetic investigation of Tunisian sheep breeds using a genome-wide scan of approximately 50,000 SNPs was performed. Genetic analysis of relationship between breeds highlighted the genetic differentiation of Noire de Thibar breed from the other local breeds, reflecting the effect of past events of introgression of European gene pool. The Queue Fine de l’Ouest breed showed a genetic heterogeneity and was close to Barbarine. The D'Man breed shared a considerable gene flow with the thin-tailed Queue Fine de l'Ouest breed. Native small ruminants breeds, are capable to be efficiently productive if essential ingredients and coherent breeding schemes are implemented and followed. Assessing the status of genetic variability of native sheep breeds could provide important clues for research and policy makers to devise better strategies for the conservation and management of genetic resources.

Keywords: sheep, farming systems, diversity, SNPs.

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Authors: Lillian Musila, Valerie Oundo, Daniel Erwin, Willie Sang

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Staphylococcus aureus infections are a major cause of nosocomial infections in Kenya. Methicillin resistant S. aureus (MRSA) infections are a significant burden to public health and are associated with considerable morbidity and mortality. At a hospital in Western Kenya two clusters of MRSA cases emerged within short periods of time. In this study we explored whether these clusters represented a nosocomial outbreak by characterizing the isolates using phenotypic and molecular assays and examining epidemiological data to identify possible transmission patterns. Specimens from the site of infection of the subjects were collected, cultured and S. aureus isolates identified phenotypically and confirmed by APIStaph™. MRSA were identified by cefoxitin disk screening per CLSI guidelines. MRSA were further characterized based on their antibiotic susceptibility patterns and spa gene typing. Characteristics of cases with MRSA isolates were compared with those with MSSA isolated around the same time period. Two cases of MRSA infection were identified in the two week period between 21 April and 4 May 2015. A further 2 MRSA isolates were identified on the same day on 7 September 2015. The antibiotic resistance patterns of the two MRSA isolates in the 1st cluster of cases were different suggesting that these were distinct isolates. One isolate had spa type t2029 and the other had a novel spa type. The 2 isolates were obtained from urine and an open skin wound. In the 2nd cluster of MRSA isolates, the antibiotic susceptibility patterns were similar but isolates had different spa types: one was t037 and the other a novel spa type different from the novel MRSA spa type in the first cluster. Both cases in the second cluster were admitted into the hospital but one infection was community- and the other hospital-acquired. Only one of the four MRSA cases was classified as an HAI from an infection acquired post-operatively. When compared to other S. aureus strains isolated within the same time period from the same hospital only one spa type t2029 was found in both MRSA and non-MRSA strains. None of the cases infected with MRSA in the two clusters shared any common epidemiological characteristic such as age, sex or known risk factors for MRSA such as prolonged hospitalization or institutionalization. These data suggest that the observed MRSA clusters were multi strain clusters and not an outbreak of a single strain. There was no clear relationship between the isolates by spa type suggesting that no transmission was occurring within the hospital between these cluster cases but rather that the majority of the MRSA strains were circulating in the community. There was high diversity of spa types among the MRSA strains with none of the isolates sharing spa types. Identification of disease clusters in space and time is critical for immediate infection control action and patient management. Spa gene typing is a rapid way of confirming or ruling out MRSA outbreaks so that costly interventions are applied only when necessary.

Keywords: cluster, Kenya, MRSA, spa typing

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Authors: M. Acin-Albiac, P. Filannino, R. Coda, Carlo G. Rizzello, M. Gobbetti, R. Di Cagno

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Demand for smart management of large amounts of agro-food by-products has become an area of major environmental and economic importance worldwide. Brewers' spent grain (BSG), the most abundant by-product generated in the beer-brewing process, represents an example of valuable raw material and source of health-promoting compounds. To the date, the valorization of BSG as a food ingredient has been limited due to poor technological and sensory properties. Tailored bioprocessing through lactic acid bacteria (LAB) fermentation is a versatile and sustainable means for the exploitation of food industry by-products. Indigestible carbohydrates (e.g., hemicelluloses and celluloses), high phenolic content, and mostly lignin make of BSG a hostile environment for microbial survival. Hence, the selection of tailored starters is required for successful fermentation. Our study investigated the metabolic strategies of Leuconostoc pseudomesenteroides and Lactobacillus plantarum strains to exploit BSG as a food ingredient. Two distinctive BSG samples from different breweries (Italian IT- and Finish FL-BSG) were microbially and chemically characterized. Growth kinetics, organic acid profiles, and the evolution of phenolic profiles during the fermentation in two BSG model media were determined. The results were further complemented with gene expression targeting genes involved in the degradation cellulose, hemicelluloses building blocks, and the metabolism of anti-nutritional factors. Overall, the results were LAB genus dependent showing distinctive metabolic capabilities. Leuc. pseudomesenteroides DSM 20193 may degrade BSG xylans while sucrose metabolism could be furtherly exploited for extracellular polymeric substances (EPS) production to enhance BSG pro-technological properties. Although L. plantarum strains may follow the same metabolic strategies during BSG fermentation, the mode of action to pursue such strategies was strain-dependent. L. plantarum PU1 showed a great preference for β-galactans compared to strain WCFS1, while the preference for arabinose occurred at different metabolic phases. Phenolic compounds profiling highlighted a novel metabolic route for lignin metabolism. These findings will allow an improvement of understanding of how lactic acid bacteria transform BSG into economically valuable food ingredients.

Keywords: brewery by-product valorization, metabolism of plant phenolics, metabolism of lactic acid bacteria, gene expression

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Authors: Muhammad Haroon, LI Xiangju

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C. communis L. is an important weed of many crop, but very little information about the adaptation strategies of C. communis L. biotypes under drought stress. We investigated five biotypes of C. communis L under drought stress to identify the adaptation mechanism. The expression of drought stress related genes (DRS1, EREB and HRB1) was up-regulated in biotypes, while in some biotypes their expression was down regulated. All five biotypes can thus regulate water balance to consume less water to maintain their status under drought stress condition. This result concluded that C. communis L. biotypes can survive longer under drought stress condition. Weed scientist should seek more effective management strategies to deal with C. communis L.

Keywords: C. communis, biotypes, drought stress, gene expression

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Authors: Angel Champion

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Chemotherapy and radiation use an acidified approach to induce apoptosis, which only kills mature cancer cells while resulting in gene and cell damage with significant levels of toxicity in tumor-affected tissues and organs. The acid approach, where the cells exterminated are not differentiated, induces the disappearance of white blood cells from the blood. This increases susceptibility to infection in severe forms of cancer spread. However, chemotherapy and radiation cannot kill cancer stem cells that metastasize, being the leading cause of 98% of cancer fatalities. With over 12 million new cancer cases symptomatic each year, including common malignancies such as Hepatocellular Carcinoma (HCC), this study aims to assess the bioactive constituents and phytochemical composition of Taraxacum Officinale (Dandelion). This analysis enables pharmaceutical quality and potency to be applied to studies on cancer cell proliferation and apoptosis. A phytochemical screening is carried out to identify the antioxidant components of Dandelion root, stem, and flower extract. The constituents tested for are phlorotannins, carbohydrates, glycosides, saponins, flavonoids, alkaloids, sterols, triterpenes, and anthraquinone glycosides. To conserve the existing phenolic compounds, a portion of the constituent tests will be examined with an acid, alcohol, or aqueous solvent. As a result, the qualitative and quantitative variations within the Dandelion extract that measure uniform effective potency are vital to the conformity for producing medicinal products. These medicines will be constructed with a consistent, uniform composition that physicians can use to control and effectively eradicate malignant diseases safely. Taraxacum Officinale's phytochemical composition comprises a highly-graded potency due to present bioactive contents that will essentially drive out malignant disease within the human body. Its high potency rate is powerful enough to eliminate both mature cancer cells and cancer stem cells without the cell and gene damage induced by chemotherapy and radiation. Correspondingly, the high margins of cancer mortality on a global scale are mitigated. This remarkable contribution to modern therapeutics will essentially optimize the margins of natural products and their derivatives, which account for 50% of pharmaceuticals in modern therapeutics, while preventing the adverse effects of radiation and chemotherapy drugs.

Keywords: antioxidant, apoptosis, metastasize, phytochemical, proliferation, potency

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Authors: M. Sakthivel, A. Devaki, D. Balasubramanyam, P. Kumarasamy, A. Raja, R. Anilkumar, H. Gopi

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The New Zealand White breed of rabbit is one of the most commonly used, well adapted exotic breeds in India. Earlier studies were limited only to analyze the environmental factors affecting the growth and reproductive performance. In the present study, the population of the New Zealand White rabbits in a closed herd was evaluated for its genetic structure. Data on pedigree information (n=2508) for 18 years (1995-2012) were utilized for the study. Pedigree analysis and the estimates of population genetic parameters based on gene origin probabilities were performed using the software program ENDOG (version 4.8). The analysis revealed that the mean values of generation interval, coefficients of inbreeding and equivalent inbreeding were 1.489 years, 13.233 percent and 17.585 percent, respectively. The proportion of population inbred was 100 percent. The estimated mean values of average relatedness and the individual increase in inbreeding were 22.727 and 3.004 percent, respectively. The percent increase in inbreeding over generations was 1.94, 3.06 and 3.98 estimated through maximum generations, equivalent generations, and complete generations, respectively. The number of ancestors contributing the most of 50% genes (fₐ₅₀) to the gene pool of reference population was 4 which might have led to the reduction in genetic variability and increased amount of inbreeding. The extent of genetic bottleneck assessed by calculating the effective number of founders (fₑ) and the effective number of ancestors (fₐ), as expressed by the fₑ/fₐ ratio was 1.1 which is indicative of the absence of stringent bottlenecks. Up to 5th generation, 71.29 percent pedigree was complete reflecting the well-maintained pedigree records. The maximum known generations were 15 with an average of 7.9 and the average equivalent generations traced were 5.6 indicating of a fairly good depth in pedigree. The realized effective population size was 14.93 which is very critical, and with the increasing trend of inbreeding, the situation has been assessed to be worse in future. The proportion of animals with the genetic conservation index (GCI) greater than 9 was 39.10 percent which can be used as a scale to use such animals with higher GCI to maintain balanced contribution from the founders. From the study, it was evident that the herd was completely inbred with very high inbreeding coefficient and the effective population size was critical. Recommendations were made to reduce the probability of deleterious effects of inbreeding and to improve the genetic variability in the herd. The present study can help in carrying out similar studies to meet the demand for animal protein in developing countries.

Keywords: effective population size, genetic structure, pedigree analysis, rabbit genetics

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Authors: Atsuko Okazaki, Jurg Ott

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Some genetic diseases (‘digenic traits’) are due to the interaction between two DNA variants. For example, certain forms of Retinitis Pigmentosa (a genetic form of blindness) occur in the presence of two mutant variants, one in the ROM1 gene and one in the RDS gene, while the occurrence of only one of these mutant variants leads to a completely normal phenotype. Detecting such digenic traits by genetic methods is difficult. A common approach to finding disease-causing variants is to compare 100,000s of variants between individuals with a trait (cases) and those without the trait (controls). Such genome-wide association studies (GWASs) have been very successful but hinge on genetic effects of single variants, that is, there should be a difference in allele or genotype frequencies between cases and controls at a disease-causing variant. Frequent pattern mining (FPM) methods offer an avenue at detecting digenic traits even in the absence of single-variant effects. The idea is to enumerate pairs of genotypes (genotype patterns) with each of the two genotypes originating from different variants that may be located at very different genomic positions. What is needed is for genotype patterns to be significantly more common in cases than in controls. Let Y = 2 refer to cases and Y = 1 to controls, with X denoting a specific genotype pattern. We are seeking association rules, ‘X → Y’, with high confidence, P(Y = 2|X), significantly higher than the proportion of cases, P(Y = 2) in the study. Clearly, generally available FPM methods are very suitable for detecting disease-associated genotype patterns. We use fpgrowth as the basic FPM algorithm and built a framework around it to enumerate high-frequency digenic genotype patterns and to evaluate their statistical significance by permutation analysis. Application to a published dataset on opioid dependence furnished results that could not be found with classical GWAS methodology. There were 143 cases and 153 healthy controls, each genotyped for 82 variants in eight genes of the opioid system. The aim was to find out whether any of these variants were disease-associated. The single-variant analysis did not lead to significant results. Application of our FPM implementation resulted in one significant (p < 0.01) genotype pattern with both genotypes in the pattern being heterozygous and originating from two variants on different chromosomes. This pattern occurred in 14 cases and none of the controls. Thus, the pattern seems quite specific to this form of substance abuse and is also rather predictive of disease. An algorithm called Multifactor Dimension Reduction (MDR) was developed some 20 years ago and has been in use in human genetics ever since. This and our algorithms share some similar properties, but they are also very different in other respects. The main difference seems to be that our algorithm focuses on patterns of genotypes while the main object of inference in MDR is the 3 × 3 table of genotypes at two variants.

Keywords: digenic traits, DNA variants, epistasis, statistical genetics

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Authors: Rebecca Richards Steed, James Van Derslice, Ken Smith, Richard Medina, Amanda Bakian

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Elucidating gene-environment interactions for heritable disease outcomes is an emerging area of disease research, with genetic studies informing hypotheses for environment and gene interactions underlying some of the most confounding diseases of our time, like autism spectrum disorder (ASD). Geography has thus far played a key role in identifying environmental factors contributing to disease, but its use can be broadened to include genetic and environmental factors that have a synergistic effect on disease. Through the use of family pedigrees and disease outcomes with life-course residential histories, space-time clustering of generations at critical developmental windows can provide further understanding of (1) environmental factors that contribute to disease patterns in families, (2) susceptible critical windows of development most impacted by environment, (3) and that are most likely to lead to an ASD diagnosis. This paper introduces a retrospective case-control study that utilizes pedigree data, health data, and residential life-course location points to find space-time clustering of ancestors with a grandchild/child with a clinical diagnosis of ASD. Finding space-time clusters of ancestors at critical developmental windows serves as a proxy for shared environmental exposures. The authors refer to geographic life-course exposures as geographic legacies. Identifying space-time clusters of ancestors creates a bridge for researching exposures of past generations that may impact modern-day progeny health. Results from the space-time cluster analysis show multiple clusters for the maternal and paternal pedigrees. The paternal grandparent pedigree resulted in the most space-time clustering for birth and childhood developmental windows. No statistically significant clustering was found for adolescent years. These results will be further studied to identify the specific share of space-time environmental exposures. In conclusion, this study has found significant space-time clusters of parents, and grandparents for both maternal and paternal lineage. These results will be used to identify what environmental exposures have been shared with family members at critical developmental windows of time, and additional analysis will be applied.

Keywords: family pedigree, environmental exposure, geographic legacy, medical geography, transgenerational inheritance

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Authors: Zelikha Labbani

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The in vitro isolated microspore culture is the most powerful androgenic pathway to produce doubled haploid plants in the short time. To deviate a microspore toward embryogenesis, a number of factors, different for each species, must concur at the same time and place. Once induced, the microspore undergoes numerous changes at different levels, from overall morphology to gene expression. Induction of microspore embryogenesis not only implies the expression of an embryogenic program, but also a stress-related cellular response and a repression of the gametophytic program to revert the microspore to a totipotent status. As haploid single cells, microspore became a strategy to achieve various objectives particularly in genetic engineering. In this communication we would show the most recent advances in the producing haploid embryos via in vitro isolated microspore culture.

Keywords: in vitro isolated microspore culture, success, haploid cells, bioinformatics, biomedicine

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Authors: Amarjit S Tanda

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Integrated Pest Management Technology (IPMT) offers a crop protection model with sustainable agriculture production with minimum damage to the environment and human health. A concept of agro-ecological crop protection seems unsuitable under dynamic environmental systems. To remedy this, we are proposing Genetically Engineered Crop Protection System (GECPS), as an alternate concept in IPMT that suggests how GE cultivars can be optimally put to the service of crop protection. Genetically engineered cultivars which are developed by gene editing biotechnology may provide a preventive defense against the insect pests and plant diseases, a suitable alternative crop system for blending in IPMT program, in the future agro-industry.

Keywords: integrated, pest, management, technology

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Authors: Judit Perjessy, Zsolt Zalan, Ferenc Hegyi, Eniko Horvath-Szanics, Krisztina Takacs, Andras Nagy, Adel Klupacs, Erika Koppany-Szabo, Zhirong Wang, Kaituo Wang, Muying Du, Jianquan Kan

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The post-harvest diseases cause great economic losses in the fruit and vegetables; the prevention of these deterioration has great importance. Against the fungi, which cause most of the diseases, are extensively used the fungicides. However, there are increasing consumer concerns over the presence of pesticide residues in food. An alternative and in recent years, increasingly studied method for the prevention of the diseases is biocontrol, where antagonistic microorganisms are used for the control of fungi. The genera of Lactobacillus is well known and extensively studied, but its applicability as biocontrol agents in post-harvest preservation of fruit and vegetables is poorly investigated. However these bacteria can be found on the surface of the plants and have great antimicrobial activity. In our study we have investigated the chitinase activity, the antifungal effect and the applicability of several Lactobacillus strains to select potential biocontrol agents. We investigated the determination of the environmental parameters of a gene (encoding chitinase) expression and we also investigated the relationship between actual antifungal activity and potential chitinase activity. Mixed cultures were also developed to enhance the antifungal activity and determined the optimal mold spore and bacteria concentration ratio for the appropriate efficacy. Five Lactobacillus strains (L. acidophilus N2, L. delbrueckii subsp. bulgaricus B397, L. sp. 2231, L. sake subsp. sake 2471, L. buchneri 1145) possess chitinase-coding gene from the 43 investigated Lactobacillus strains. Proteins with similar molecular weight and separation properties like bacterial chitinases were detected from these strains, which also possess chitin-binding property. Nevertheless, they were inactive, lacks the chitinolytic activity. In point of the cumulative activity of inhibition, our results showed that certain strains were statistically significant in a positive direction compared to other strains, e.g., L. rhamnosus VT1 and L. Casey 154 have shown great general antifungal effect against 11 molds from the genera Penicillium and Botrytis and isolated from spoiled fruit and vegetables. Also, some mixed cultures (L. rhamnosus VT1 - L. Plantarum 299v) showed significant antifungal effects against the indigenous molds on the surface of apple fruit during the industrial storage experiment. Thus, they could be promising for post-harvest biopreservation.

Keywords: biocontrol, chitinase, Lactobacillus, post-harvest

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Authors: Virupakshi Hiremata, Ratnakar M. Shet, Raghavendra Gunnaiah, Prashantha A.

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Muskmelon is a health-beneficial and refreshing dessert vegetable with a low shelf life. Mangalore melon, a genetic homeologue of muskmelon, has a shelf life of more than six months and is mostly used for culinary purposes. Understanding the genetics of shelf life, yield and yield-related traits and identification of markers linked to such traits is helpful in transfer of extended shelf life from Mangalore melon to the muskmelon through intra-specific hybridization. For QTL mapping, 276 F2 mapping population derived from the cross Arka Siri × SS-17 was genotyped with 40 polymorphic markers distributed across 12 chromosomes. The same population was also phenotyped for yield, shelf life and fruit quality traits. One major QTL (R2 >10) and fourteen minor QTLs (R2 <10) localized on four linkage groups, governing different traits were mapped in F2 mapping population developed from the intraspecific cross with a LOD > 5.5. The phenotypic varience explained by each locus varied from 3.63 to 10.97 %. One QTL was linked to shelf-life (qSHL-3-1), five QTLs were linked to TSS (qTSS-1-1, qTSS-3-3, qTSS-3-1, qTSS-3-2 and qTSS-1-2), two QTLs for flesh thickness (qFT-3-1, and qFT-3-2) and seven QTLs for fruit yield per vine (qFYV-3-1, qFYV-1-1, qFYV-3-1, qFYV1-1, qFYV-1-3, qFYV2-1 and qFYV6-1). QTL flanking markers may be used for marker assisted introgression of shelf life into muskmelon. Important QTL will be further fine-mapped for identifying candidate genes by QTLseq and RNAseq analysis. Fine-mapping of Important Quantitative Trait Loci (QTL) holds immense promise in elucidating the genetic basis of complex traits. Leveraging advanced techniques like QTLseq and RNA sequencing (RNA seq) is crucial for this endeavor. QTLseq combines next-generation sequencing with traditional QTL mapping, enabling precise identification of genomic regions associated with traits of interest. Through high-throughput sequencing, QTLseq provides a detailed map of genetic variations linked to phenotypic variations, facilitating targeted investigations. Moreover, RNA seq analysis offers a comprehensive view of gene expression patterns in response to specific traits or conditions. By comparing transcriptomes between contrasting phenotypes, RNA seq aids in pinpointing candidate genes underlying QTL regions. Integrating QTLseq with RNA seq allows for a multi-dimensional approach, coupling genetic variation with gene expression dynamics.

Keywords: QTL, shelf life, TSS, muskmelon and Mangalore melon

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Authors: Jérémie Ochin

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Soccer analytics are built on two data sources: the frame-by-frame position of each player on the terrain and the sequences of events, such as ball drive, pass, cross, shot, throw-in... With more than 2000 ball-events per soccer game, their precise and exhaustive annotation, based on a monocular video stream such as a TV broadcast, remains a tedious and costly manual task. State-of-the-art methods for spatio-temporal action detection from a monocular video stream, often based on 3D convolutional neural networks, are close to reach levels of performances in mean Average Precision (mAP) compatibles with the automation of such task. Nevertheless, to meet their expectation of exhaustiveness in the context of data analytics, such methods must be applied in a regime of high recall – low precision, using low confidence score thresholds. This setting unavoidably leads to the detection of false positives that are the product of the well documented overconfidence behaviour of neural networks and, in this case, their limited access to contextual information and understanding of the game: their predictions are highly unstructured. Based on the assumption that professional soccer players’ behaviour, pose, positions and velocity are highly interrelated and locally driven by the player performing a ball-action, it is hypothesized that the addition of information regarding surrounding player’s appearance, positions and velocity in the prediction methods can improve their metrics. Several methods are compared to build a proper representation of the game surrounding a player, from handcrafted features of the local graph, based on domain knowledge, to the use of Graph Neural Networks trained in an end-to-end fashion with existing state-of-the-art 3D convolutional neural networks. It is shown that the inclusion of information regarding surrounding players helps reaching higher metrics.

Keywords: fine-grained action recognition, human action recognition, convolutional neural networks, graph neural networks, spatio-temporal action recognition

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Authors: Elene Zhuravliova, Tamar Barbakadze, Irina Kalandadze, Elnari Zaalishvili, Lali Shanshiashvili, David Mikeladze

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Background: Multiple sclerosis (MS) is an inflammatory, neurodegenerative disease, which is accompanied by demyelination and autoimmune response to myelin proteins. Among post-translational modifications, which mediate the modulation of inflammatory pathways during MS, methylation is the main one. The methylation of DNA, also amino acids lysine and arginine, occurs in the cell. It was found that decreased trans-methylation is associated with neuroinflammatory diseases. Therefore, abnormal regulation of the methyl cycle could induce demyelination through the action on PAD (peptidyl-arginine-deiminase) gene promoter. PAD takes part in protein citrullination and targets myelin basic protein (MBP), which is affected during demyelination. To determine whether MBP charge isomers are changing the methyl cycle, we have estimated the concentrations of methyl cycle metabolites in MBP-activated primary astrocytes and oligodendrocytes. For this purpose, the action of the citrullinated MBP- C8 and the most cationic MBP-C1 isomers on the primary cells were investigated. Methods: Primary oligodendrocyte and astrocyte cell cultures were prepared from whole brains of 2-day-old Wistar rats. The methyl cycle metabolites, including homocysteine, S-adenosylmethionine (SAM), and S-adenosylhomocysteine (SAH), were estimated by HPLC analysis using fluorescence detection and prior derivatization. Results: We found that the action of MBP-C8 and MBP-C1 induces a decrease in the concentration of both methyl cycle metabolites, S-adenosylmethionine (SAM) and S-adenosylhomocysteine (SAH), in astrocytes compared to the control cells. As for oligodendrocytes, the concentration of SAM was increased by the addition of MBP-C1, while MBP-C8 has no significant effect. As for SAH, its concentration was increased compared to the control cells by the action of both MBP-C1 and MBP-C8. A significant increase in homocysteine concentration was observed by the action of the MBP-C8 isomer in both oligodendrocytes and astrocytes. Conclusion: These data suggest that MBP charge isomers change the concentration of methyl cycle metabolites. MBP-C8 citrullinated isomer causes elevation of homocysteine in astrocytes and oligodendrocytes, which may be the reason for decreased astrocyte proliferation and increased oligodendrocyte cell death which takes place in neurodegenerative processes. Elevated homocysteine levels and subsequent abnormal regulation of methyl cycles in oligodendrocytes possibly change the methylation of DNA that activates PAD gene promoter and induces the synthesis of PAD, which in turn provokes the process of citrullination, which is the accompanying process of demyelination. Acknowledgment: This research was supported by the SRNSF Georgia RF17_534 grant.

Keywords: myelin basic protein, astrocytes, methyl cycle metabolites, homocysteine, oligodendrocytes

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Authors: Lakmini Wijesooriya, Vicki Chalker, Jessica Day, Priyantha Perera, N. P. Sunil-Chandra

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M. pneumoniae has been identified as an etiology for exacerbation of asthma (EQA), although viruses play a major role in EOA. M. pneumoniae infection is treated empirically with macrolides, and its antibiotic sensitivity is not detected routinely. Characterization of the organism by genotyping and determination of macrolide resistance is important epidemiologically as it guides the empiric antibiotic treatment. To date, there is no such characterization of M. pneumoniae performed in Sri Lanka. The present study describes the characterization of M. pneumoniae detected from a child with EOA following a screening of 100 children with EOA. Of the hundred children with EOA, M. pneumoniae was identified only in one child by Real-Time polymerase chain reaction (PCR) test for identifying the community-acquired respiratory distress syndrome (CARDS) toxin nucleotide sequences. The M. pneumoniae identified from this patient underwent detection of macrolide resistance via conventional PCR, amplifying and sequencing the region of the 23S rDNA gene that contains single nucleotide polymorphisms that confer resistance. Genotyping of the isolate was performed via nested Multilocus Sequence Typing (MLST) in which eight (8) housekeeping genes (ppa, pgm, gyrB, gmk, glyA, atpA, arcC, and adk) were amplified via nested PCR followed by gene sequencing and analysis. As per MLST analysis, the M. pneumoniae was identified as sequence type 14 (ST14), and no mutations that confer resistance were detected. Resistance to macrolides in M. pneumoniae is an increasing problem globally. Establishing surveillance systems is the key to informing local prescriptions. In the absence of local surveillance data, antibiotics are started empirically. If the relevant microbiological samples are not obtained before antibiotic therapy, as in most occasions in children, the course of antibiotic is completed without a microbiological diagnosis. This happens more frequently in therapy for M. pneumoniae which is treated with a macrolide in most patients. Hence, it is important to understand the macrolide sensitivity of M. pneumoniae in the setting. The M. pneumoniae detected in the present study was macrolide sensitive. Further studies are needed to examine a larger dataset in Sri Lanka to determine macrolide resistance levels to inform the use of macrolides in children with EOA. The MLST type varies in different geographical settings, and it also provides a clue to the existence of macrolide resistance. The present study enhances the database of the global distribution of different genotypes of M. pneumoniae as this is the first such characterization performed with the increased number of samples to determine macrolide resistance level in Sri Lanka. M. pneumoniae detected from a child with exacerbation of asthma in Sri Lanka was characterized as ST14 by MLST and no mutations that confer resistance were detected.

Keywords: mycoplasma pneumoniae, Sri Lanka, characterization, macrolide resistance

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Authors: Gail Louw, Helena Boshoff, Taeksun Song, Clifton Barry

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Drug resistance in Mycobacterium tuberculosis is primarily attributed to mutations in target genes. These mutations incur a fitness cost and result in bacterial generations that are less fit, which subsequently acquire compensatory mutations to restore fitness. We hypothesize that mutations in specific drug target genes influence bacterial metabolism and cellular function, which affects its ability to develop subsequent resistance to additional agents. We aim to determine whether the sequential acquisition of drug resistance and specific mutations in a well-defined clinical M. tuberculosis strain promotes or limits the development of additional resistance. In vitro mutants resistant to pretomanid, linezolid, moxifloxacin, rifampicin and kanamycin were generated from a pan-susceptible clinical strain from the Beijing lineage. The resistant phenotypes to the anti-TB agents were confirmed by the broth microdilution assay and genetic mutations were identified by targeted gene sequencing. Growth of mono-resistant mutants was done in enriched medium for 14 days to assess in vitro fitness. Double resistant mutants were generated against anti-TB drug combinations at concentrations 5x and 10x the minimum inhibitory concentration. Subsequently, mutation frequencies for these anti-TB drugs in the different mono-resistant backgrounds were determined. The initial level of resistance and the mutation frequencies observed for the mono-resistant mutants were comparable to those previously reported. Targeted gene sequencing revealed the presence of known and clinically relevant mutations in the mutants resistant to linezolid, rifampicin, kanamycin and moxifloxacin. Significant growth defects were observed for mutants grown under in vitro conditions compared to the sensitive progenitor. Mutation frequencies determination in the mono-resistant mutants revealed a significant increase in mutation frequency against rifampicin and kanamycin, but a significant decrease in mutation frequency against linezolid and sutezolid. This suggests that these mono-resistant mutants are more prone to develop resistance to rifampicin and kanamycin, but less prone to develop resistance against linezolid and sutezolid. Even though kanamycin and linezolid both inhibit protein synthesis, these compounds target different subunits of the ribosome, thereby leading to different outcomes in terms of fitness in the mutants with impaired cellular function. These observations showed that oxazolidinone treatment is instrumental in limiting the development of multi-drug resistance in M. tuberculosis in vitro.

Keywords: oxazolidinones, mutations, resistance, tuberculosis

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Authors: Mao Huasong, Tang Siqi, Cheng Yu

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The cognition and practice of Chinese landscapes have distinct uniqueness. The intergenerational inheritance of urban and rural landscapes is a common objective fact which has created a unique type of heritage in China - scenic heritage. The current generalization of the concept of scenic heritage has affected the lack of innovation in corresponding protection practices. Therefore, clarifying the concepts and connotations of scenery and scenic heritage, clarifying the protection objects of scenic heritage and the methods and approaches in intergenerational inheritance can provide theoretical support for the practice of Chinese scenic heritage and contribute Chinese wisdom to the transformation of world heritage sites. Taking ancient Shaoxing, which has a long time span and rich descriptions of scenic types and quantities, as the research object and using local chronicles as the basic research material, based on text analysis, word frequency analysis, case statistics, and historical, geographical spatial annotation methods, this study traces back to ancient scenic practices and conducts in-depth descriptions in both text and space. it have constructed a scenic heritage identification method based on the basic connotation characteristics and morphological representation characteristics of natural and cultural correlations, combined with the intergenerational and representative characteristics of scenic heritage; Summarized the bidirectional integration of "scenic spots" and "form scenic spots", "outstanding people" and "local spirits" in the formation process of scenic heritage; In inheritance, guided by Confucian values of education; In communication, the cultural interpretation constructed by scenery and the way of landscape life are used to strengthen the intergenerational inheritance of natural, artificial material elements, and intangible spirits. As a unique type of heritage in China, scenic heritage should improve its standards, values, and connotations in current protection practices and actively absorb historical experience.

Keywords: scenic heritage, heritage protection, cultural landscape, shaoxing, chinese landscape

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Authors: Likith Reddy Pinninti, Fredrik Ribsskog Staven, Leslie Robert Noble, Jorge Manuel de Oliveira Fernandes, Deepti Manjari Patel, Torstein Kristensen

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Understanding fish behavior is essential to improve animal welfare in aquaculture research. Behavioral traits can have a strong influence on fish health and habituation. To identify the genes and biological pathways responsible for lumpfish behavior, we performed an experiment to understand the interspecies relationship (mutualism) between the lumpfish and salmon. Also, we tested the correlation between the gene expression data vs. observational/physiological data to know the essential genes that trigger stress and swimming behavior in lumpfish. After the de novo assembly of the brain transcriptome, all the samples were individually mapped to the available lumpfish (Cyclopterus lumpus L.) primary genome assembly (fCycLum1.pri, GCF_009769545.1). Out of ~16749 genes expressed in brain samples, we found 267 genes to be statistically significant (P > 0.05) found only in odor and control (1), model and control (41) and salmon and control (225) groups. However, genes with |LogFC| ≥0.5 were found to be only eight; these are considered as differentially expressed genes (DEG’s). Though, we are unable to find the differential genes related to the behavioral traits from RNA-Seq data analysis. From the correlation analysis, between the gene expression data vs. observational/physiological data (serotonin (5HT), dopamine (DA), 3,4-Dihydroxyphenylacetic acid (DOPAC), 5-hydroxy indole acetic acid (5-HIAA), Noradrenaline (NORAD)). We found 2495 genes found to be significant (P > 0.05) and among these, 1587 genes are positively correlated with the Noradrenaline (NORAD) hormone group. This suggests that Noradrenaline is triggering the change in pigmentation and skin color in lumpfish. Genes related to behavioral traits like rhythmic, locomotory, feeding, visual, pigmentation, stress, response to other organisms, taxis, dopamine synthesis and other neurotransmitter synthesis-related genes were obtained from the correlation analysis. In KEGG pathway enrichment analysis, we find important pathways, like the calcium signaling pathway and adrenergic signaling in cardiomyocytes, both involved in cell signaling, behavior, emotion, and stress. Calcium is an essential signaling molecule in the brain cells; it could affect the behavior of fish. Our results suggest that changes in calcium homeostasis and adrenergic receptor binding activity lead to changes in fish behavior during stress.

Keywords: behavior, De novo, lumpfish, salmon

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Authors: Jamileh Ahmed, Helena Hernandez, Gabriel De Erausquin

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H1N1 virus susceptibility of iPSC-derived DA neurons from schizophrenia patients and controls will compared. C57/BL-6 fibroblasts were reprogrammed into iPSCs using a lenti-viral vector containing SOKM genes. Pluripotency verification with the AP assay and immunocytochemistry ensured iPSC presence. The experimental outcome of ISPCs from DA neuron differentiation will be discussed in the Results section. Fibroblasts from patients and controls will be reprogrammed into iPSCs using a sendai-virus vector containing SOKM. IPSCs will be characterized using the AP assay, immunocytochemistry and RT-PCR. IPSCs will then be differentiated into DA neurons. Gene methylation will be compared for both groups with custom-designed microarrays.

Keywords: schizophrenia, iPSCs, stem cells, neuroscience

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Authors: Fereydoon Bondarian, Samira Shaygan

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Today, many nutritionists recommend the consumption of plants, fruits, and vegetables to provide the antioxidants needed by the body because the use of plant antioxidants usually causes fewer side effects and better treatment. Natural antioxidants increase the power of plasma antioxidants and reduce the incidence of some diseases, such as cancer. Bad lifestyles and environmental factors play an important role in increasing the incidence of cancer. In this study, different extracts of white teas taken from two types of tea available in Iran (clone 100 and Chinese hybrid) due to the presence of a hydroxyl functional group in their structure to inhibit free radicals and anticancer properties, using 3 aqueous, methanolic and aqueous-methanolic methods were used. The total polyphenolic content was calculated using the Folin-Ciocalcu method, and the percentage of inhibition and trapping of free radicals in each of the extracts was calculated using the DPPH method. With the help of high-performance liquid chromatography, a small amount of each catechin in the tea samples was obtained. Clone 100 white tea was found to be the best sample of tea in terms of all the examined attributes (total polyphenol content, antioxidant properties, and individual amount of each catechin). The results showed that aqueous and aqueous-methanolic extracts of Clone 100 white tea have the highest total polyphenol content with 27.59±0.08 and 36.67±0.54 (equivalent gallic acid per gram dry weight of leaves), respectively. Due to having the highest level of different groups of catechin compounds, these extracts have the highest property of inhibiting and trapping free radicals with 66.61±0.27 and 71.74±0.27% (mg/l) of the extracted sample against ascorbic acid). Using the MTT test, the inhibitory effect of clone 100 white tea extract in inhibiting the growth of HCT-116 colon cancer cells was investigated and the best time and concentration treatments were 500, 150 and 1000 micrograms in 8, 16 and 24 hours, respectively. To investigate gene expression changes, selected genes, including tumorigenic genes, proto-oncogenes, tumor suppressors, and genes involved in apoptosis, were selected and analyzed using the real-time PCR method and in the presence of concentrations obtained for white tea. White tea extract at a concentration of 1000 μg/ml 3 times 16, 8, and 24 hours showed the highest growth inhibition in cancer cells with 53.27, 55.8, and 86.06%. The concentration of 1000 μg/ml aqueous extract of white tea under 24-hour treatment increased the expression of tumor suppressor genes compared to the normal sample.

Keywords: catechin, gene expression, suppressor genes, colon cell line

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Authors: Seok Woo Chang, Kee Yeon Kum, Kwang Shik Bae, WooCheol Lee

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Aim: The objective of this study was to compare the biocompatibilities and mineralization potential of ProRoot MTA and newly developed calcium phosphate based cement, Capseal. Materials and Methods: The biocompatibilities and mineralization-related gene expressions (Bone sialoprotein (BSP) and osteocalcin (OCN)) of ProRoot MTA and Capseal were also compared by a methylthiazol tetrazolium (MTT) assay and reverse transcription-polymerization chain reaction (RT-PCR) analysis on 1, 3, and 7 days, respectively. Empty rings were used as control group. The results were statistically analyzed by Kruskal-Wallis test with a Bonferroni correction. P-value of < 0.05 was considered significant. Results: The biocompatibilities of ProRoot MTA and Capseal were equally favorable. ProRoot MTA and Capseal affected the messenger RNA expression of osteocalcin and osteonectin. Conclusions: Based on the results, both ProRoot MTA and Capseal could be a useful biomaterial in clinical endodontics.

Keywords: biocompatibility, calcium silicate cement, MTT, RT-PCR

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Authors: Valeria Velasco, Ana M. Bonilla, José L. Vergara, Alcides Lofa, Jorge Campos, Pedro Rojas-García

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Staphylococcus aureus is both commensal bacterium and opportunistic pathogen that can cause different diseases in humans and can rapidly develop antimicrobial resistance. Since this bacterium has the ability to colonize the nares and skin of humans and animals, there is a risk of contamination of food in different steps of the food chain supply. Emerging strains have been detected in food-producing animals and meat, such as methicillin-resistant S. aureus (MRSA). The aim of this study was to determine the prevalence and oxacillin susceptibility of S. aureus in the pork chain supply in Chile and to suggest some natural antimicrobials for control. A total of 487 samples were collected from pigs (n=332), carcasses (n=85), and retail pork meat (n=70). Presumptive S. aureus colonies were isolated by selective enrichment and culture media. The confirmation was carried out by biochemical testing (Api® Staph) and molecular technique PCR (detection of nuc and mecA genes, associated with S. aureus and methicillin resistance, respectively). The oxacillin (β-lactam antibiotic that replaced methicillin) susceptibility was assessed by minimum inhibitory concentration (MIC) using the Epsilometer test (Etest). A preliminary assay was carried out to test thymol, carvacrol, oregano essential oil (Origanum vulgare L.), Maqui or Chilean wineberry extract (Aristotelia chilensis (Mol.) Stuntz) as anti-staphylococcal agents using the disc diffusion method at different concentrations. The overall prevalence of S. aureus in the pork chain supply reached 33.9%. A higher prevalence of S. aureus was determined in carcasses (56.5%) than in pigs (28.3%) and pork meat (32.9%) (P ≤ 0.05). The prevalence of S. aureus in pigs sampled at farms (40.6%) was higher than in pigs sampled at slaughterhouses (23.3%) (P ≤ 0.05). The contamination of no packaged meat with S. aureus (43.1%) was higher than in packaged meat (5.3%) (P ≤ 0.05). The mecA gene was not detected in S. aureus strains isolated in this study. Two S. aureus strains exhibited oxacillin resistance (MIC ≥ 4µg/mL). Anti-staphylococcal activity was detected in solutions of thymol, carvacrol, and oregano essential oil at all concentrations tested. No anti-staphylococcal activity was detected in Maqui extract. Finally, S. aureus is present in the pork chain supply in Chile. Although the mecA gene was not detected, oxacillin resistance was found in S. aureus and could be attributed to another resistance mechanism. Thymol, carvacrol, and oregano essential oil could be used as anti-staphylococcal agents at low concentrations. Research project Fondecyt No. 11140379.

Keywords: antimicrobials, mecA gen, nuc gen, oxacillin susceptibility, pork meat

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Authors: Senol Dogan, Gunay Karli

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Identification of relevant publications based on a Medline query is time-consuming and error-prone. An all based process has the potential to solve this problem without any manual work. To the best of our knowledge, our study is the first to investigate the ability of machine learning to identify relevant articles accurately. 5 different machine learning algorithms were tested using 23 predictors based on several metadata fields attached to publications. We find that the Boosted model is the best-performing algorithm and its overall accuracy is 96%. In addition, specificity and sensitivity of the algorithm is 97 and 93%, respectively. As a result of the work, we understood that we can apply the same procedure to understand cancer gene expression big data.

Keywords: prediction of publications, machine learning, algorithms, bariatric surgery, comparison of algorithms, boosted, tree, logistic regression, ANN model

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Authors: Christelle E. Chua, Alicia L. Ho

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The development of a panel of differential gene expression signatures has been of interest in the field of biomarker discovery for radiation exposure. In the absence of the availability of exposed human subjects, lymphocyte cell lines have often been used as a surrogate to human whole blood, when performing ex vivo irradiation studies. The extent of variation between different lymphocyte cell lines is currently unclear, especially with regard to the expression of extracellular miRNA. This study compares the expression profile of extracellular miRNA isolated from different lymphocyte cell lines. It also compares the profile of miRNA obtained when different exosome isolation kits are used. Lymphocyte cell lines were created using lymphocytes isolated from healthy adult males of similar racial descent (Chinese American and Chinese Singaporean) and immortalised with Epstein-Barr virus. The cell lines were cultured in exosome-free cell culture media for 72h and the cell culture supernatant was removed for exosome isolation. Two exosome isolation kits were used. Total exosome isolation reagent (TEIR, ThermoFisher) is a polyethylene glycol (PEG)-based exosome precipitation kit, while ExoSpin (ES, Cell Guidance Systems) is a PEG-based exosome precipitation kit that includes an additional size exclusion chromatography step. miRNA from the isolated exosomes were isolated using miRNEASY minikit (Qiagen) and analysed using nCounter miRNA assay (Nanostring). Principal component analysis (PCA) results suggested that the overall extracellular miRNA expression profile differed between the lymphocyte cell line originating from the Chinese American donor and the cell line originating from the Chinese Singaporean donor. As the gender, age and racial origins of both donors are similar, this may suggest that there are other genetic or epigenetic differences that account for the variation in extracellular miRNA gene expression in lymphocyte cell lines. However, statistical analysis showed that only 3 miRNA genes had a fold difference > 2 at p < 0.05, suggesting that the differences may not be of that great a significance as to impact overall conclusions drawn from different cell lines. Subsequent analysis using cell lines from other donors will give further insight into the reproducibility of results when difference cell lines are used. PCA results also suggested that the method of exosome isolation impacted the expression profile. 107 miRNA had a fold difference > 2 at p < 0.05. This suggests that the inclusion of an additional size exclusion chromatography step altered the subset of the extracellular vesicles that were isolated. In conclusion, these results suggest that extracellular miRNA can be isolated and analysed from exosomes derived from lymphocyte cell lines. However, care must be taken in the choice of cell line and method of exosome isolation used.

Keywords: biomarker, extracellular miRNA, isolation methods, lymphocyte cell line

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Authors: Fakhrosadat Sajjadian

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The majority of deaths in cancer patients are caused by distant metastasis. Breast cancer shows a unique spread pattern, often affecting bone, liver, lung, and brain. Breast cancer can be categorized into various subtypes according to gene expression patterns, and these subtypes exhibit specific preferences for organs where metastasis occurs. Breast tumors with luminal characteristics have a preference for spreading to the bone, whereas basal-like breast cancer (BLBC) shows a tendency to metastasize to the lungs. Still, the mechanisms behind this particular pattern of metastasis in organs have yet to be fully understood. In this evaluation, we will outline the latest progress in molecular signaling pathways and treatment methods for breast cancer lung metastasis.

Keywords: lung cancer, liver cancer, diagnosis, BLBC, metastasis

Procedia PDF Downloads 48

Authors: Alsu F. Saifitdinova, Alexey S. Komissarov, Svetlana A. Galkina, Elena I. Koshel, Maria M. Kulak, Stephen J. O'Brien, Elena R. Gaginskaya

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The mystery of sex determination is one of the most ancient and still not solved until the end so far. In many species, sex determination is genetic and often accompanied by the presence of dimorphic sex chromosomes in the karyotype. Genomic sequencing gave the information about the gene content of sex chromosomes which allowed to reveal their origin from ordinary autosomes and to trace their evolutionary history. Female-specific W chromosome in birds as well as mammalian male-specific Y chromosome is characterized by the degeneration of gene content and the accumulation of repetitive DNA. Tandem repeats complicate the analysis of genomic data. Despite the best efforts chicken W chromosome assembly includes only 1.2 Mb from expected 55 Mb. Supplementing the information on the sex chromosome composition not only helps to complete the assembly of genomes but also moves us in the direction of understanding of the sex-determination systems evolution. A whole-genome survey to the assembly Gallus_gallus WASHUC 2.60 was applied for repeats search in assembled genome and performed search and assembly of high copy number repeats in unassembled reads of SRR867748 short reads datasets. For cytogenetic analysis conventional methods of fluorescent in situ hybridization was used for previously cloned W specific satellites and specifically designed directly labeled synthetic oligonucleotide DNA probe was used for bioinformatically identified repetitive sequence. Hybridization was performed with mitotic chicken chromosomes and manually isolated giant meiotic lampbrush chromosomes from growing oocytes. A novel chicken W specific satellite (GGAAA)n which is not co-localizes with any previously described classes of W specific repeats was identified and mapped with high resolution. In the composition of autosomes this repeat units was found as a part of upstream regions of gonad specific protein coding sequences. These findings may contribute to the understanding of the role of tandem repeats in sex specific differentiation regulation in birds and sex chromosome evolution. This work was supported by the postdoctoral fellowships from St. Petersburg State University (#1.50.1623.2013 and #1.50.1043.2014), the grant for Leading Scientific Schools (#3553.2014.4) and the grant from Russian foundation for basic researches (#15-04-05684). The equipment and software of Research Resource Center “Chromas” and Theodosius Dobzhansky Center for Genome Bioinformatics of Saint Petersburg State University were used.

Keywords: birds, lampbrush chromosomes, sex chromosomes, tandem repeats

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Authors: Ji Su Kim, Bo Ram Choi, Ju Yeon Cho, Hyukjin Lee

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Epidermal growth factor receptor (EGFR) 19 deletion mutation gene is over-expressed in carcinoma patient. EGFR 19 deletion mutation is known as typical biomarker of non-small cell lung cancer (NSCLC), which one section in the coding exon 19 of EGFR is deleted. Therefore, there have been many attempts over the years to detect EGFR 19 deletion mutation for replacing conventional diagnostic method such as PCR and tissue biopsy. We developed a simple and facile detection platform based on Rolling Circle Amplification (RCA), which provides highly amplified products in isothermal amplification of the ligated DNA template. Limit of detection (~50 nM) and a faster detection time (~30 min) could be achieved by introducing RCA.

Keywords: EGFR19, cancer, diagnosis, rolling circle amplification (RCA), hydrogel

Procedia PDF Downloads 255

Authors: Nazish Badar

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In early 2009, Pandemic type A (H1N1) Influenza virus emerged globally. Since then, it has continued circulation causing considerable morbidity and mortality. The purpose of this study was to evaluate the evolutionary changes in Influenza A (H1N1) pdm09 viruses from 2009-15 and their relevance with the current vaccine viruses. Methods: Respiratory specimens were collected with influenza-like illness and Severe Acute Respiratory Illness. Samples were processed according to CDC protocol. Sequencing and phylogenetic analysis of Haemagglutinin (HA) and neuraminidase (NA) genes was carried out comparing representative isolates from Pakistan viruses. Results: Between Jan2009 - Feb 2016, 1870 (13.2%) samples were positive for influenza A out of 14086. During the pandemic period (2009–10), Influenza A/ H1N1pdm 09 was the dominant strain with 366 (45%) of total influenza positives. In the post-pandemic period (2011–2016), a total of 1066 (59.6%) cases were positive Influenza A/ H1N1pdm 09 with co-circulation of different Influenza A subtypes. Overall, the Pakistan A(H1N1) pdm09 viruses grouped in two genetic clades. Influenza A(H1N1)pdm09 viruses only ascribed to Clade 7 during the pandemic period whereas viruses belong to clade 7 (2011) and clade 6B (2015) during the post-pandemic years. Amino acid analysis of the HA gene revealed mutations at positions S220T, I338V and P100S specially associated with outbreaks in all the analyzed strains. Sequence analyses of post-pandemic A(H1N1)pdm09 viruses showed additional substitutions at antigenic sites; S179N,K180Q (SA), D185N, D239G (CA), S202A (SB) and at receptor binding sites; A13T, S200P when compared with pandemic period. Substitution at Genetic markers; A273T (69%), S200P/T (15%) and D239G (7.6%) associated with severity and E391K (69%) associated with virulence was identified in viruses isolated during 2015. Analysis of NA gene revealed outbreak markers; V106I (23%) among pandemic and N248D (100%) during post-pandemic Pakistan viruses. Additional N-Glycosylation site; HA S179N (23%), NA I23T(7.6%) and N44S (77%) in place of N386K(77%) were only found in post-pandemic viruses. All isolates showed histidine (H) at position 275 in NA indicating sensitivity to neuraminidase inhibitors. Conclusion: This study shows that the Influenza A(H1N1)pdm09 viruses from Pakistan clustered into two genetic clades, with co-circulation of some variants. Certain key substitutions in the receptor binding site and few changes indicative of virulence were also detected in post-pandemic strains. Therefore, it is imperative to continue monitoring of the viruses for early identification of potential variants of high virulence or emergence of drug-resistant variants.

Keywords: Influenza A (H1N1) pdm09, evolutionary analysis, post pandemic period, Pakistan

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Authors: Mary Rose Eunice S. Gundayao, Manolo M. Fernandez

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Metachromatic leukodystrophy (MLD) is a rare lysosomal storage disorder with an autosomal recessive inheritance pattern. Lysosomal storage disorders are often severe, follow a progressively neurodegenerative path, and may result in multi-organ failure, potentially leading to death within 5 to 6 years in cases of early-onset forms. There are limited data regarding cases of MLD in Filipino children. This is the case of a 2-year-old Filipino girl who presented with progressive neurological deterioration and was diagnosed with metachromatic leukodystrophy by molecular genetic testing. This case report aims to present this patient’s clinical history, neurological findings, diagnosis and novel genetic mutations causing MLD. A concise review of updated literature on MLD will be discussed.

Keywords: metachromatic leukodystrophy, ARSA gene, peripheral neuropathy, case report, demyelinating disease

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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

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