Search results for: interferon stimulated genes

Authors: Rebiahi Sid Ahmed, Boutarfi Zakaria, Rahmoun Malika, Antonio Galvez

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The objective of this study was to explore the possible correlation between resistance to antibiotics and tolerance to biocides in Gram-negative bacilli isolated from the University Hospital Center of Tlemcen. This study focused on 175 clinical isolates of Gram-negative bacilli, it is a question of exploring: their level and profile of resistance to antibiotics, their tolerance to biocides, as well as the identification of the genetic supports of this resistance. Enterobacter spp. was the most predominant bacterial genus, all isolates harbored at least one of the studied genes with significant resistance capacity. Our results show, in some cases, a possible positive correlation between the presence of biocide tolerance genes and those of antibiotic resistance; in fact, tolerance to biocides could be one of the co-selection factors for antibiotic resistance. The results of this study should encourage the good practice of hygiene measures as well as the rational use of antimicrobials in order to hinder the development and emergence of resistance in our hospital departments.Mots clés : Antibiotiques, Biocides, Enterobacter, Hôpital, Résistance,

Keywords: antibiotic, biocides, enterobacter, hospital, resistance

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Authors: Mohammad Jamal

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Non-alcoholic fatty liver disease (NAFLD) has become one of the most chronic liver diseases, prevalent among people with morbid obesity. NAFLD does not develop clinically significant liver disease, however cirrhosis and liver cancer develop in subset and currently there are no approved therapies for the treatment of NAFLD. The study is aimed to understand the various key genes involved in the mechanism of NAFLD which can be valuable for developing diagnostic and predictive biomarkers based on their histologic stage of liver. The study was conducted on 16 male Sprague Dawley rats. The animals were divided in two groups: control group (n=8) fed on ad libitum normal chow and regular water and the cafeteria group (CAF)) (n=8) fed on high fatty/ carbohydrate diet. The animals received their respective diet from 4 weeks onwards from D.O.B until 25 weeks. Liver was extracted and RT² Profiler PCR Array was used to assess the NAFLD related genes. Histological evaluation was performed using H&E stain in liver tissue sections. Our PCR array results showed that genes involved in anti-inflammatory activity (Ifng, IL10), fatty acid uptake/oxidation (Fabp5), apoptosis (Fas), lipogenesis (Gck and Srebf1), Insulin signalling (Igfbp1) and metabolic pathway (pdk4) were upregulated in the liver of cafeteria fed obese rats. Bloated hepatocytes, displaced nucleus and higher lipid content were seen in the liver of cafeteria fed obese rats. Although Liver biopsies remain the gold standard in evaluating NAFLD, however an approach towards non-invasive markers could be used in understanding the physiology, therapeutic potential, and the targets to combat NAFLD.

Keywords: biomarkers, cafeteria diet, obesity, NAFLD

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Authors: Guna Raj Dhungana, Roshan Nepal, Apshara Parajuli, , Archana Maharjan, Shyam K. Mishra, Pramod Aryal, Rajani Malla

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Introduction: Klebsiella pneumoniae is a well-known opportunistic human pathogen, primarily causing healthcare-associated infections. The global emergence of carbapenemase-producing K. pneumoniaeis a major public health burden, which is often extensively multidrug resistant.Thus, because of the difficulty to treat these ‘superbug’ and menace and some term as ‘apocalypse’ of post antibiotics era, an alternative approach to controlling this pathogen is prudent and one of the approaches is phage mediated control and/or treatment. Objective: In this study, we aimed to isolate novel bacteriophage against carbapenemase-producing K. pneumoniaeand characterize for potential use inphage therapy. Material and Methods: Twenty lytic phages were isolated from river water using double layer agar assay and purified. Biological features, physiochemical characters, burst size, host specificity and activity spectrum of phages were determined. One most potent phage: Phage TU_Kle10O was selected and characterized by electron microscopy. Whole genome sequences of the phage were analyzed for presence/absence of virulent factors, and other lysin genes. Results: Novel phage TU_Kle10O showed multiple host range within own genus and did not induce any BIM up to 5th generation of host’s life cycle. Electron microscopy confirmed that the phage was tailed and belonged to Caudovirales family. Next generation sequencing revealed its genome to be 166.2 Kb. bioinformatical analysis further confirmed that the phage genome ‘did not’ contain any ‘bacterial genes’ within phage genome, which ruled out the concern for transfer of virulent genes. Specific 'lysin’ enzyme was identified phages which could be used as 'antibiotics'. Conclusion: Extensively multidrug resistant bacteria like carbapenemase-producing K. pneumoniaecould be treated efficiently by phages.Absence of ‘virulent’ genes of bacterial origin and presence of lysin proteins within phage genome makes phages an excellent candidate for therapeutics.

Keywords: bacteriophage, Klebsiella pneumoniae, MDR, phage therapy, carbapenemase,

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Authors: O. H. Gebril, N. A. Meguid

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Background: Iron had been a focus of interest recently as a main exaggerating factor for oxidative stresses in the central nervous system and a link to various neurological disorders is suspected. Many studies with various techniques showed evidence of disturbed iron-related proteins in the cell in human and animal models of neurodegenerative disorders. Also, linkage to significant pathological changes had been evidenced e.g. apoptosis and cell signaling. On the other hand, the role of iron in neurodevelopmental disorders is still unclear. With increasing prevalence of autism worldwide, some changes in iron parameters and its stores were documented in many studies. This study includes Haemochromatosis HFE gene polymorphisms (p.H63D and p.C282Y) and ferroportin gene (SLC40A1) Q248H polymorphism in autism and control children. Materials and Methods: Whole genome DNA was extracted; p.H63D and p.C282Y genotyping was studied using specific sequence amplification followed by restriction enzyme digestion on a sample of autism patients (25 cases) and twenty controls. Results: The p.H63D is seen more than the C282Y among both autism and control samples, with no significant association of p.H63D or p.C282Y polymorphism and autism was revealed. Also, no association with Q248H polymorphism was evidenced. Conclusion: The study results do not prove the role of cellular iron genes polymorphisms as risk factors for neurodevelopmental disorders, and in turn highlights the specificity of cellular iron related pathways in neurodegeneration. These results demand further gene expression studies to elucidate the main pathophysiological pathways that are disturbed in autism and other neurodevelopmental disorders.

Keywords: iron, neurodevelopmental, oxidative stress, haemohromatosis, ferroportin, genes

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Authors: Shima Mahmoudi, Babak Pourakbari, Setareh Mamishi, Mostafa Teymuri, Majid Marjani

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Although cytokine analysis has greatly contributed to the understanding of tuberculosis (TB) pathogenesis, data on cytokine profiles that might distinguish progression from latency of TB infection are scarce. Since PE/PPE proteins are known to induce strong humoral and cellular immune responses, the aim of this study was to evaluate the diagnostic potential of interleukin-2 (IL-2) as biomarker after specific antigen stimulation with PE35 and PPE68 for the discrimination of active and latent tuberculosis infection (LTBI). The production of IL-2 was measured in the antigen-stimulated whole-blood supernatants following stimulation with recombinant PE35 and PPE68. All the patients with active TB and LTBI had positive QuantiFERON-TB Gold in Tube test. The level of IL-2 following stimulation with recombinant PE35 and PPE68 were significantly higher in LTBI group than in patients with active TB infection or control group. The discrimination performance (assessed by the area under ROC curve) for IL-2 following stimulation with recombinant PE35 and PPE68 between LTBI and patients with active TB were 0.837 (95%CI: 0.72-0.97) and 0.75 (95%CI: 0.63-0.89), respectively. Applying the 12.4 pg/mL cut-off for IL-2 induced by PE35 in the present study population resulted in sensitivity of 78%, specificity of 78%, PPV of 78% and NPV of 100%. In addition, a sensitivity of 81%, specificity of 70%, PPV of 67% and 87% of NPV was reported based on the 4.4 pg/mL cut-off for IL-2 induced by PPE68. In conclusion, peptides of the antigen PE35 and PPE68, absent from commonly used BCG strains, stimulated strong IL-2- positive T cell responses in patients with LTBI. This study confirms IL-2 induced by PE35 and PPE68 as a sensitive and specific biomarker and highlights IL-2 as new promising adjunct markers for discriminating of LTBI and Active TB infection.

Keywords: IL-2, PE35, PPE68, tuberculosis

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Authors: Kgaugelo Lekota, Ayesha Hassim, Henriette Van Heerden

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Bacillus anthracis is the causative agent of anthrax that is composed of three genetic groups, namely A, B, and C. Clade-A is distributed world-wide, while sub-clades B has been identified in Kruger National Park (KNP), South Africa. KNP is one of the endemic anthrax regions in South Africa with distinctive genetic diversity. Genomic surveillance of KNP B. anthracis strains was employed on the historical culture collection isolates (n=67) dated from the 1990’s to 2015 using a whole genome sequencing approach. Whole genome single nucleotide polymorphism (SNPs) and pan-genomics analysis were used to define the B. anthracis genetic population structure. This study showed that KNP has heterologous B. anthracis strains grouping in the A-clade with more prominent ABr.005/006 (Ancient A) SNP lineage. The 2012 and 2015 anthrax isolates are dispersed amongst minor sub-clades that prevail in non-stabilized genetic evolution strains. This was augmented with non-parsimony informative SNPs of the B. anthracis strains across minor sub-clades of the Ancient A clade. Pan-genomics of B. anthracis showed a clear distinction between A and B-clade genomes with 11 374 predicted clusters of protein coding genes. Unique accessory genes of B-clade genomes that included biosynthetic cell wall genes and multidrug resistant of Fosfomycin. South Africa consists of diverse B. anthracis strains with unique defined SNPs. The sequenced B. anthracis strains in this study will serve as a means to further trace the dissemination of B. anthracis outbreaks globally and especially in South Africa.

Keywords: bacillus anthracis, whole genome single nucleotide polymorphisms, pangenomics, kruger national park

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Authors: Mahmoud M. Zakaria, Omnia F. Elmoursi, Mahmoud M. Gabr, Camelia A. AbdelMalak, Mohamed A. Ghoneim

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Many protocols were publicized for differentiation of human mesenchymal stem cells (MSCS) into insulin-producing cells (IPCs) in order to excrete insulin hormone ingoing to treat diabetes disease. Our aim is to evaluate relative gene expression for each independent protocol. Human bone marrow cells were derived from three volunteers that suffer diabetes disease. After expansion of mesenchymal stem cells, differentiation of these cells was done by three different protocols (the one-step protocol was used conophylline protein, the two steps protocol was depending on trichostatin-A, and the three-step protocol was started by beta-mercaptoethanol). Evaluation of gene expression was carried out by real-time PCR: Pancreatic endocrine genes, transcription factors, glucose transporter, precursor markers, pancreatic enzymes, proteolytic cleavage, extracellular matrix and cell surface protein. Quantitation of insulin secretion was detected by immunofluorescence technique in 24-well plate. Most of the genes studied were up-regulated in the in vitro differentiated cells, and also insulin production was observed in the three independent protocols. There were some slight increases in expression of endocrine mRNA of two-step protocol and its insulin production. So, the two-step protocol was showed a more efficient in expressing of pancreatic endocrine genes and its insulin production than the other two protocols.

Keywords: mesenchymal stem cells, insulin producing cells, conophylline protein, trichostatin-A, beta-mercaptoethanol, gene expression, immunofluorescence technique

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Authors: Maria Lina Garrido

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This paper aims to reflect upon instruction in English classes with the specific purpose of reading comprehension development, having as its paradigm the considerations presented by William Grabe, in his book Reading in a Second Language: Moving from theory to practice. His concerns regarding the connection between research findings and instructional practices have stimulated the present author to re-evaluate both her long practice as an English reading teacher and as the author of two reading textbooks for graduate students. Elements of the reading process such as linguistic issues, prior knowledge, reading strategies, critical evaluation, and motivation are the main foci of this analysis as far as the activities developed in the classroom are concerned. The experience with university candidates on postgraduate courses with different levels of English knowledge in Bahia, Brazil, has definitely demanded certain adjustments to this author`s classroom setting. Word recognition based on cognates, for example, has been emphasized given the fact that academic texts use many Latin words which have the same roots as the Brazilian Portuguese lexicon. Concerning syntactic parsing, the tenses/verbal aspects, modality and linking words are included in the curriculum, but not with the same depth as the general English curricula. Reading strategies, another essential predictor for developing reading skills, have been largely stimulated in L2 classes in order to compensate for a lack of the appropriate knowledge of the foreign language. This paper presents results that demonstrate that this author`s teaching practice is compatible with the implications and instruction concerning the reading process outlined by Grabe, however, it admits that each class demands specific instructions to meet the needs of that particular group.

Keywords: classroom practice, instructional activities, reading comprehension, reading skills

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Authors: Anyaphat Srithanasuwan, Noppason Pangprasit, Montira Intanon, Phongsakorn Chuammitri, Witaya Suriyasathaporn, Ynte H. Schukken

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Streptococcus uberis is one of the most common mastitis-causing pathogens, with a wide range of intramammary infection (IMI) durations and pathogenicity. This study aimed to compare shared or unique virulence factor gene clusters distinguishing persistent and transient strains of S. uberis. A total of 139 S. uberis strains were isolated from three small-holder dairy herds with a high prevalence of S. uberis mastitis. The duration of IMI was used to categorize bacteria into two groups: transient and persistent strains with an IMI duration of less than 1 month and longer than 2 months, respectively. Six representative S. uberis strains, three from each group (transience and persistence) were selected for analysis. All transient strains exhibited multi-locus sequence types (MLST), indicating a highly diverse population of transient S. uberis. In contrast, MLST of persistent strains was available in an online database (pubMLST). Identification of virulence genes was performed using whole-genome sequencing (WGS) data. Differences in genomic size and number of virulent genes were found. For example, the BCA gene or alpha-c protein and the gene associated with capsule formation (hasAB), found in persistent strains, are important for attachment and invasion, as well as the evasion of the antimicrobial mechanisms and survival persistence, respectively. These findings suggest a genetic-level difference between the two strain types. Consequently, a comprehensive study of 139 S. uberis isolates will be conducted to perform an in-depth genetic assessment through WGS analysis on an Illumina platform.

Keywords: Streptococcus Uberis, mastitis, whole genome sequence, intramammary infection, persistent S. Uberis, transient s. Uberis

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Authors: Jafar Ahmadi, Nafiseh Noormohammadi, Sedegeh Fabriki Ourang

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GRF, Growth regulating factor, genes encode a novel class of plant-specific transcription factors. The GRF proteins play a role in the regulation of cell numbers in young and growing tissues and may act as transcription activations in growth and development of plants. Identification of GRF genes and their expression are important in plants to performance of the growth and development of various organs. In this study, to better understanding the structural and functional differences of GRFs family, 45 GRF proteins sequences in A. thaliana, Z. mays, O. sativa, B. napus, B. rapa, H. vulgare, and S. bicolor, have been collected and analyzed through bioinformatics data mining. As a result, in secondary structure of GRFs, the number of alpha helices was more than beta sheets and in all of them QLQ domains were completely in the biggest alpha helix. In all GRFs, QLQ, and WRC domains were completely protected except in AtGRF9. These proteins have no trans-membrane domain and due to have nuclear localization signals act in nuclear and they are component of unstable proteins in the test tube.

Keywords: domain, gene family, GRF, motif

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Authors: Alexandra Emmanuelle Membangbi, Jacky Njiki Bikoï, Esther Del-florence Moni Ndedi, Marie Joseph Nkodo Mindimi, Donatien Serge Mbaga, Elsa Nguiffo Makue, André Chris Mikangue Mbongue, Martha Mesembe, George Ikomey Mondinde, Eric Walter Perfura-yone, Sara Honorine Riwom Essama

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Background: Tuberculosis (TB) is one of the top lethal infectious diseases worldwide. In recent years, interferon-γ (INF-γ) release assays (IGRAs) have been established as routine tests for diagnosing TB infection. However, produced INF-γ assessment failed to distinguish active TB (ATB) from latent TB infection (LTBI), especially in TB epidemic areas. In addition to IFN-γ, interleukin-2 (IL-2), another cytokine secreted by activated T cells, is also involved in immune response against Mycobacterium tuberculosis. The aim of the study was to assess the capacity of IFN-γ and IL2 to evaluate the therapeutic response of patients on anti-tuberculosis treatment. Material and Methods: We conducted a cross-sectional study in the Pneumonology Departments of the Jamot Hospital in Yaoundé between May and August 2021. After signed the informed consent, the sociodemographic data, as well as 5 mL of blood, were collected in the crook of the elbow of each participant. Sixty-one subjects were selected (n= 61) and divided into 4 groups as followed: group 1: resistant tuberculosis (n=13), group 2: active tuberculosis (n=19), group 3 cured tuberculosis (n=16), and group 4: presumed healthy persons (n=13). The cytokines of interest were determined using an indirect Enzyme-linked Immuno-Sorbent Assay (ELISA) according to the manufacturer's recommendations. P-values < 0.05 were interpreted as statistically significant. All statistical calculations were performed using SPSS version 22.0 Results: The results showed that men were more 14/61 infected (31,8%) with a high presence in active and resistant TB groups. The mean age was 41.3±13.1 years with a 95% CI = [38.2-44.7], the age group with the highest infection rate was ranged between 31 and 40 years. The IL-2 and INF-γ means were respectively 327.6±160.6 pg/mL and 26.6±13.0 pg/mL in active tuberculosis patients, 251.1±30.9 pg/mL and 21.4±9.2 pg/mL in patients with resistant tuberculosis, while it was 149.3±93.3 pg/mL and 17.9±9.4 pg/mL in cured patients, 15.1±8.4 pg/mL and 5.3±2.6 pg/mL in participants presumed healthy (p <0.0001). Significant differences in IFN-γ and IL-2 rates were observed between the different groups. Conclusion: Monitoring the serum levels of INF-γ and IL-2 would be useful to evaluate the therapeutic response of anti-tuberculosis patients, particularly in the both cytokines association case, that could improve the accuracy of routine examinations.

Keywords: antibiotic therapy, interferon gamma, interleukin 2, tuberculosis

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Authors: Elif Coskun Daggecen, Seyma Dokucu, Yekta Gezginc, Ismail Akyol

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Fermented dairy food quality is mainly determined by the sensory perception and influenced by many factors. Today, starter cultures for fermented foods are being developed to have a constant quality in these foods. Streptococcus thermophilus is one of the main species of most a starter cultures of yogurt fermentation. This species produces lactate by lactose fermentation from pyruvate. On the other hand, a small amount of pyruvate can alternatively be converted to various typical yoghurt flavor compounds such as diacetyl, acetoin, acetaldehyde, or acetic acid, for which the activity of three genes are shown to be especially important; ldh, nox and als. Up to date, commercially produced yoghurts have not yet met the desired aromatic properties that Turkish consumers find in traditional homemade yoghurts. Therefore, it is important to select starters carrying favorable metabolic characteristics from natural isolates. In this study, 30 strains of Str. Thermophilus were isolated from traditional Turkish yoghurts obtained from different regions of the country. In these strains, transcriptional levels of ldh, nox and als genes were determined via a newly developed qPCR protocol, which is a more reliable and precision method for analyzing the quantitative and qualitative expression of specific genes in different experimental conditions or in different organisms compared to conventional analytical methods. Additionally, the metabolite production potentials of the isolates were measured. Of all the strains examined, 60% were found to carry the metabolite production potential and the gene activity which appeared to be suitable to be used as a starter culture. Probable starter cultures were determined according to real-time PCR results.

Keywords: gene expression, RT-PCR, starter culture, Streptococcus thermophilus

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Authors: Amin Abbasi, Mahdi Asghari Ozma

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Background and Objective:Enterococcus faecium is a normal flora of the human gastrointestinal tract that causes infection in the host body under conditions such as biofilm formation, in which the use of antibiotics causes changes in these pathogenic mechanisms. In this study, we aimed to evaluate comprehensively the changes in E.faecium when exposed to sub-MIC of the gentamicin,especiallythe biofilm formation rate. Materials and Methods: For this study, the keywords "Enterococcus faecium ", "Biofilm", and "Gentamicin" in the databases PubMed, Google Scholar, Sid, and MagIran between 2015 and 2021 were searched, and 14 articles were chosen, studied, and analyzed. Results: Gentamicin significantly had increased biofilm formation in most of the isolates in the studies. Increased expression of the genes (efaA and esp) and proteins involved in biofilm formation and decreased expression of the genes (gelE and cylA) involved in spreading and proteins involved in metabolism and cell division in E.faecium were the most significant cause of the biofilm formation, which were increased in sub-MIC gentamicin-treated situation. Conclusion: Inadequate use of gentamicin intensify biofilm formation of E.faecium, which can make the treatment of infections caused by this bacterium difficult.

Keywords: biofilm, enterococcus faecium, gentamicin, proteome

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Authors: Sajewicz-Krukowska Joanna, Domańska-Blicharz Katarzyna, Tarasiuk Karolina, Marzec-Kotarska Barbara

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Astroviral infections pose a significant problem in the poultry industry, leading to multiple adverse effects such as decreased egg production, breeding disorders, poor weight gain, and even increased mortality. Commonly observed chicken astrovirus (CAstV) was recently reported to be responsible for "white chicks syndrome" associated with increased embryo/chick mortality. The CAstV-mediated pathogenesis in chicken occurs due to complex interactions between the infectious pathogen and the immune system. Many aspects of CAstV-chicken interactions remain unclear, and there is no information available regarding gene expression changes in the chicken's spleen in response to CAstV infection. We aimed to investigate the molecular background triggered by CAstV infection. Ten 21-day-old SPF White Leghorn chickens were divided into two groups of 5 birds each. One group was inoculated with CAstV, and the other was used as the negative control. On 4th dpi, spleen samples were collected and immediately frozen at -70°C for RNA isolation. We analysed transcriptional profiles of the chickens' spleens at the 4th day following infection using RNA-seq to establish differentially expressed genes (DEGs). The RNA-seq findings were verified by quantitative real-time PCR (qRT-PCR). A total of 31959 transcripts were identified in response to CAstV infection. Eventually 45 DEGs (p-value<0.05; Log2Foldchange>1)were recognized in the spleen after CAstV infection (26 upregulated DEGs and 19 downregulated DEGs). qRT-PCR performed on 4 genes (IFIT5, OASL, RASD1, DDX60) confirmed RNAseq results. Top differentially expressed genes belonged to novel putative IFN-induced CAstV restriction factors. Most of the DEGs were associated with RIG-I–like signalling pathway or, more generally, with an innate antiviral response(upregulated: BLEC3, CMPK2, IFIT5, OASL, DDX60, IFI6, and downregulated: SPIK5, SELENOP, HSPA2, TMEM158, RASD1, YWHAB). The study provided a global analysis of host transcriptional changes that occur during CAstV infection in vivo and proved the cell cycle in the spleen and immune signalling in chickens were predominantly affected upon CAstV infection.

Keywords: chicken astrovirus, CastV, RNA-seq, transcriptome, spleen

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Authors: Salama A. Ouf, Amera A. El-Adly, Abdelaleam H. Mohamed

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Dermatophytosis is the infection of keratinized tissues such as hair, nail and the stratum corneum of the skin by dermatophytic fungi. Infection is generally cutaneous and restricted to the non-living cornified layers because of the inability of the fungi to penetrate the deeper tissues or organs of immunocompetent hosts. In Saudi Arabia, Onychomycosis is the most frequent infection (40.3%), followed by tinea capitis (21.9%), tinea pedis (16%), tinea cruris (15.1%), and tinea corporis (6.7%). Several azole compounds have been tried to control dermatophytic infection, however, the azole-containing medicines may interfere with the activity of hepatic microsomal enzymes, sex and thyroid hormones, and testosterone biosynthesis. In this research, antibody-conjugated nanoparticles stimulated by cold plasma and laser were evaluated in vitro against some dermatophytes isolated from the common types of tinea. Different types of nanomaterials were tested but silver nanoparticles (AgNPs) were proved to be most effective against the dermatophytes under test. The use of cold plasma coupled with antibody-conjugated nano-particles has severe impact on dermatophytes where the inhibition of growth, spore germination keratinase activity was more than 88% in the case of Trichophyton rubrum, T. violaceum, Microsprum canis and M. gypseum. Complete inhibition of growth for all dermatophytes was brought about by the interaction of conjugated nanoparticles, with cold plasma and laser treatment. The in vivo test with inoculated guinea pigs achieved promising results where the recovery from the infection reached 95% in the case of M. canis –inoculated pigs treated with AgNPs pretreated with cold plasma and laser.

Keywords: cold plasma, dermatophytes, laser, silver nanoparticles

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Authors: Hyeona Kim, Kichang Lee, Seunghee Lee, Jeongsu An, Kyungjun Min

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Contrast videofluoroscopy is the diagnostic imaging technique for evaluating cat with dysphagia. Generally, videofluoroscopic studies have been done with the cat restrained in lateral recumbency. It is different from the neutral position such as standing or sternal recumbency which is actual swallowing posture. We hypothesized that measurement of esophageal transit and peristalsis would be affected by body position. This experimental study analyzed the imaging findings of barium esophagram in 5 cats. Each cat underwent videofluoroscopy during swallowing of liquid barium and barium-soaked kibble in standing position and lateral recumbency. Esophageal transit time and the number of esophageal peristaltic waves were compared among body positions. Transit time in the cervical esophagus (0.57s), cranial thoracic esophagus (2.5s), and caudal thoracic esophagus(1.10s) was delayed when cats were in lateral recumbency for liquid barium. For kibble, transit time was more delayed than that of liquid through the entire esophagus in lateral recumbency. Liquid and kibble frequently started to delay at thoracic inlet region, transit time in the thoracic esophagus was significantly delayed than the cervical esophagus. In standing position, 60.2% of liquid swallows stimulated primary esophageal peristalsis. In lateral recumbency, 50.5% of liquid swallows stimulated primary esophageal peristalsis. Other variables were not significantly different. Lateral body positioning increases entire esophageal transit time and thoracic esophageal transit time is most significantly delayed. Thus, lateral recumbency decreases the number of primary esophageal peristalsis.

Keywords: barium esophagram, body positioning, cat, videofluoroscopy

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Authors: Ni Luh Putu Harta Wedari

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Background: Clostridium difficile has two main virulence factors, namely TcdA and TcdB. TcdA encoded by the tcdA gene acts as an enterotoxin, pro-inflammatory and fluid accumulation, while TcdB encoded by the tcdB gene is cytotoxic, causes disruption of the actin cytoskeleton, and causes disruption of tight junctions in colon cells. This study aims to explore the relationship between the tcdA and tcdB genes and the duration of diarrhea in elderly patients. Method: This research was an observational analytic with a prospective cross-sectional with samples of elderly diarrhea patients who met the inclusion criteria in Denpasar City health service facilities from 1 December 2022 until 30 June 2023, and then their feces were analyzed using the real-time PCR method. Results: In this study, 40 elderly diarrhea patients met the inclusion criteria and in accordance with the minimum sample size, 28 (70%) men and 12 (30%) women. 5 patients (12.5%) had a history of azithromycin, 4 (10%) levofloxacin, 17 (42.5%) ciprofloxacin, 8 (20%) metronidazole, 1 (2.5%) cefoperazone, 5 (12, 5%) doxycycline. Comorbids, namely 13 (32.5%) type II diabetes mellitus, 4 (10%) chronic kidney disease, 10 (25%) malignancies, 7 (17.5%) urinary tract infections, 3 (7.5%) %) immunocompromised, 2 (5%) cardiac heart failure, and 1 (2.5%) acute on chronic kidney disease. The overall diarrhea duration average was 5 days. 8 samples (20%) were positive for 16s rRNA, and there was no significant difference in diarrhea duration with negative samples (p=0.166). The relationship between the tcdA gene and the duration of diarrhea could not be performed because all samples were negative. Likewise, relationship analysis between the coexistence of tcdA and tcdB could not be performed. There was no significant difference between tcdB positive 3 (7.5%) and negative with diarrhea duration (p=0.739). Conclusion: There is no significant relationship between the presence of the 16s rRNA and tcdB C. difficile genes with the duration of diarrhea in elderly patients.

Keywords: clostridium, difficile, diarrhea, elderly, tcdA, tcdB

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Authors: Hannah R. Devens, Phillip L. Davidson, Dione Deaker, Kathryn E. Smith, Gregory A. Wray, Maria Byrne

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Marine invertebrate species with calcifying larvae are especially vulnerable to ocean acidification (OA) caused by rising atmospheric CO₂ levels. Acidic conditions can delay development, suppress metabolism, and decrease the availability of carbonate ions in the ocean environment for skeletogenesis. These stresses often result in increased larval mortality, which may lead to significant ecological consequences including alterations to the larval settlement, population distribution, and genetic connectivity. Importantly, many of these physiological and developmental effects are caused by genetic and molecular level changes. Although many studies have examined the effect of near-future oceanic pH levels on gene expression in marine invertebrates, little is known about the impact of OA on gene expression in a developmental context. Here, we performed mRNA-sequencing to investigate the impact of environmental acidity on gene expression across three developmental stages in the sea urchin Heliocidaris erythrogramma. We collected RNA from gastrula, early larva, and 1-day post-metamorphic juvenile sea urchins cultured at present-day and predicted future oceanic pH levels (pH 8.1 and 7.7, respectively). We assembled an annotated reference transcriptome encompassing development from egg to ten days post-metamorphosis by combining these data with datasets from two previous developmental transcriptomic studies of H. erythrogramma. Differential gene expression and time course analyses between pH conditions revealed significant alterations to developmental transcription that are potentially associated with pH stress. Consistent with previous investigations, genes involved in biomineralization and ion transport were significantly upregulated under acidic conditions. Differences in gene expression between the two pH conditions became more pronounced post-metamorphosis, suggesting a development-dependent effect of OA on gene expression. Furthermore, many differences in gene expression later in development appeared to be a result of broad downregulation at pH 7.7: of 539 genes differentially expressed at the juvenile stage, 519 of these were lower in the acidic condition. Time course comparisons between pH 8.1 and 7.7 samples also demonstrated over 500 genes were more lowly expressed in pH 7.7 samples throughout development. Of the genes exhibiting stage-dependent expression level changes, over 15% of these diverged from the expected temporal pattern of expression in the acidic condition. Through these analyses, we identify novel candidate genes involved in development, metabolism, and transcriptional regulation that are possibly affected by pH stress. Our results demonstrate that pH stress significantly alters gene expression dynamics throughout development. A large number of genes differentially expressed between pH conditions in juveniles relative to earlier stages may be attributed to the effects of acidity on transcriptional regulation, as a greater proportion of mRNA at this later stage has been nascent transcribed rather than maternally loaded. Also, the overall downregulation of many genes in the acidic condition suggests that OA-induced developmental delay manifests as suppressed mRNA expression, possibly from lower transcription rates or increased mRNA degradation in the acidic environment. Further studies will be necessary to determine in greater detail the extent of OA effects on early developing marine invertebrates.

Keywords: development, gene expression, ocean acidification, RNA-sequencing, sea urchins

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Authors: Zainab Dashti, Leila Vali

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Background: The Middle East, in particular Kuwait, contains one of the highest rates of patients with Diabetes in the world. Generally, infections resistant to antibiotics among the diabetic population has been shown to be on the rise. This is the first study in Kuwait to compare the antibiotic resistance profiles and genotypic differences between the resistant isolates of Enterobacteriaceae obtained from diabetic and non-diabetic patients. Material/Methods: In total, 65 isolates were collected from diabetic patients consisting of 34 E. coli, 15 K. pneumoniae and 16 other Enterobacteriaceae species (including Salmonella spp. Serratia spp and Proteus spp.). In our control group, a total of 49 isolates consisting of 37 E. coli, 7 K. pneumoniae and 5 other species (including Salmonella spp. Serratia spp and Proteus spp.) were included. Isolates were identified at the species level and antibiotic resistance profiles, including Colistin, were determined using initially the Vitek system followed by double dilution MIC and E-test assays. Multi drug resistance (MDR) was defined as isolates resistant to a minimum of three antibiotics from three different classes. PCR was performed to detect ESBL genes (blaCTX-M, blaTEM & blaSHV), flouroquinolone resistance genes (qnrA, qnrB, qnrS & aac(6’)-lb-cr) and carbapenem resistance genes (blaOXA, blaVIM, blaGIM, blaKPC, blaIMP, & blaNDM) in both groups. Pulse field gel electrophoresis (PFGE) was performed to compare clonal relatedness of both E. coli and K.pneumonaie isolates. Results: Colistin resistance was determined in three isolates with MICs of 32-128 mg/L. A significant difference in resistance to ampicillin (Diabetes 93.8% vs control 72.5%, P value <0.002), augmentin (80% vs 52.5%, p value < 0.003), cefuroxime (69.2% vs 45%, p value < 0.0014), ceftazadime (73.8% vs 42.5%, p value <0.001) and ciprofloxacin (67.6% vs 40%, p value < 0.005) were determined. Also, a significant difference in MDR rates between the two groups (Diabetes 76.9%, control 57.5%, p value <0.036 were found. All antibiotic resistance genes showed a higher prevalence among the diabetic group, except for blaCTX-M, which was higher among the control group. PFGE showed a high rate of diversity between each group of isolates. Conclusions: Our results suggested an alarming rate of antibiotic resistance, in particular Colistin resistance (1.8%) among K. pneumoniea isolated from diabetic patients in Kuwait. MDR among Enterobacteriaceae infections also seems to be a worrying issue among the diabetics of Kuwait. More efforts are required to limit the issue of antibiotic resistance in Kuwait, especially among patients with diabetes mellitus.

Keywords: antibiotic resistance, diabetes, enterobacreriacae, multi antibiotic resistance

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Authors: Mukul Sharma, Madhusmita Das, Sundeep Chaitanya Vedithi

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Leprosy is a chronic human disease caused by Mycobacterium leprae, that cannot be cultured in vitro. Though treatable with multidrug therapy (MDT), recently, bacteria reported resistance to multiple antibiotics. Targeting DNA replication and repair pathways can serve as the foundation of developing new anti-leprosy drugs. Due to the absence of an axenic culture medium for the propagation of M. leprae, studying cellular processes, especially those belonging to DNA repair pathways, is challenging. Genomic understanding of M. Leprae harbors several protein-coding genes with no previously assigned function known as 'hypothetical proteins'. Here, we report identification and expression of known and hypothetical DNA repair genes from a human skin biopsy and mouse footpads that are involved in base excision repair, direct reversal repair, and SOS response. Initially, a bioinformatics approach was employed based on sequence similarity, identification of known protein domains to screen the hypothetical proteins in the genome of M. leprae, that are potentially related to DNA repair mechanisms. Before testing on clinical samples, pure stocks of bacterial reference DNA of M. leprae (NHDP63 strain) was used to construct standard graphs to validate and identify lower detection limit in the qPCR experiments. Primers were designed to amplify the respective transcripts, and PCR products of the predicted size were obtained. Later, excisional skin biopsies of newly diagnosed untreated, treated, and drug resistance leprosy cases from SIHR & LC hospital, Vellore, India were taken for the extraction of RNA. To determine the presence of the predicted transcripts, cDNA was generated from M. leprae mRNA isolated from clinically confirmed leprosy skin biopsy specimen across all the study groups. Melting curve analysis was performed to determine the integrity of the amplification and to rule out primer‑dimer formation. The Ct values obtained from qPCR were fitted to standard curve to determine transcript copy number. Same procedure was applied for M. leprae extracted after processing a footpad of nude mice of drug sensitive and drug resistant strains. 16S rRNA was used as positive control. Of all the 16 genes involved in BER, DR, and SOS, differential expression pattern of the genes was observed in terms of Ct values when compared to human samples; this was because of the different host and its immune response. However, no drastic variation in gene expression levels was observed in human samples except the nth gene. The higher expression of nth gene could be because of the mutations that may be associated with sequence diversity and drug resistance which suggests an important role in the repair mechanism and remains to be explored. In both human and mouse samples, SOS system – lexA and RecA, and BER genes AlkB and Ogt were expressing efficiently to deal with possible DNA damage. Together, the results of the present study suggest that DNA repair genes are constitutively expressed and may provide a reference for molecular diagnosis, therapeutic target selection, determination of treatment and prognostic judgment in M. leprae pathogenesis.

Keywords: DNA repair, human biopsy, hypothetical proteins, mouse footpads, Mycobacterium leprae, qPCR

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Authors: Ali Bayram, Burak Uz, Remzi Yiğiter

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The impairment of lipid metabolism in the central nervous system has been suggested as a critical factor of Alzheimer’s disease (AD) pathogenesis. Homo sapiens acyl-coenyme A synthetase short-chain family member 2 (ACSS2) gene encodes the enzyme acetyl-Coenzyme A synthetase (AMP forming; AceCS) providing acetyl-coenzyme A (Ac-CoA) for various physiological processes, such as cholesterol and fatty acid synthesis, as well as the citric acid cycle. We investigated ACSS2, transcript variant 1 (ACSS2*1), mRNA levels in the peripheral blood mononuclear cells (PBMC) of patients with AD and compared them with the controls. The study group comprised 50 patients with the diagnosis of AD who have applied to Gaziantep University Faculty of Medicine, and Department of Neurology. 49 healthy individuals without any neurodegenerative disease are included as controls. ACSS2 mRNA expression in PBMC of AD/control patients was 0.495 (95% confidence interval: 0.410-0.598), p= .000000001902). Further studies are needed to better clarify this association.

Keywords: Alzheimer’s disease, ACSS2 Genes, mRNA expression, RT-PCR

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Authors: I. Nava-Arenas, N. Ruiz-Ordaz, C. J. Galindez-Mayer, M. L. Luna-Guido, S. L. Ruiz-López, A. Cabrera-Orozco, D. Nava-Arenas

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Among the most important herbicides, the organochlorine compounds are of considerable interest due to their recalcitrance to the chemical, biological, and photolytic degradation, their persistence in the environment, their mobility, and their bioacummulation. The most widely used herbicides in North America are primarily 2,4-dichlorophenoxyacetic acid (2,4-D), the triazines (atrazine and simazine), and to a lesser extent diuron. The contamination of soils and water bodies frequently occurs by mixtures of these xenobiotics. For this reason, in this work, the operational stability to changes in the composition of the medium supplied to an aerobic biofilm reactor was studied. The reactor was packed with fragments of volcanic rock that retained a complex microbial film, able to degrade a mixture of organochlorine herbicides atrazine, simazine, diuron and 2,4-D, and whose members have microbial genes encoding the main catabolic enzymes atzABCD, tfdACD and puhB. To acclimate the attached microbial community, the biofilm reactor was fed continuously with a mineral minimal medium containing the herbicides (in mg•L-1): diuron, 20.4; atrazine, 14.2, simazine, 11.4, and 2,4-D, 59.7, as carbon and nitrogen sources. Throughout the bioprocess, removal efficiencies of 92-100% for herbicides, 78-90% for COD, 92-96% for TOC and 61-83% for dehalogenation were reached. In the microbial community, the genes encoding catabolic enzymes of different herbicides tfdACD, puhB and, occasionally, the genes atzA and atzC were detected. After the acclimatization, the triazine herbicides were eliminated from the mixture formulation. Volumetric loading rates of the mixture 2,4-D and diuron were continuously supplied to the reactor (1.9-21.5 mg herbicides •L-1 •h-1). Along the bioprocess, the removal efficiencies obtained were 86-100% for the mixture of herbicides, 63-94% for for COD, 90-100% for COT, and dehalogenation values of 63-100%. It was also observed that the genes encoding the enzymes in the catabolism of both herbicides, tfdACD and puhB, were consistently detected; and, occasionally, the atzA and atzC. Subsequently, the triazine herbicide atrazine and simazine were restored to the medium supply. Different volumetric charges of this mixture were continuously fed to the reactor (2.9 to 12.6 mg herbicides •L-1 •h-1). During this new treatment process, removal efficiencies of 65-95% for the mixture of herbicides, 63-92% for COD, 66-89% for TOC and 73-94% of dehalogenation were observed. In this last case, the genes tfdACD, puhB and atzABC encoding for the enzymes involved in the catabolism of the distinct herbicides were consistently detected. The atzD gene, encoding the cyanuric hydrolase enzyme, could not be detected, though it was determined that there was partial degradation of cyanuric acid. In general, the community in the biofilm reactor showed some catabolic stability, adapting to changes in loading rates and composition of the mixture of herbicides, and preserving their ability to degrade the four herbicides tested; although, there was a significant delay in the response time to recover to degradation of the herbicides.

Keywords: biodegradation, biofilm reactor, microbial community, organochlorine herbicides

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Authors: Hye Kyung Kim, Myung-Gyou Kim, Kang-Hyun Leem

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The prickly pear cactus (Opuntia ficus-indica) has a global distribution and has been used for medicinal benefits such as artherosclerosis, diabetes, gastritis, and hyperglycemia. The prickly pear variety Opuntia ficus-indica var. Saboten (OFS) is widely cultivated in Cheju Island, the southwestern region of Korea, and used as a functional food. The present study investigated the effects of OFS on adipogenesis, lipolysis, glucose uptake, and glucose transporter (GLUT4) expression using preadipocyte 3T3-L1 cells. Adipogenesis was determined by preadipocyte differentiation and triglyceride accumulation assessed by Oil Red O staining. Lipolysis was determined as the rate of glycerol release. Insulin-stimulated glucose uptake and GLUT4 expression were measured using fluorescent glucose analogue, 2-NBDG, and ELISA, respectively. Quantitative real-time RT-PCR was performed to investigate the effects of OFS on the mRNA expression of peroxisome proliferator-activated receptor γ (PPARγ), a regulator of adipocyte differentiation. Ethanol extracts of OFS dose-dependently enhanced adipocyte differentiation and cellular triglyceride levels indicating the enhancement of the differentiation of preadipocytes into adipocytes. Insulin-stimulated glucose uptake and GLUT4 expression were also dose-dependently increased by OFS treatment. Furthermore, OFS treatment also increased the mRNA levels of PPARγ. These effects of OFS on adipocytes suggest that OFS is potentially beneficial for type 2 diabetes by due to its enhanced glucose uptake and balanced adipogenesis and lipolysis properties.

Keywords: 3T3-L1 preadipocyte cell, adipogenesis, GLUT4, lipolysis, Opuntia ficus-indica var. Saboten, PPARγ, prickly pear cactus

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Authors: Debatosh Das, Moxian Chen, Jianhua Zhang, Caroline Gutjahr

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Arbuscular mycorrhiza (AM) is a mutualistic symbiosis between plant roots and Glomeromycotina fungi, which is activated under low but inhibited by high phosphate. The effect of phosphate on AM development has been observed for many years, but mechanisms regulating it under contrasting phosphate levels remain unknown. Based on previous observations that promoters of several AM functional genes contain PHR binding motifs, we hypothesized that PHR2, a master regulator of phosphate starvation response in rice, was recruited to regulate AM symbiosis development. We observed a drastic reduction in root colonization and significant AM transcriptome modulation in phr2. PHR2 targets genes required for root colonization and AM signaling. The role of PHR2 in improving root colonization, mycorrhizal phosphate uptake, and growth response was confirmed in field soil. In conclusion, rice PHR2, which is considered a master regulator of phosphate starvation responses, acts as a positive regulator of AM symbiosis between Glomeromycotina fungi and rice roots. PHR2 directly targets the transcription of plant strigolactone and AM genes involved in the establishment of this symbiosis. Our work facilitates an understanding of ways to enhance AMF propagule populations introduced in field soils (as a biofertilizer) in order to restore the natural plant-AMF networks disrupted by modern agricultural practices. We show that PHR2 is required for AM-mediated improvement of rice yield in low phosphate paddy field soil. Thus, our work contributes knowledge for rational application of AM in sustainable agriculture. Our data provide important insights into the regulation of AM by the plant phosphate status, which has a broad significance in agriculture and terrestrial ecosystems.

Keywords: biofertilizer, phosphate, mycorrhiza, rice, sustainable, symbiosis

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Authors: Pawinee Innark, Hudsaya Punyanitikul, Chanuluk Khanobdee, Chatchawan Jantasuriyarat, Sompid Samipak

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One of the most devastating diseases in cucumber is downy mildew caused by the fungus Pseudoperonospora cubensis. To enable the use of marker-assisted breeding for resistance cultivars, sixty six microsatellite markers were used to map (quantitative trait loci) QTLs for DM resistance. Total of 315 F2 population from the cross between DM-resistant inbred line CSL0067 and susceptible CSL0139 were evaluated for downy mildew resistance in cotyledon, first and second true leaf at 7, 10, and 14 day after inoculation. The QTL analysis revealed that the downy mildew resistant genes were controlled by multiple recessive genes. From eight linkage groups (LG 1.1, 1.2, 2, 3, 4, 5.1, 5.2 and 6), fourteen QTL positions were detected on 4 linkage groups (LG 1.1, 2, 5.1 and 6) with the log of odd scores ranged from 3.538 to 9.165. Among them, Cot7_5.1_2 and Cot10_5.1 had major-effect QTL with the R2 values of 10.9 and 12.5%, respectively. The flanking markers for Cot7_5.1_2 were SSR19172 - SSR07531 markers and for Cot10_5.1 were SSR03943 - SSR00772. Besides QTLs on chromosome 1, 5 and 6 that were previously reported, this study also revealed a QTL for DM resistance on chromosome 2 that can be used as a new source in cucumber breeding program.

Keywords: cucumber, DNA marker, downy mildew, QTL

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Authors: K. Swapna, Sk. Mahamuda, Ch, Annapurna, A. Srinivasa Rao, G. Vijaya Prakash

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Samarium ions doped Alkali Fluoro Tungsten Tellurite (AFTT) Glasses have been prepared by using the melt quenching technique and characterized through various spectroscopic techniques such as optical absorption, excitation, emission and decay spectral studies. From the measured absorption spectra of Sm3+ ions in AFTT glasses, the optical band gap and Urbach energies have been evaluated. The spectroscopic parameters such as oscillator strengths (f), Judd-Ofelt (J-O) intensity parameters (Ωλ), spontaneous emission probability (AR), branching ratios (βR) and radiative lifetimes (τR) of various excited levels have been determined from the absorption spectrum by using J-O analysis. A strong luminescence in the reddish-orange spectral region has been observed for all the Sm3+ ions doped AFTT glasses. It consisting four emission transitions occurring from the 4G5/2metastable state to the lower lying states 6H5/2, 6H7/2, 6H9/2 and 6H11/2 upon exciting the sample with a 478 nm line of an argon ion laser. The stimulated emission cross-sections (σe) and branching ratios (βmeas) were estimated from the emission spectra for all emission transitions. Correlation of the radiative lifetime with the experimental lifetime measured from the day curves allows us to measure the quantum efficiency of the prepared glasses. In order to know the colour emission of the prepared glasses under near UV excitation, the emission intensities were analyzed using CIE 1931 colour chromaticity diagram. The aforementioned spectral studies carried out on Sm3+ ions doped AFTT glasses allowed us to conclude that, these glasses are best suited for orange-red visible lasers.

Keywords: fluoro tungsten tellurite glasses, judd-ofelt intensity parameters, lifetime, stimulated emission cross-section

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Authors: Al-Mutary M., Alhimaidi A., Al-Ghadi M. Iwamoto D., Javed Ahmad. Abdulaziz A. Al-Khedhairy

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The aim of the present study was to evaluate the effect of ovine follicular fluid supplementation during IVM of sheep oocytes on the resumption of meiosis, glutathione (GSH) content and expression of Bax, Bcl-2, and HSPB1 genes. Sheep ovaries were collected from Riyadh slaughterhouse, KSA. Oocytes were aspirated from 3-6 mm follicles. Ovine oocytes were cultured in maturation medium with 0% (control), 10%, 20%, 40% of ovine follicular fluid for 24 h. Results indicated that the rate of oocyte maturation was significantly (P≤0.05) decreased in 40% OFF (36.87%) versus the control (61.3%), 10% OFF (63.95%) and 20% OFF (64.08%). Supplementation of 10% OFF to IVM medium induced an intra-oocyte GSH concentration significantly higher than that found in ovine oocytes cultured with 20% OFF and 40% OFF and similar to the GSH content in oocytes cultured without FF. Real time polymerase chain reaction analysis for gene expression revealed no differences in Bax, Bcl-2, HSPB1 genes between control and 10% OFF group, whereas they were strongly expressed in 20% OFF and 40% OFF (P < 0.05) when compared to the control and 10% OFF. In conclusion the addition of 10% OFF to the IVM culture of sheep oocytes is recommended to support cytoplasmic maturation and increase oocytes competence.

Keywords: IVM, oocyte maturation, gene expression, follicular fluid

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Authors: Jin Young Kim, Kwon Kyoo Kang

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The SGR1 (STAYGREEN1) protein is a critical regulator of plant leaves in chlorophyll degradation and senescence. The functions and mechanisms of tomato SGR1 action are poorly understood and worthy of further investigation. To investigate the function of the SGR1 gene, we generated a SGR1-knockout (KO) null line via clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene editing and conducted RNA sequencing and gas chromatography tandem mass spectrometry (GC-MS/MS) analysis to identify the differentially expressed genes. The SlSGR1 (Solanum lycopersicum SGR1) knockout null line clearly showed a turbid brown color with significantly higher chlorophyll and carotenoid content compared to wild-type (WT) fruit. Differential gene expression analysis revealed 728 differentially expressed genes (DEGs) between WT and sgr1 #1-6 line, including 263 and 465 downregulated and upregulated genes, respectively, for which fold change was >2, and the adjusted p-value was <0.05. Most of the DEGs were related to photosynthesis and chloroplast function. In addition, the pigment, carotenoid changes in sgr1 #1-6 line was accumulated of key primary metabolites such as sucrose and its derivatives (fructose, galactinol, raffinose), glycolytic intermediates (glucose, G6P, Fru6P) and tricarboxylic acid cycle (TCA) intermediates (malate and fumarate). Taken together, the transcriptome and metabolite profiles of SGR1-KO lines presented here provide evidence for the mechanisms underlying the effects of SGR1 and molecular pathways involved in chlorophyll degradation and carotenoid biosynthesis.

Keywords: tomato, CRISPR/Cas9, null line, RNA-sequencing, metabolite profiling

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Authors: Salman Naveed, Nitant Gandhi, Grant Billings, Zachary Jones, B. Todd Campbell, Michael Jones, Sachin Rustgi

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Cotton (Gossypium spp.) is the primary source of natural fiber in the U.S. and a major crop in the Southeastern U.S. Despite constant efforts to increase the cotton fiber yield, the yield gain has stagnated. Therefore, we undertook a novel approach to improve the cotton fiber yield by altering its growth habit from perennial to annual. In this effort, we identified genotypes with high-expression alleles of five floral induction and meristem identity genes (FT, SOC1, FUL, LFY, and AP1) from an upland cotton mini-core collection and crossed them in various combinations to develop cotton lines with annual growth habit, optimal flowering time and enhanced productivity. To facilitate the characterization of genotypes with the desired combinations of stacked alleles, we identified markers associated with the gene expression traits via genome-wide association analysis using a 63K SNP Array (Hulse-Kemp et al. 2015 G3 5:1187). Over 14,500 SNPs showed polymorphism and were used for association analysis. A total of 396 markers showed association with expression traits. Out of these 396 markers, 159 mapped to genes, 50 to untranslated regions, and 187 to random genomic regions. Biased genomic distribution of associated markers was observed where more trait-associated markers mapped to the cotton D sub-genome. Many quantitative trait loci coincided at specific genomic regions. This observation has implications as these traits could be bred together. The analysis also allowed the identification of candidate regulators of the expression patterns of these floral induction and meristem identity genes whose functions will be validated via virus-induced gene silencing.

Keywords: cotton, GWAS, QTL, expression traits

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Authors: Anida Causevic-Ramosevac, Sabina Semiz

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The aim of this study was to investigate the association of four single nucleotide polymorphisms (SNPs) - rs673548, rs693 in ApoB gene, rs1800775 in CETP gene and rs4846914 in GALNT2 gene with parameters of type 2 diabetes (T2D) and diabetic dyslipidemia in the population of Bosnia and Herzegovina (BH). Materials and methods: Our study involved 352 patients with T2D and 156 healthy subjects. Biochemical and anthropometric parameters were measured in all participants. DNA was extracted from the peripheral blood for the purpose of genetic testing. Polymorphisms in ApoB (rs673548, rs693), CETP (rs1800775) and GALNT2 (rs4846914) genes were analyzed by using Sequenom IPLEX platform. Results: Our results demonstrated significant associations for rs180075 polymorphism in CETP gene with levels of fasting insulin (p = 0.020; p = 0.027; p = 0.044), triglycerides (p = 0.046) and ALT (p = 0.031) activity in control group. In group of diabetic patients, results showed a significant association of rs673548 in ApoB gene with levels of fasting insulin (p = 0.008), HOMA-IR (p = 0.013), VLDL-C (p = 0.037) and CRP (p = 0.029) and rs693 in ApoB gene with BMI (p = 0.025), systolic blood pressure (p = 0.027), fasting insulin (p = 0.037) and HOMA-IR (p = 0.023) levels. Significant associations were also observed for rs1800775 in CETP gene with triglyceride (p = 0.023) levels and rs4846914 in GALNT2 gene with HbA1C (p = 0.013) and triglyceride (p = 0.043) levels. Conclusion: In conclusion, this is the first study that examined the impact of variations of candidate genes on a wide range of metabolic parameters in BH population. Our results suggest an association of variations of ApoB, CETP and GALNT2 genes with specific markers of T2D and dyslipidemia. Further studies would be needed in order to confirm these genetic effects in other ethnic groups as well.

Keywords: ApoB, CETP, dyslipidemia, GALNT2, type 2 diabetes

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