Search results for: bacterial gene clusters

Authors: Chamilani Nikapitiya, Mahanama De Zoysa, Jehee Lee

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Most of the bacterial diseases are associated with high mortalities in aquaculture species and causing huge economic losses. Different approaches have been taken to prevent or control of bacterial diseases including use of vaccines, probiotics, chemotherapy, water quality management, etc. Antibiotics are widely applying as chemotherapy to control bacterial diseases, however, it has been shown that frequent use of antibiotics is favored to develop multi-drug resistance bacteria. Therefore, phages and phage encoded lytic proteins are known to be one of the most promising alternatives for antibiotics to avoid the emergence of antibiotic-resistant bacteria. We isolated and characterized the two lytic phages, namely pAh-1 and pAs-1 against pathogenic Aeromonas hydrophila and Aeromonas salmonicida, respectively. Morphological characteristics were analyzed by Transmission electron microscopy (TEM) and host strain specificities were tested with Aeromonas and other closely related bacterial strains. TEM analysis revealed that both pAh-1 and pAsm-1 are composed of an icosahedral head and a segmented tail, and we suggest that, they are new members of Myoviridae family. Genome sizes of isolated phages were estimated by restriction enzyme digestion of genomic DNA using selected endonucleases followed by agarose gel electrophoresis. Estimated genome size of pAh-1 and pAs-1 were approximately 64 Kbp and 120 Kbp, respectively. Both pAh-1 and pAs-1 have shown narrow host specificity. Moreover, protective effects of phage therapy against fish pathogenic A. hydrophila were investigated in zebrafish model. The survival rate was 40% higher when zebrafish received intra-peritoneal injection (i.p.) of pAh-1 were simultaneously challenge A. hydrophila (2 x 106 CFU/fish) compared to that without phage treatment. Overall results suggest that both pAh-1 and pAs-1 can be used as a potential phage therapy to control Aeromonas infections in aquaculture.

Keywords: Aeromonas infections, antibiotic resistance, bacteriophage, bio-control, lytic phage

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Authors: Thobela Conco, Sheena Kumari, Chika Nnadozie, Mahmoud Nasr, Thor A. Stenström, Mushal Ali, Arshad Ismail, Faizal Bux

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The discharge of antibiotics and its residues into the wastewater treatment plants (WWTP’s) create a conducive environment for the development of antibiotic resistant pathogens. This presents a risk of potential dissemination of antibiotic resistant pathogens and antibiotic resistance genes into the environment. It is, therefore, necessary to study the level of antibiotic resistance genes (ARG’s) among bacterial pathogens that proliferate in biological wastewater treatment systems. In the current study, metagenomic and meta-transcriptomic sequences of samples collected from the influents, secondary effluents and post chlorinated effluents of three wastewater treatment plants treating domestic and hospital effluents in Durban, South Africa, were analyzed for profiling of ARG’s among bacterial pathogens. Results show that a variety of ARG’s, mostly, aminoglycoside, β-lactamases, tetracycline and sulfonamide resistance genes were harbored by diverse bacterial genera found at different stages of treatment. A significant variation in diversity of pathogen and ARGs between the treatment plant was observed; however, treated final effluent samples from all three plants showed a significant reduction in bacterial pathogens and detected ARG’s. Both pre- and post-chlorinated samples showed the presence of mobile genetic elements (MGE’s), indicating the inefficiency of chlorination to remove of ARG’s integrated with MGE’s. In conclusion, the study showed the wastewater treatment plant efficiently caused the reduction and removal of certain ARG’s, even though the initial focus was the removal of biological nutrients.

Keywords: antibiotic resistance, mobile genetic elements, wastewater, wastewater treatment plants

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Authors: Zerrin Orbak, Busra Demir

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Osteopetrosis is a rare genetic disease characterized by impaired bone resorption and increased bone sclerosis. Clinical presentation is very different in osteopetrosis. It can be asymptomatic or can be seen with typical symptoms. Here, a case of osteopetrosis was presented when evaluated for nystagmus. She was 10 months old. Parents were second-degree relatives. On physical examination, pigeon chest deformity and horizontal nystagmus were observed. There was a failure of thrive but no fracture. The cardiovascular examination was normal. Cranial, vertebral and long bone roentgenograms revealed characteristic deformities of osteopetrosis and diffuse sclerosis. The diagnosis was confirmed by genetic testing. A Homozygous mutation was detected in the TNFRSF11A gene (c.508A>G p.(Arg170Gly)). RANKL is encoded by the tumor necrosis factor ligand superfamily member 11 (TNFSF11) gene, and the binding to its receptor RANK, encoded by the TNFRSF11A gene, determines the activation of the downstream pathway that drives osteoclast differentiation and activation (51). The complete absence of osteoclasts is the key feature of the osteoclast-poor form of osteopetrosis (46). Patients are characterized by the absence of TRAP-positive osteoclasts in bone biopsies. The osteoclast-poor subtype of osteopetrosis caused by mutations in TNFSF11 gene is ultra-rare in humans. Clinical presentation is usually severe, with onset in early infancy or in fetal life. But here, a case was presented with horizontal nystagmus. A case presented with horizontal nystagmus, which was evaluated by neurology and diagnosed incidentally, was shared.

Keywords: osteopetrosis, nystagmus, bone, osteoclast-poor

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Authors: Vivek Anand, Rainer Naegele

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Industry 4.0 is a global mega-trend revolutionizing the world of advanced manufacturing, but also bringing up challenges for SMEs. In response, many regional, as well as digital Industry 4.0 Platforms, have been set up to boost the competencies of established enterprises as well as SMEs. The concept of 'Clusters' is a policy tool that aims to be a starting point to establish sustainable and self-supporting structures in industries of a region by identifying competencies and supporting cluster actors with services that match their growth needs. This paper is motivated by the idea that Clusters have the potential to enable firms, particularly SMEs, to accelerate the innovation process and transition to digital technologies. In this research, the efficacy of Industry 4.0 platforms as Cluster ecosystems is evaluated, especially for SMEs. Focusing on the Baden Wurttemberg region in Germany, an action research method is employed to study how SMEs leverage other actors on Industry 4.0 Platforms to further their Industry 4.0 journeys. The aim is to evaluate how such Industry 4.0 platforms stimulate innovation, cooperation and competitiveness. Additionally, the barriers to these platforms fulfilling their promise to serve as capacity building cluster ecosystems for SMEs in a region will also be identified. The findings will be helpful for academicians and policymakers alike, who can leverage a ‘cluster policy’ to enable Industry 4.0 ecosystems in their regions. Furthermore, relevant management and policy implications stem from the analysis. This will also be of interest to the various players in a cluster ecosystem - like SMEs and service providers - who benefit from the cooperation and competition. The paper will improve the understanding of how a dialogue orientation, a bottom-up approach and active integration of all involved cluster actors enhance the potential of Industry 4.0 Platforms. A strong collaborative culture is a key driver of digital transformation and technology adoption across sectors, value chains and supply chains; and will position Industry 4.0 Platforms at the forefront of the industrial renaissance. Motivated by this argument and based on the results of the qualitative research, a roadmap will be proposed to position Industry 4.0 Platforms as effective clusters ecosystems to support Industry 4.0 adoption in a region.

Keywords: cluster policy, digital transformation, industry 4.0, innovation clusters, innovation policy, SMEs and startups

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Authors: Renuka G. Oka

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From chowks to streets to verandahs to courtyards; residential open spaces are very significantly placed in traditional urban neighborhoods of India. At various levels of intersection, the open spaces with their attributes like juxtaposition with the built fabric, scale, climate sensitivity and response, multi-functionality, etc. reflect and respond to the patterns of human interactions. Also, these spaces tend to be quite well utilized. On the other hand, it is a common specter to see an imbalanced utilization of open spaces in newly/recently planned residential clusters. This is maybe due to lack of activity generators around or wrong locations or excess provisions or improper incorporation of aforementioned design attributes. These casual observations suggest the necessity for a systematic study of current residential open spaces. The exploratory study thus attempts to draw lessons through a structured inspection of residential open spaces to understand the effective environment as revealed through their use patterns. Here, residential open spaces are considered in a wider sense to incorporate all the un-built fabric around. These thus, include both use spaces and access space. For the study, open spaces in ten exemplary housing clusters/societies built during the last ten years across India are studied. A threefold inquiry is attempted in this direction. The first relates to identifying and determining the effects of various physical functions like space organization, size, hierarchy, thermal and optical comfort, etc. on the performance of residential open spaces. The second part sets out to understand socio-cultural variations in values, lifestyle, and beliefs which determine activity choices and behavioral preferences of users for respective residential open spaces. The third inquiry further observes the application of these research findings to the design process to derive meaningful and qualitative design advice. However, the study also emphasizes to develop a suitable framework of analysis and to carve out appropriate methods and approaches to probe into these aspects of the inquiry. Given this emphasis, a considerable portion of the research details out the conceptual framework for the study. This framework is supported by an in-depth search of available literature. The findings are worked out for design solutions which integrate the open space systems with the overall design process for residential clusters. The open spaces in residential areas present great complexities both in terms of their use patterns and determinants of their functional responses. The broad aim of the study is, therefore, to arrive at reconsideration of standards and qualitative parameters used by designers – on the basis of more substantial inquiry into the use patterns of open spaces in residential areas.

Keywords: open spaces, physical and social determinants, residential clusters, use patterns

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Authors: Bindu I. Somarajan, Viney Gupta, Gagandeep Kaur Walia, Jasbir Kaur, Sunil Kumar, Shikha Gupta, Abadh K. Chaurasia, Dinesh Gupa, Abhinav Kaushik, Aditi Mehta, Vipin Gupta, Arundhati Sharma

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Background: Juvenile onset primary open angle glaucoma (JOAG), affects individuals under the age of 40 years. Studies on a few families of JOAG, that led to the discovery of the Myocilin gene, reported the disease to have an autosomal dominant pattern of inheritance. However, sporadic forms of JOAG been seen to be more common in some populations. Most pathological homozygous mutations in the CYP1B1 gene associated with JOAG have been seen among sporadic cases. Given the higher prevalence of sporadic JOAG cases in our population, we aimed to look for common mutations E229K and R368H, the two most common variants in the CYP1B1 gene associated with glaucoma. Objective: To determine the frequency and evaluate genotype phenotype correlation of CYP1B1 E229K and R368H mutations in a cohort of 120 sporadic Juvenile open angle glaucoma patients.Methods: Unrelated JOAG patients whose first degree relatives had been examined and found to be unaffected were included in the study. The patients and their parents were screened for E229K and R368H mutations. The phenotypic characteristics were compared between probands with and with out these mutations by SPSS v16. Results: Out of 120 JOAG patients included in the study, the E229K mutation was seen in 9 probands (7.5%) and R368H in 7 (5.8%). The average age of onset of the disease (p=0.3) and the highest untreated IOP (p=0.4) among those carrying mutations was not significantly different from those who did not have these mutations. The proportion of probands with angle dysgenesis among those with E229K and R368H mutations was 70% (11 out of 16) in comparison to 65% (67 out of 104) of those who did not harbour these mutations (p=0.56). Similarly the probands with moderate to high myopia among those with E229K and R368H mutations was 20% (3 out of 16) in comparison to 18% (18 out of 104) of those who did not harbour these mutations(p=0.59). Conclusion: The frequency of E229K and R368H mutations of the CYP1B1 gene is low even among sporadic JOAG patients. Moreover there is no clinical correlation between the presence of these mutations and disease severity

Keywords: CYP1B1, gene, IOP, JOAG, mutation

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Authors: C. Kridtayopas, W. Danvilai, P. Sopannarath, A. Kayan, W. Loongyai

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Both Betong chicken (KU Line) and Thai Native chickens were the high quality of the meat and low carcass fat compared to broiler chickens. The objective of this study was to determine the growth performance, carcass characteristic, meat quality and association of polymorphism in the ApoVLDL-II gene with fat accumulation in the female broiler, Thai Native and Betong (KU line) chickens at 4-14 weeks. The chickens were used and reared under the same environment and management (100 chicks per breed). The results showed that body weight (BW) of broiler chickens was significantly higher than Thai Native and Betong (KU line) chickens (P < 0.01) through all the experiment. At 4-8 weeks of age, feed conversion ratio (FCR) of broiler chickens was significantly better than Thai Native and Betong (KU line) chickens (P < 0.01), then increased at week 8-14. The percentage of breast, abdominal fat and subcutaneous fat of broiler chickens was significantly greater than Thai Native and Betong (KU line) chickens (P < 0.01). However, Thai Native chickens showed the highest percentage of liver (P < 0.01) when compared to other breeds. In addition, the percentage of wing of Thai Native and Betong (KU line) chickens were significantly (P < 0.01) higher than broiler chickens. Meat quality was also determined and found that, pH of breast meat left from slaughter 45 minutes (pH45) and 24 hours (pH24) of broiler was significantly higher than Thai Native and Betong (KU line) (P < 0.01) whereas the percentage of drip loss, thawing loss, cooking loss and shear force was not significantly different between breeds. The polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used to genotype the polymorphism in the ApoVLDL-II gene in the broiler, Thai Native and Betong (KU line) chickens. The results found that, the polymorphism in the ApoVLDL-II gene at VLDL6 loci was not associated with fat accumulation in those studied population.

Keywords: ApoVLDL-II gene, Betong (KU line) chickens, broiler chickens, carcass characteristic, growth performance, meat quality, Thai native chickens

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Authors: Vivian A. Panes, Raymond John S. Rebong, Miel Q. Diaz

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Moringa oleifera Lam. is known mainly for its high nutritional value and medicinal properties contributing to its popular reputation as a 'miracle plant' in the tropical climates where it usually grows. The main objective of this study is to discover the genes and gene products involved in abiotic stress-induced activity that may impact the M. oleifera Lam. mature seeds as well as their corresponding functions. In this study, RNA-sequencing and de novo transcriptome assembly were performed using two assemblers, Trinity and Oases, which produced 177,417 and 120,818 contigs respectively. These transcripts were then subjected to various bioinformatics tools such as Blast2GO, UniProt, KEGG, and COG for gene annotation and the analysis of relevant metabolic pathways. Furthermore, FPKM analysis was performed to identify gene expression levels. The sequences were filtered according to the 'response to stress' GO term since this study dealt with stress response. Clustered Orthologous Groups (COG) showed that the highest frequencies of stress response gene functions were those of cytoskeleton which make up approximately 14% and 23% of stress-related sequences under Trinity and Oases respectively, recombination, repair and replication at 11% and 14% respectively, carbohydrate transport and metabolism at 23% and 9% respectively and defense mechanisms 16% and 12% respectively. KEGG pathway analysis determined the most abundant stress-response genes in the phenylpropanoid biosynthesis at counts of 187 and 166 pathways for Oases and Trinity respectively, purine metabolism at 123 and 230 pathways, and biosynthesis of antibiotics at 105 and 102. Unique and cumulative GO term counts revealed that majority of the stress response genes belonged to the category of cellular response to stress at cumulative counts of 1,487 to 2,187 for Oases and Trinity respectively, defense response at 754 and 1,255, and response to heat at 213 and 208, response to water deprivation at 229 and 228, and oxidative stress at 508 and 488. Lastly, FPKM was used to determine the levels of expression of each stress response gene. The most upregulated gene encodes for thiamine thiazole synthase chloroplastic-like enzyme which plays a significant role in DNA damage tolerance. Data analysis implies that M. oleifera stress response genes are directed towards the effects of climate change more than other stresses indicating the potential of M. oleifera for cultivation in harsh environments because it is resistant to climate change, pathogens, and foreign invaders.

Keywords: stress response, genes, Moringa oleifera, transcriptomics

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Authors: Felicia Segeth, Florian G. Klein, Lea Berger, Andreas Kolk, Per S. Holm

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The entry of oncolytic viruses (OVs) into clinical application opens groundbreaking changes in current and future treatment regimens. However, despite their potent anti-cancer activity in vitro, clinical studies revealed limitations of OVs as monotherapy. The same applies to CDK 4/6 inhibitors (CDK4/6i) targeting cell cycle as well as bromodomain and extra-terminal domain inhibitors (BETi) targeting gene expression. In this study, the anti-tumoral effect of XVir-N-31, an YB-1 dependent oncolytic adenovirus, was evaluated in combination with Ribociclib, a CDK4/6i, and JQ1, a BETi. The head and neck squamous cell carcinoma (HNSCC) cell lines Fadu, SAS, and Cal-33 were used. DNA replication and gene expression of XVir-N-31 was measured by RT-qPCR, protein expression by western blotting, and cell lysis by SRB assays. Treatment with CDK4/6i and BETi increased viral gene expression, viral DNA replication, and viral particle formation. The data show that the combination of oncolytic adenovirus XVir-N-31 with CDK4/6i & BETi acts highly synergistic in cancer cell lysis. Furthermore, additional molecular analyses on this subject demonstrate that the positive transcription elongation factor P-TEFb plays a decisive role in this regard, indicating an influence of the combinational therapy on gene transcription control. The combination of CDK4/6i & BETi and XVir-N-31 is an attractive strategy to achieve substantial cancer cell killing and is highly suitable for clinical testing.

Keywords: adenovirus, BET, CDK4/6, HNSCC, P-TEFb, YB-1

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Authors: Beatriz Suárez López, Gabriela Forman

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Kombucha (a symbiotic culture of bacteria and yeast) produces material capable of acquiring multiple shapes and textures that change significantly under different environment or temperature variations (e.g., when it is exposed to wet conditions), properties that may be explored in the scenic industry. This paper presents an analysis of its specific characteristics, exploring them as a non-conventional material for arts and performance. Costume Design uses surfaces as a powerful way of expression to represent concepts and stories; it may apply the unique features of nano bacterial cellulose (NBC) as assets in this artistic context. A mix of qualitative and quantitative (interventionist) methodology approaches were used -review of relevant literature to deepen knowledge on the research topic (crossing bibliography from different fields of studies: Biology, Art, Costume Design, etc.); as well as descriptive methods: laboratorial experiments, document quantities, observation to identify material properties and possibilities used to express a multiple narrative ideas, concepts and feelings. The results confirmed that NBC is an interactive and versatile material viable to be used in an alternative scenic context; its unique aesthetic and performative qualities, which change in contact to moisture, is a resource that can be used to show a visual and poetic impact on stage.

Keywords: biotechnological materials, contemporary dance, costume design, nano bacterial cellulose, performing arts

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Authors: M.F. Elkady, Sahar Zaki, Desouky Abd-El-Haleem

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Silver nanoparticles (AgNPs) are already widely prepared using different technologies. However, there are limited data on the effects of hydrogen ion concentration on nano-silver production. In this investigation, the impact of the pH reaction medium toward the particle size, agglomeration and the yield of the produced bio-synthesized silver were established. Quasi-spherical silver nanoparticles were synthesized through the biosynthesis green production process using the Egyptian E. coli bacterial strain 23N at different pH values. The formation of AgNPs has been confirmed with ultraviolet–visible spectra through identification of their characteristic peak at 410 nm. The quantitative production yield and the orientation planes of the produced nano-silver were examined using X-ray spectroscopy (EDS) and X-ray diffraction (XRD). Quantitative analyses indicated that the silver production yield was promoted at elevated pH regarded to increase the reduction rate of silver precursor through both chemical and biological processes. As a result, number of the nucleus and thus the size of the silver nanoparticles were tunable through changing pH of the reaction system. Accordingly, the morphological structure and size of the produced silver and its aggregates were determined using scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images. It was considered that the increment in pH value of the reaction media progress the aggregation of silver clusters. However, the presence of stain 23N biomass decreases the possibility of silver aggregation at the pH 7.

Keywords: silver nanoparticles, biosynthesis, reaction media pH, nano-silver characterization

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Authors: Mudassar Mohiuddin, Zahid Iqbal

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Introduction: Clostridium perfringens is an important pathogen responsible for causing enteric diseases in both human and animals. The bacteria produce several toxins. These toxins play vital role in the pathogenesis of various fatal enteric diseases and are classified into five types, on the basis of the differential production of Alpha, Beta, Epsilon and Iota toxins. In addition to the so-called major toxins, there are other toxins like beta2 toxin, produced by some strains of C. perfringens which may play a role in the pathogenesis of disease. Aim of the study: In this study a multiplex PCR assay was developed and used for detection of cpb2 gene to identify the Beta2 harboring isolates among different types of C. perfringens. Objectives: The primary objective of this study was to identify the prevalence of β2-toxin gene in local isolates of Clostridium perfringens. Methodology: This was an experimental study. Random sampling technique was used. A total of 97 sheep and goats were included in this study. All were Pakistani local breeds. The samples were collected during the period from Sep, 2014 to Mar, 2015 from selected districts of Punjab province (Pakistan). Faecal samples were cultured in cooked meat media. The identification of Clostridium perfringens was made on the basis of biochemical tests. Multiplex PCR was performed to identify the toxin genes. Results: A total of 43 C. perfringens isolates were genotyped using multiplex PCR assay. The gene encoding C. perfringens β2-toxin (cpb2) was present in more than 50% of the isolates genotyped. However, the prevalence of this gene varied between sheep and goat isolates. Conclusion: The present study suggests the high occurrence of C. perfringens b2-toxin (cpb2) in the local isolates of Pakistan. As β2-toxin is present in both healthy and diseased animals, so further studies are suggested to establish the role of β2-toxin in pathogenesis of the clostridial enteric diseases.

Keywords: beta 2 toxin gene, clostridium perfringens, enteric diseases, goats, multiplex PCR, sheep

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Authors: Saleh Alkarri, Melinda Frame, Dimple Sharma, John Cairney, Lee Maddan, Jin H. Kim, Jonathan O. Rayner, Teresa M. Bergholz, Muhammad Rabnawaz

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Reported herein is an investigation of anti-bacterial and anti-virus properties, mode of action of Mg(OH)₂ and copper-infused Mg(OH)₂ nanoplatelets (NPs) on melt-compounded and thermally embossed polypropylene (PP) surfaces. The anti-viral activity for the NPs was studied in aqueous liquid suspensions against SARS-CoV-2, and the mode of action was investigated on neat NPs and PP samples that were thermally embossed with NPs. Anti-bacterial studies for melt-compounded NPs in PP confirmed approximately 1 log reduction of E. coli populations in 24 h, while for thermally embossed NPs, an 8 log reduction of E. coli populations was observed. In addition, the NPs exhibit anti-viral activity against SARS-CoV-2. Fluorescence microscopy revealed that reactive oxygen species (ROS) is the main mode of action through which Mg(OH)₂ and Cu-Infused Mg(OH)₂act against microbes. Plastics with anti-microbial surfaces from where biocides are non-leachable are highly desirable. This work provides a general fabrication strategy for developing anti-microbial plastic surfaces.

Keywords: anti-microbial activity, E. coli K-12 MG1655, anti-viral activity, SARS-CoV-2, copper-infused magnesium hydroxide, non-leachable, ROS, compounding, surface embossing, dyes

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Authors: Chen Zhang, Fengxue Xin, Jianzhong He

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A unique Clostridium beijerinckii species strain BGS1 was obtained from grass land samples, which is capable of producing 8.43g/L butanol and 3.21 isopropanol from 60g/L glucose while generating 4.68g/L volatile fatty acids (VFAs) from 30g/L xylan. The concentration of isopropanol produced by culture BGS1 is ~15% higher than previously reported wild-type Clostridium beijerinckii under similar conditions. Compared to traditional Acetone-Butanol-Ethanol (ABE) fermentation species, culture BGS1 only generates negligible amount of ethanol and acetone, but produces butanol and isopropanol as biosolvent end-products which are pure alcohols and more economical than ABE. More importantly, culture BGS1 can consume acetone to produce isopropanol, e.g., 1.84g/L isopropanol from 0.81g/L acetone in 60g/L glucose medium containing 6.15g/L acetone. The analysis of BGS1 draft genome annotated by RAST server demonstrates that no ethanol production is caused by the lack of pyruvate decarboxylase gene – related to ethanol production. In addition, an alcohol dehydrogenase (adhe gene) was found in BGS1 which could be a potential gene responsible for isopropanol-generation. This is the first report on Isopropanol-Butanol (IB) fermentation by wild-type Clostridium strain and its application for isopropanol and butanol production.

Keywords: acetone conversion, butanol, clostridium, isopropanol

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Authors: Mayada Mazher, Ahmed Moustafa, Ahmed Abdellatif

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Background: Autophagy is a eukaryotic, highly conserved catabolic process implicated in many pathophysiologies such as wound healing. Autophagy-associated genes serve as a scaffolding platform for signal transduction of macrophage polarization during the inflammatory phase of wound healing and tissue repair process. In the current study, we report a model for the interplay between autophagy-associated genes and macrophages polarization associated genes. Methods: In silico analysis was performed on 249 autophagy-related genes retrieved from the public autophagy database and gene expression data retrieved from Gene Expression Omnibus (GEO); GSE81922 and GSE69607 microarray data macrophages polarization 199 DEGS. An integrated protein-protein interaction network was constructed for autophagy and macrophage gene sets. The gene sets were then used for GO terms pathway enrichment analysis. Common transcription factors for autophagy and macrophages' polarization were identified. Finally, microRNAs enriched in both autophagy and macrophages were predicated. Results: In silico prediction of common transcription factors in DEGs macrophages and autophagy gene sets revealed a new role for the transcription factors, HOMEZ, GABPA, ELK1 and REL, that commonly regulate macrophages associated genes: IL6,IL1M, IL1B, NOS1, SOC3 and autophagy-related genes: Atg12, Rictor, Rb1cc1, Gaparab1, Atg16l1. Conclusions: Autophagy and macrophages' polarization are interdependent cellular processes, and both autophagy-related proteins and macrophages' polarization related proteins coordinate in tissue remodelling via transcription factors and microRNAs regulatory network. The current work highlights a potential new role for transcription factors HOMEZ, GABPA, ELK1 and REL in wound healing.

Keywords: autophagy related proteins, integrated network analysis, macrophages polarization M1 and M2, tissue remodelling

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Authors: Elif Tugce Aksun Tumerkan, Chris Lowe, Hannah Krupa

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Fluorescent proteins are self-sufficient in forming chromophores with a visible wavelength from 3 amino acids sequence within their own polypeptide structure. This chromophore – a molecule that absorbs a photon of light and exhibits an energy transition equal to the energy of the absorbed photon. Fluorescent proteins (FPs) consisted of a chain of 238 amino acid residues and composed of 11 beta strands shaped in a cylinder surrounding an alpha helix structure. A better understanding of the system of the chromospheres and the increasing advance in protein engineering in recent years, the properties of FPs offers the potential for new applications. They have used sensors and probes in molecular biology and cell-based research that giving a chance to observe these FPs tagged cell localization, structural variation and movement. For clarifying functional uses of fluorescent proteins, electrophoretic properties of these proteins are one of the most important parameters. Sodium dodecyl sulphate polyacrylamide gel electrophoresis (SDS-PAGE) analysis is used for determining electrophoretic properties commonly. While there are many techniques are used for determining the functionality of protein-based research, SDS-PAGE analysis can only provide a molecular level assessment of the proteolytic fragments. Before SDS-PAGE analysis, fluorescent proteins need to successfully purified. Due to directly purification of the target, FPs is difficult from the animal, gene expression is commonly used which must be done by transformation with the plasmid. Furthermore, used gel within electrophoresis and staining agents properties have a key role. In this review, the different factors that have the impact on the electrophoretic properties of fluorescent proteins explored. Fluorescent protein separation and purification are the essential steps before electrophoresis that should be done very carefully. For protein purification, gene expression process and following steps have a significant function. For successful gene expression, the properties of selected bacteria for expression, used plasmid are essential. Each bacteria has own characteristics which are very sensitive to gene expression, also used procedure is the important factor for fluorescent protein expression. Another important factors are gel formula and used staining agents. Gel formula has an effect on the specific proteins mobilization and staining with correct agents is a key step for visualization of electrophoretic bands of protein. Visuality of proteins can be changed depending on staining reagents. Apparently, this review has emphasized that gene expression and purification have a stronger effect than electrophoresis protocol and staining agents.

Keywords: cell biology, gene expression, staining agents, SDS-page

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Authors: Mhuji Kilonzo, Patrick Ndakidemi, Musa Chacha

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Objective: To evaluate antibacterial activity from four selected medicinal plants namely Mystroxylon aethiopicum, Lonchocarpus capassa, Albizia anthelmentica and Myrica salicifolia used for management of bacterial infection in Tanzania. Methods: Minimum Inhibitory Concentration (MIC) of plants extracts against the tested bacterial species was determined by using 96 wells microdilution method. In this method, 50 μL of nutrient broth were loaded in each well followed by 50 μL of extract (100 mg/mL) to make a final volume of 100 μL. Subsequently, 50 μL were transferred from first rows of each well to the second rows and the process was repeated down the columns to the last wells from which 50 μL were discarded. Thereafter, 50 μL of the selected bacterial suspension were added to each well thus making a final volume of 100 μL. The lowest concentration which showed no bacterial growth was considered as MIC. Results: It was revealed that L. capassa leaf ethyl acetate extract exhibited antibacterial activity against Salmonella kisarawe and Salmonella typhi with MIC values of 0.39 and 0.781 mg/mL respectively. Likewise, L. capassa root bark ethyl acetate extracts inhibited growth of S. typhi and E. coli with MIC values of 0.39 and 0.781 mg/mL respectively. The M. aethiopicum leaf and root bark chloroform extracts displayed antibacterial activity against S. kisarawe and S. typhi respectively with MIC value of 0.781 mg/mL. The M. salicifolia stem bark ethyl acetate exhibited antibacterial activity against P. aeruginosa with MIC value of 0.39 mg/mL whereas the methanolic stem and root bark of the same plant inhibited the growth of Proteus mirabilis and Klebsiella pneumoniae with MIC value of 0.781 mg/mL. Conclusion: It was concluded that M. aethiopicum, L. capassa, A. anthelmentica and M. salicifolia are potential source of antibacterial agents. Further studies to establish structures of antibacterial and evaluate active ingredients are recommended.

Keywords: Albizia anthelmentica, Lonchocarpus capassa, Mystroxylon aethiopicum, Myrica salicifolia

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Authors: R. Majidzadeh Heravi, M. Sankian, H. Kermanshahi, M. R. Nassiri, A. Heravi Moussavi, S. A. Lari, A. R. Varasteh

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The use of probiotics engineered to express specific enzymes has been the subject of considerable attention in poultry industry because of increased nutrient availability and reduced cost of enzyme supplementation. Phytase enzyme is commonly added to poultry feed to improve digestibility and availability of phosphorus from plant sources. To construct a probiotic with potential of phytate degradation, phytase gene (appA) from E. coli was cloned and transformed into two probiotic bacteria Lactobacillus salivarius and Lactococcus lactis. L. salivarous showed plasmid instability, unable to express the gene. The expression of appA gene in L. lactis was analyzed by detecting specific RNA and zymography assay. Phytase enzyme was isolated from cellular extracts of recombinant L. lactis, showing a 46 kDa band upon the SDS-PAGE analysis. Zymogram also confirmed the phytase activity of the 46 kDa band corresponding to the enzyme. An enzyme activity of 4.9U/ml was obtained in cell extracts of L. lactis. The growth of native and recombinant L. lactis was similar in the presence of two concentrations of ox bile.

Keywords: Lactobacillus salivarus, Lactococcuslactis, recombinant, phytase, poultry

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Authors: F. A. Ogundolie, F. Okogue, D. V. Adegunloye

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Greywater samples were obtained from three restaurants in the Federal University of Technology; Akure coded SSR, MGR and GGR. Fungi isolates obtained include Rhizopus stolonifer, Aspergillus niger, Mucor mucedo, Aspergillus flavus, Saccharomyces cerevisiae. Of these fungi isolates obtained, R. stolonifer, A. niger and A. flavus showed significant degradation ability on grey water and was used for this research. A simple bioreactor was constructed using biodegradation process in purification of waste water samples. Waste water undergoes primary treatment; secondary treatment involves the introduction of the isolated organisms into the waste water sample and the tertiary treatment which involved the use of filter candle and the sand bed filtration process to achieve the end product without the use of chemicals. A. niger brought about significant reduction in both the bacterial load and the fungi load of the greywater samples of the three respective restaurants with a reduction of (1.29 × 108 to 1.57 × 102 cfu/ml; 1.04 × 108 to 1.12 × 102 cfu/ml and 1.72 × 108 to 1.60 × 102 cfu/ml) for bacterial load in SSR, MGR and GGR respectively. Reduction of 2.01 × 104 to 1.2 × 101; 1.72 × 104 to 1.1 × 101, and 2.50 × 104 to 1.5 × 101 in fungi load from SSR, MGR and GGR respectively. Result of degradation of these selected waste water by the fungi showed that A. niger was probably more potent in the degradation of organic matter and hence, A. niger could be used in the treatment of wastewater.

Keywords: Aspergillus niger, greywater, bacterial, fungi, microbial load, bioreactor, biodegradation, purification, organic matter and filtration

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Authors: Vinod Kumar Gupta, Narendrakumar M. Chaudhari, Suchismitha Iskepalli, Chitra Dutta

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Background-The community composition of the human microbiome is known to vary at distinct anatomical niches. But little is known about the nature of variations if any, at the genome/sub-genome levels of a specific microbial community across different niches. The present report aims to explore, as a case study, the variations in gene repertoire of 28 Prevotella reference draft genomes derived from different body-sites of human, as reported earlier by the Human Microbiome Consortium. Results-The analysis reveals the exclusive presence of 11798, 3673, 3348 and 934 gene families and exclusive absence of 17, 221, 115 and 645 gene families in Prevotella genomes derived from the human oral cavity, gastro-intestinal tracts (GIT), urogenital tract (UGT) and skin, respectively. The pan-genome for Prevotella remains “open”. Distribution of various functional COG categories differs appreciably among the habitat-specific genes, within Prevotella pan-genome and between the GIT-derived Bacteroides and Prevotella. The skin and GIT isolates of Prevotella are enriched in singletons involved in Signal transduction mechanisms, while the UGT and oral isolates show higher representation of the Defense mechanisms category. No niche-specific variations could be observed in the distribution of KEGG pathways. Conclusion-Prevotella may have developed distinct genetic strategies for adaptation to different anatomical habitats through selective, niche-specific acquisition and elimination of suitable gene-families. In addition, individual microorganisms tend to develop their own distinctive adaptive stratagems through large repertoires of singletons. Such in situ, habitat-driven refurbishment of the genetic makeup can impart substantial intra-lineage genome diversity within the microbes without perturbing their general taxonomic heritage.

Keywords: body niche adaptation, human microbiome, pangenome, Prevotella

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Authors: Yahia Massinissa, Yahia Mouloud

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Cystic fibrosis (CF), the most common lethal genetic disease in the Europe population, is caused by mutations in the transmembrane conductance regulator gene (CFTR). It affects most organs including an epithelial tissue, base of hydroelectrolytic transepithelial transport, notably that aerial ways, the pancreas, the biliary ways, the intestine, sweat glands and the genital tractus. The gene whose anomalies are responsible of the cystic fibrosis codes for a protein Cl channel named CFTR (cystic fibrosis transmembrane conductance regulator) that exercises multiple functions in the cell, one of the most important in control of sodium and chlorine through epithelia. The deficient function translates itself notably by an abnormal production of viscous secretion that obstructs the execrator channels of this target organ: one observes then a dilatation, an inflammation and an atrophy of these organs. It also translates itself by an increase of the concentration in sodium and in chloride in sweat, to the basis of the sweat test. In order to do a phenotypical and genotypical diagnosis at a part of the Algerian population, our survey has been carried on 16 patients with evocative symptoms of the cystic fibrosis at that the clinical context has been confirmed by a sweat test. However, anomalies of the CFTR gene have been determined by electrophoresis in gel of polyacrylamide of the PCR products (polymerase chain reaction), after enzymatic digestion, then visualized to the ultraviolet (UV) after action of the ethidium bromide. All mutations detected at the time of our survey have already been identified at patients attained by this pathology in other populations of the world. However, the important number of found mutation with regard to the one of the studied patients testifies that the origin of this big clinical variability that characterizes the illness in the consequences of an enormous diversity of molecular defects of the CFTR gene.

Keywords: cystic fibrosis, CFTR gene, polymorphism, algerian population, sweat test, genotypical diagnosis

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Authors: Maryam Monazzah, Ronak Samadpour, Mehdi Nasr-esfahani, Fatemeh Qalavand, Marziye Motamedi

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Bipolaris sorokiniana, and Heterodera filipjevi, are important wheat diseases that lead to yield losses worldwide. Identifying novel resistant sources helps us combat these devastating diseases. In this study, we studied the role of Cre3 gene and antioxidant enzymes in the immune responses of wheat genotypes to H. filipjevi and B. sorokiniana. Therefore, real-time PCR analysis using Cre3 gene marker, a resistant gene to cereal cyst nematodes, was conducted on leaves and roots, along with changes ‎in the activity of antioxidant enzymes, peroxidase, and catalase. Enzyme activity assay was performed on roots attacked by nematode and in leaves infected with Bipolaris. Wheat accessions including “Bam” (resistant), “Parsi” (moderately-resistant), “Azar2”, “Ohadi”, “Homa” (highly-susceptible) were previously screened against both stresses under greenhouse and field conditions. Results showed that Cre3 expression against cyst nematodes was significantly higher in resistant cultivars compared to susceptible cultivars. Cre3 was used in marker-assisted selection programs to identify genotypes carrying resistant genes to cyst nematodes. Interestingly, Cre3 was also up-regulated in both tissues of resistant cultivars to B. sorokiniana. Therefore, Cre3 in wheat similarly modulates immunity against B. sorokiniana and might be one of the central components of the induced immune system in wheat. The activity of antioxidant enzymes also indicated the highest increase in resistant genotypes upon both stresses that subsequently neutralize oxidative stress in tissues and decrease damage. Further studies on these resistance components may help us gain insight into the molecular basis of resistance and shed new light on the interaction and overlap between different forms of stress.

Keywords: Bipolaris sorokiniana, Heterodera filipjevi, resistant gene expression, wheat

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Authors: Sweta Pandey, Samridhi Dhyani, Susmita Chaudhuri

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Klebsiella pneumoniae causes a wide range of infections, including urinary tract infections, sepsis, bacteremia, pneumonia, and liver abscesses. The emergence of multi-drug resistance in this bacterium led to a major setback for clinical management. WHO also endorsed a need for finding alternative therapy to antibiotics for the treatment of these infections. Development of vaccines and passive antibody therapy has been proven as a potent alternative to antibiotics in the case of MDR, XDR, and PDR Klebsiella infections. Siderophore receptors have been demonstrated to be overexpressed for the internalization of iron siderophore complexes during infections in most Gram-negative bacteria. For the present study, immune response to siderophore receptors to establish this protein as a potential immunogen for the development of therapeutic leads was explored. Clinical strains of Klebsiella pneumoniae were grown in iron-deficient conditions, and the iron-regulated outer membrane proteins were extracted and characterized through mass spectrometry for specific identification. The gene for identified protein was cloned in pET- 28a vector and expressed in E. coli. The native protein and the recombinant protein were isolated and purified and used as antigens for the generation of immune response in BALB/c mice. The native protein of Klebsiella pneumoniae grown in iron-deficient conditions was identified as FepA (Ferrienterobactin receptor) and other siderophore receptors. This 80 kDa protein generated an immune response in BALB/c mice. The antiserum from mice after subsequent booster doses was collected and showed binding with FepA protein in western blot and phagocytic uptake of the K. pneumoniae in the presence antiserum from immunized mice also observed from the animal studies after bacterial challenge post immunisation in mice have shown bacterial clearance. The antiserum from mice showed binding and clearance of the Klebsiella pneumoniae bacteria in vitro and in vivo. These antigens used for generating an active immune response in mice can further be used for therapeutic monoclonal antibody development against Klebsiella pneumoniae infections.

Keywords: antiserum, FepA, Klebsiella pneumoniae, multi drug resistance, siderophore receptor

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Authors: Yong Chen

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To understand the detailed molecular mechanisms of memory formation in engram cells is one of the most fundamental questions in neuroscience. Recent single-cell RNA-seq (scRNA-seq) and single-nucleus RNA-seq (snRNA-seq) techniques have allowed us to explore the sparsely activated engram ensembles, enabling access to the molecular mechanisms that underlie experience-dependent memory formation and consolidation. However, the absence of specific and powerful computational methods to detect memory-related genes (modules) and their regulatory relationships in the sc/snRNA-seq datasets has strictly limited the analysis of underlying mechanisms and memory coding principles in mammalian brains. Here, we present a deep-learning method named SCENTBOX, to detect memory-related gene modules and causal regulatory relationships among themfromsc/snRNA-seq datasets. SCENTBOX first constructs codifferential expression gene network (CEGN) from case versus control sc/snRNA-seq datasets. It then detects the highly correlated modules of differential expression genes (DEGs) in CEGN. The deep network embedding and attention-based convolutional neural network strategies are employed to precisely detect regulatory relationships among DEG genes in a module. We applied them on scRNA-seq datasets of TRAP; Ai14 mouse neurons with fear memory and detected not only known memory-related genes, but also the modules and potential causal regulations. Our results provided novel regulations within an interesting module, including Arc, Bdnf, Creb, Dusp1, Rgs4, and Btg2. Overall, our methods provide a general computational tool for processing sc/snRNA-seq data from case versus control studie and a systematic investigation of fear-memory-related gene modules.

Keywords: sc/snRNA-seq, memory formation, deep learning, gene module, causal inference

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Authors: Yantao Li, Jun Zheng

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Food poison caused by consumption of contaminated food, especially seafood, is one of most serious public health threats worldwide. Vibrio parahaemolyticus is emerging bacterial pathogen and the leading cause of human gastroenteritis associated with food poison, especially in the southern coastal region of China. To successfully cause disease in host, bacterial pathogens need to overcome the host-derived stresses encountered during infection. One of the toxic chemical species elaborated by the host is nitric oxide (NO). NO is generated by acidified nitrite in the stomach and by enzymes of the inducible NO synthase (iNOS) in the host cell, and is toxic to bacteria. Bacterial pathogens have evolved some mechanisms to battle with this toxic stress. Such mechanisms include genes to sense NO produced from immune system and activate others to detoxify NO toxicity, and genes to repair the damage caused by toxic reactive nitrogen species (RNS) generated during NO toxic stress. However, little is known about the NO resistance in V. parahaemolyticus. In this study, a transposon coupled with next generation sequencing (Tn-seq) technology will be utilized to identify genes for NO resistance in V. parahaemolyticus. Our strategy will include construction the saturating transposon insertion library, transposon library challenging with NO, next generation sequencing (NGS), bioinformatics analysis and verification of the identified genes in vitro and in vivo.

Keywords: vibrio parahaemolyticus, nitric oxide, tn-seq, virulence

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Authors: Xiaohan Bookman, Xiaoyan Zhu

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The outputs of non-linear feed-forward neural network are positive, which could be treated as probability when they are normalized to one. If we take Entropy-Based Principle into consideration, the outputs for each sample could be represented as the distribution of this sample for different clusters. Entropy-Based Principle is the principle with which we could estimate the unknown distribution under some limited conditions. As this paper defines two processes in Feed-Forward Neural Network, our limited condition is the abstracted features of samples which are worked out in the abstraction process. And the final outputs are the probability distribution for different clusters in the clustering process. As Entropy-Based Principle is considered into the feed-forward neural network, a clustering method is born. We have conducted some experiments on six open UCI data sets, comparing with a few baselines and applied purity as the measurement. The results illustrate that our method outperforms all the other baselines that are most popular clustering methods.

Keywords: feed-forward neural network, clustering, max-entropy principle, probabilistic models

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Authors: Ruchi Yadav, Shivani Pandey, Prachi Srivastava

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Microarrays provide a rich source of data on the molecular working of cells. Each microarray reports on the abundance of tens of thousands of mRNAs. Virtually every human disease is being studied using microarrays with the hope of finding the molecular mechanisms of disease. Bioinformatics analysis plays an important part of processing the information embedded in large-scale expression profiling studies and for laying the foundation for biological interpretation. A basic, yet challenging task in the analysis of microarray gene expression data is the identification of changes in gene expression that are associated with particular biological conditions. Careful statistical design and analysis are essential to improve the efficiency and reliability of microarray experiments throughout the data acquisition and analysis process. One of the most popular platforms for microarray analysis is Bioconductor, an open source and open development software project based on the R programming language. This paper describes specific procedures for conducting quality assessment, visualization and preprocessing of Affymetrix Gene Chip and also details the different bioconductor packages used to analyze affymetrix microarray data and describe the analysis and outcome of each plots.

Keywords: microarray analysis, R language, affymetrix visualization, bioconductor

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Authors: Ahmad Ali Shahid, Mukhtar Ahmed

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The demand for long staple fiber having better strength and length is increasing with the introduction of modern spinning and weaving industry in Pakistan. Work on gene discovery from developing cotton fibers has helped to identify dozens of genes that take part in cotton fiber development and several genes have been characterized for their role in fiber development. Sucrose synthase (SuS) is a key enzyme in the metabolism of sucrose in a plant cell, in cotton fiber it catalyzes a reversible reaction, but preferentially converts sucrose and UDP into fructose and UDP-glucose. UDP-glucose (UDPG) is a nucleotide sugar act as a donor for glucose residue in many glycosylation reactions and is essential for the cytosolic formation of sucrose and involved in the synthesis of cell wall cellulose. The study was focused on successful Agrobacterium-mediated stable transformation of SuS gene in pCAMBIA 1301 into cotton under a CaMV35S promoter. Integration and expression of the gene were confirmed by PCR, GUS assay, and real-time PCR. Young leaves of SuS overexpressing lines showed increased total soluble sugars and plant biomass as compared to non-transgenic control plants. Cellulose contents from fiber were significantly increased. SEM analysis revealed that fibers from transgenic cotton were highly spiral and fiber twist number increased per unit length when compared with control. Morphological data from field plants showed that transgenic plants performed better in field conditions. Incorporation of genes related to cotton fiber length and quality can provide new avenues for fiber improvement. The utilization of this technology would provide an efficient import substitution and sustained production of long-staple fiber in Pakistan to fulfill the industrial requirements.

Keywords: agrobacterium-mediated transformation, cotton fiber, sucrose synthase gene, staple length

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Authors: Neda Menbari, Ramin Mehdiabadi

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

Keywords: breast cancer, gene expression, FOXM1, microRNA

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Authors: Samira B. R. Prado, Paulo R. Melfi, Beatriz T. Minguzzi, João P. Fabi

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Fruit softening is the main change that occurs during papaya (Carica papaya L.) ripening. It is characterized by the depolymerization of cell wall polysaccharides, especially the pectic fractions, which causes cell wall disassembling. However, it is uncertain how the modification of the two main pectin polysaccharides fractions (water-soluble – WSF, and oxalate-soluble fractions - OSF) accounts for fruit softening. The aim of this work was to correlate molecular weight changes of WSF and OSF with the gene expression of pectin-solubilizing enzymes (pectinases) during papaya ripening. Papaya fruits obtained from a producer were harvest and storage under specific conditions. The fruits were divided in five groups according to days after harvesting. Cell walls from all groups of papaya pulp were isolated and fractionated (WSF and OSF). Expression profiles of pectinase genes were achieved according to the MIQE guidelines (Minimum Information for publication of Quantitative real-time PCR Experiments). The results showed an increased yield and a decreased molecular weight throughout ripening for WSF and OSF. Gene expression data support that papaya softening is achieved by polygalacturonases (PGs) up-regulation, in which their actions might have been facilitated by the constant action of pectinesterases (PMEs). Moreover, BGAL1 gene was up-regulated during ripening with a simultaneous galactose release, suggesting that galactosidases (GALs) could also account for pulp softening. The data suggest that a solubilization of galacturonans and a depolymerization of cell wall components were caused mainly by the action of PGs and GALs.

Keywords: carica papaya, fruit ripening, galactosidases, plant cell wall, polygalacturonases

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