Search results for: reverse transcriptase polymerase chain reaction

Authors: Vandana Deopanée Tomar, Gurpreet Kaur Sidhu, Panchsheela Nogia, Rajesh Mehrotra, Sandhya Mehrotra

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The cyanobacterial CO₂ concentrating mechanism (CCM) operates to raise the levels of CO₂ in the vicinity of the main carboxylation enzyme Rubisco which is encapsulated in protein micro compartments called carboxysomes. Thus, due to the presence of CCM, cyanobacterial cells are able to work with high photosynthetic efficiency even at low Ci conditions and can accumulate 1000 folds high internal concentrations of Ci than external environment. Engineering of some useful CCM components into higher plants is one of the plausible approaches to improve their photosynthetic performance. The first step and the simplest approach for attaining this objective would be the transfer of cyanobacterial bicarbonate transporter such as SbtA to inner chloroplast envelope of C₃ plants. For this, SbtA transporter gene from Synechococcus elongatus PCC 7942 was fused to a transit peptide element to generate chimeric constructs in order to direct it to chloroplast inner envelope. Two transit peptides namely, TnaXTP (transit peptide from AT3G56160) and TMDTP (transit peptide from AT2G02590) were shortlisted from Arabidopsis thaliana genome and cloned in plant expression vector pCAMBIA1302 having mgfp5 as a reporter gene. Plant transformation was done by agro infiltration and Agrobacterium mediated co-culture. DNA, RNA, and protein were isolated from the leaves four days post infiltration, and the presence of transgene was confirmed by gene specific PCR (Polymerase Chain Reaction) analysis and by RT-PCR (Reverse Transcription Polymerase Chain Reaction). The expression was confirmed at the protein level by western blotting using anti-GFP primary antibody and horseradish peroxidase (HRP) conjugated secondary antibody. The localization of the protein was detected by confocal microscopy of isolated protoplasts. We observed chloroplastic expression for both the fusion constructs which suggest that the transit peptide sequences are capable of taking the cargo protein to the chloroplasts. These constructs are now being used to generate stable transgenic plants by Agrobacterium mediated transformation. The stability of transgene expression will be analyzed from T₀ to T₂ generation.

Keywords: agro infiltration, bicarbonate transporter, carbon concentrating mechanisms, cyanobacteria, SbtA

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Authors: Zunnu Raen Akhtar, U. Irshad, M. Majid

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Due to the widespread cultivation of transgenic cotton, intense selection pressure resulted in resistant allele in pink bollworm, Pectinophora gossypiella (Gelechiidae: Lepidoptera). A resistant strain of pink bollworm against transgenic cotton has become a challenge to Integrated Resistance Management (IRM) in the World. Laboratory and field studies were conducted to determine the resistant strains of pink bollworm by performing bioassay, extracting the DNA, conducting PCR of both laboratory as well as field collected pink bollworms to observe the developed resistance. In all of the studies, two Bt varieties FH-142 and FH-118 expressing Cry1Ac compared to non-Bt (Control) were tested against pink bollworm. In the laboratory, bioassay results showed that there was no significant mortality difference between Bt and non-Bt varieties. Similar mortality percentage was observed in transgenic and non-transgenic (control) variety. Insects which were survived after bioassay, as well as those collected from the Bt cotton fields, were selected for further molecular studies. DNA extraction followed by PCR was conducted to check the resistant strains in pink bollworm. In field studies, we also observed the population dynamics of pink boll worms on Bt as compared to non-Bt varieties. Laboratory and field studies confirmed that resistant strains occurs in Pakistani Bt cotton fields. Different strategies should be adopted to combat that serious prevailing resistance issues.

Keywords: transgenic cotton, resistance, pectinophora gossypiella, , integrated resistance management (IRM), polymerase chain reaction (PCR)

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Authors: Emad Al-Abdallat, Faris G. Bakri, Azmi Mahafza, Rayyan Al Ali, Nidaa Ababneh, Ahmed Idhair

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Background: Morgues are high-risk areas for the spread of infection from the cadavers to the staff during the postmortem examination. Infection can spread from corpses to workers by the airborne route, by direct contact, or from needle and sharp object injuries. Objective: Knowledge about the prevalence of these infections among autopsies is prudent to appreciate any risk of transmission and to further enforce safety measures. Method: A total of 242 autopsies were tested. Age ranged from 3 days to 94 years (median 75.5 years, mean 45.3 (21.9 ± SD)). There were 172 (71%) males. Results: The cause of death was considered natural in 137 (56.6%) cases, accidental in 89 (36.8%), homicidal in 9 (3.7%), suicidal in 4 (1.7%), and unknown in 3 (1.2%). Hepatitis B surface antigen was positive in 5 (2.1%) cases. Hepatitis C virus antibody was detected in 5 (2.1%) cases and the hepatitis C virus polymerase chain reaction was positive in 2 of them (0.8%). HIV antibody was not detected in any of the cases. Conclusions: Autopsies can be associated with exposure to blood borne viruses. Autopsies performed during the study period were tested for hepatitis B surface antigen, hepatitis C virus antibody, and human immunodeficiency virus antibody. Positive tests were subsequently confirmed by polymerase chain reaction. There is low prevalence of infections with these viruses in our autopsy cases. However, the risk of transmission remains a threat. Healthcare workers in the forensic departments should adhere to standard precautions.

Keywords: autopsy, hepatitis B virus, hepatitis C virus, human immunodeficiency virus, Jordan

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Authors: Adèle Oliva, Samuel Fosso Wamba

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This study looks at how firms can create competitive advantages through effective reserve logistics strategies. Upon using data collected from reverse supply chain managers of electronic commerce companies, the study found that improved reverse logistics management can have a positive impact on companies’ business benefits. These include playing a role in the implementation of many factors that highly influence the decision to purchase, customers’ loyalty, as well as increasing companies’ turnover. As a result, through an efficient design and management of their reverse flow, companies can decrease the costs associated to returned products.

Keywords: reverse logistics, competitive advantage, case study, business value

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Authors: Muhammad SAFDAR, Mehmet Ozaslan, Musarrat Abbas Khan

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Babesiosis is a haemoparasitic disease due to the multiplication of protozoan’s parasite, Babesia ovis in the red blood cells of the host, and contributes numerous economical losses, including sheep and goat ruminants. The early identification and successful treatment of Babesia Ovis spp. belong to the key steps of control and health management of livestock resources. The objective of this study was to construct a polymerase chain reaction (PCR) based method for the detection of Babesia spp. in small ruminants and to determine the risk factors involved in the spreading of babesiosis infections. A total of 100 blood samples were collected from 50 sheep and 50 goats along with different areas of Muzaffargarh, Pakistan, from randomly selected herds. Data on the characteristics of sheep and goats were collected through questionnaires. Of 100 blood samples examined, 18 were positive for Babesia ovis upon microscopic studies, whereas 11 were positive for the presence of Babesia spp. by PCR assay. For the recognition of parasitic DNA, a set of 500bp oligonucleotide was designed by PCR amplification with sequence 18S rRNA gene for B. ovis. The prevalence of babesiosis in small ruminant’s sheep and goat detected by PCR was significantly higher in female animals (28%) than male herds (08%). PCR analysis of the reference samples showed that the detection limit of the PCR assay was 0.01%. Taken together, all data indicated that this PCR assay was a simple, fast, specific detection method for Babesia ovis species in small ruminants compared to other available methods.

Keywords: Babesia ovis, PCR amplification, 18S rRNA, sheep and goat

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Authors: Jacintha Menezes, Ramalingam Dharmalingam, Palaiahnakote Shivakumara

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In the recent years, Omani acid lime cultivation and production has been affected by Citrus greening or Huanglongbing (HLB) disease. HLB disease is one of the most destructive diseases for citrus, with no remedies or countermeasures to stop the disease. Currently used Polymerase chain reaction (PCR) and enzyme-linked immunosorbent assay (ELISA) HLB detection tests require lengthy and labor-intensive laboratory procedures. Furthermore, the equipment and staff needed to carry out the laboratory procedures are frequently specialized hence making them a less optimal solution for the detection of the disease. The current research uses hyperspectral imaging technology for automatic detection of citrus trees with HLB disease. Omani citrus tree leaf images were captured through portable Specim IQ hyperspectral camera. The research considered healthy, nutrition deficient, and HLB infected leaf samples based on the Polymerase chain reaction (PCR) test. The highresolution image samples were sliced to into sub cubes. The sub cubes were further processed to obtain RGB images with spatial features. Similarly, RGB spectral slices were obtained through a moving window on the wavelength. The resized spectral-Spatial RGB images were given to Convolution Neural Networks for deep features extraction. The current research was able to classify a given sample to the appropriate class with 92.86% accuracy indicating the effectiveness of the proposed techniques. The significant bands with a difference in three types of leaves are found to be 560nm, 678nm, 726 nm and 750nm.

Keywords: huanglongbing (HLB), hyperspectral imaging (HSI), · omani citrus, CNN

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Authors: Junichi Hosoi

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Epidermal Langerhans cells reside in upper layer of epidermis and play a role in immune surveillance. The finding of the close association of nerve endings to Langerhans cells triggered the research on systemic regulation of Langerhans cells. They disappear from epidermis after exposure to environmental and internal stimuli and reappear about a week later. Myeloid progenitor cells are assumed to be one of the sources of Langerhans cells. We examined the effects of cortisol on the reappearance of Langerhans cells in vitro. Cord-blood derived CD34-positive cells were cultured in the medium supplemented with stem cell factor/Flt3 ligand/granulocyte macrophage-colony stimulating factor/tumor necrosis factor alpha/bone morphologic protein 7/transforming growth factor beta in the presence or absence of cortisol. Cells were analyzed by flow cytometry for CD1a (cluster differentiation 1a), a marker of Langerhans cells and dermal dendritic cells, and CD39 (cluster differentiation factor 39), extracellular adenosine triphosphatase. Both CD1a-positive cells and CD39-positive cells were decreased by treatment with cortisol (suppression by 35% and 22% compared to no stress hormone, respectively). Differentiated Langerhans cells are attracted to epidermis by chemokines that are secreted from keratinocytes. Epidermal keratinocytes were cultured in the presence or absence of cortisol and analyzed for the expression of CCL2 (C-C motif chemokine ligand 2) and CCL20 (C-C motif chemokine ligand 20), which are typical attractants of Langerhans cells, by quantitative reverse transcriptase polymerase chain reaction. The expression of both chemokines, CCL2 and CCL20, were suppressed by treatment with cortisol (suppression by 38% and 48% compared to no stress hormone, respectively). We examined the possible regulation of the suppression by cortisol with plant extracts. The extracts of Ganoderma lucidum and Iris protected the suppression of the differentiation to CD39-positive cells and also the suppression of the gene expression of LC-chemoattractants. These results suggest that cortisol, which is either systemic or locally produced, blocks the supply of epidermal Langerhans cells at 2 steps, differentiation from the precursor and attraction to epidermis. The suppression is possibly blocked by some plant extracts.

Keywords: Langerhans cell, stress, CD39, chemokine

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Authors: Lemar Blake, Chris Oura, Ayanna C. N. Phillips Savage

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Improved DNA sequencing technology has greatly enhanced bacterial identification, especially for organisms that are difficult to culture. Mycobacteriosis with consistent hyphema, bilateral exophthalmia, open mouth gape and ocular lesions, were observed in various fish populations at the School of Veterinary Medicine, Aquaculture/Aquatic Animal Health Unit. Objective: To identify the species of Mycobacterium that is affecting aquarium fish at the School of Veterinary Medicine, Aquaculture/Aquatic Animal Health Unit. Method: A total of 13 fish samples were collected and analyzed via: Ziehl-Neelsen, conventional polymerase chain reaction (PCR) and real-time PCR. These tests were carried out simultaneously for confirmation. The following combination of conventional primers: 16s rRNA (564 bp), rpoB (396 bp), sod (408 bp) were used. Concatenation of the gene fragments was carried out to phylogenetically classify the organism. Results: Acid fast non-branching bacilli were detected in all samples from homogenized internal organs. All 13 acid fast samples were positive for Mycobacterium via real-time PCR. Partial gene sequences using all three primer sets were obtained from two samples and demonstrated a novel strain. A strain 99% related to Mycobacterium marinum was also confirmed in one sample, using 16srRNA and rpoB genes. The two novel strains were clustered with the rapid growers and strains that are known to affect humans. Conclusions: Phylogenetic analysis demonstrated two novel Mycobacterium strains with the potential of being zoonotic and one strain 99% related to Mycobacterium marinum.

Keywords: polymerase chain reaction, phylogenetic, DNA sequencing, zoonotic

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Authors: Mei Han, Jinkou Zhao, Yuan Yao, Liangui Feng, Xianbin Ding, Guohui Wu, Chao Zhou, Lin Ouyang, Rongrong Lu, Bo Zhang

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To compare the HIV incidence estimated using BED capture enzyme linked immunosorbent assay (BED-CEIA) and observed in a cohort against the HIV incidence among men who have sex with men (MSM) measured by pooling polymerase chain reaction (pooling-PCR). A total of 617 MSM subjects were included in a respondent driven sampling survey in Chongqing in 2008. Among the 129 that were tested HIV antibody positive, 102 were defined with long-term infection, 27 were assessed for recent HIV infection (RHI) using BED-CEIA. The remaining 488 HIV negative subjects were enrolled to the prospective cohort and followed-up every 6 months to monitor HIV seroconversion. All of the 488 HIV negative specimens were assessed for acute HIV infection (AHI) using pooling-PCR. Among the 488 negative subjects in the open cohort, 214 (43.9%) were followed-up for six months, with 107 person-years of observation and 14 subjects seroconverted. The observed HIV incidence was 12.5 per 100 person-years (95% CI=9.1-15.7). Among the 488 HIV negative specimens, 5 were identified with acute HIV infection using pooling-PCR at an annual rate of 14.02% (95% CI=1.73-26.30). The estimated HIV-1 incidence was 12.02% (95% CI=7.49-16.56) based on BED-CEIA. The HIV incidence estimated with three different approaches was different among subgroups. In the highly HIV prevalent MSM, it costs US$ 1724 to detect one AHI case, while detection of one case of RHI with BED assay costs only US$ 42. Three approaches generated comparable and high HIV incidences, pooling PCR and prospective cohort are more close to the true level of incidence, while BED-CEIA seemed to be the most convenient and economical approach for at-risk population’s HIV incidence evaluation at the beginning of HIV pandemic. HIV-1 incidences were alarmingly high among MSM population in Chongqing, particularly within the subgroup under 25 years of age and those migrants aged between 25 to 34 years.

Keywords: BED-CEIA, HIV, incidence, pooled PCR, prospective cohort

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Authors: Siddhartha Paul, Debabrata Das

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Closed-loop supply chain (CLSC) management focuses on integrating forward and reverse flow of material as well as information to maximize value creation over the entire life-cycle of a product. Bullwhip effect in supply chain management refers to the phenomenon where a small variation in customers’ demand results in larger variation of orders at the upstream levels of supply chain. Since the quality and quantity of products returned to the collection centers (as a part of reverse logistics process) are uncertain, bullwhip effect is inevitable in CLSC. Therefore, in the present study, first, through an extensive literature survey, we identify all the important factors related to forward as well as reverse supply chain which causes bullwhip effect in CLSC. Second, we develop a system dynamics model to study the interrelationship among the factors and their effect on the performance of overall CLSC. Finally, the results of the simulation study suggest that demand forecasting, lead times, information sharing, inventory and work in progress adjustment rate, supply shortages, batch ordering, price variations, erratic human behavior, parameter correcting, delivery time delays, return rate of used products, manufacturing and remanufacturing capacity constraints are the important factors which have a significant influence on system’s performance, specifically on bullwhip effect in a CLSC.

Keywords: bullwhip effect, closed-loop supply chain, system dynamics, variance ratio

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Authors: Kanokon Chaicom, Chitima Sirijerachai, Kanchana Chansung, Pinsuda Klangsang, Boonpeng Palaeng, Prajuab Chaimanee, Pimjai Ananta

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Chronic myeloid leukemia (CML) is characterized by the consistent involvement of the Philadelphia chromosome (Ph), which is derived from a reciprocal translocation between chromosome 9 and 22, the main product of the t(9;22) (q34;q11) translocation, is found in the leukemic clone of at least 95% of CML patients. There are two major forms of the BCR/ABL fusion gene, involving ABL exon 2, but including different exons of BCR gene. The transcripts b2a2 (e13a2) or b3a2 (e14a2) code for a p210 protein. Another fusion gene leads to the expression of an e1a2 transcript, which codes for a p190 protein. Other less common fusion genes are b3a3 or b2a3, which codes for a p203 protein and e19a2 (c3a2) transcript, which codes for a p230 protein. Its frequency varies in different populations. In this study, we aimed to report the frequency of BCR-ABL fusion transcript types with CML by multiplex PCR (polymerase chain reaction) in Srinagarind Hospital, Khon Kaen, Thailand. Multiplex PCR for BCR-ABL was performed on 58 patients, to detect different types of BCR-ABL transcripts of the t (9; 22). All patients examined were positive for some type of BCR/ABL rearrangement. The majority of the patients (93.10%) expressed one of the p210 BCR-ABL transcripts, b3a2 and b2a2 transcripts were detected in 53.45% and 39.65% respectively. The expression of an e1a2 transcript showed 3.75%. Co-expression of p210/p230 was detected in 3.45%. Co-expression of p210/p190 was not detected. Multiplex PCR is useful, saves time and reliable in the detection of BCR-ABL transcript types. The frequency of one or other rearrangement in CML varies in different population.

Keywords: chronic myeloid leukemia, BCR-ABL fusion transcript types, multiplex PCR, frequency of BCR-ABL fusion

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Authors: S. Dhib, S. A. Addouche, T. Loukil, A. Elmhamedi

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In this paper, a reverse supply chain network is investigated for a decision making. This decision is surrounded by complex flows of returned products, due to the increasing quantity, the type of returned products and the variety of recovery option products (reuse, recycling, and refurbishment). The most important problem in the reverse logistic network (RLN) is to orient returned products to the suitable type of recovery option. However, returned products orientations from collect sources to the recovery disposition have not well considered in performance model. In this study, we propose a performance model for designing a network configuration on reverse logistics. Conceptual and analytical models are developed with taking into account operational, economic and environmental factors on designing network.

Keywords: reverse logistics, network design, performance model, open loop configuration

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Authors: Abdelsabour G. A. Khaled, Ahmed W. A. Abdalla And Sabry Y. M. Mahmoud

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Banana plants showing typical mosaic and yellow stripes on leaves as symptoms were collected from Assiut Governorate in Egypt. The causal agent was identified as Cucumber mosaic virus (CMV) on the basis of symptoms, transmission, serology, transmission electron microscopy and reverse transcription polymerase chain reaction (RT-PCR). Coat protein (CP) gene was amplified using gene specific primers for coat protein (CP), followed by cloning into desired cloning vector for sequencing. In this study the CMV was transmitted into propagation host either by aphid or mechanically. The transmission was confirmed through Direct Antigen Coating Enzyme Linked Immuno Sorbent Assay (DAC-ELISA). Analysis of the 120 deduced amino acid sequence of the coat protein gene revealed that the EG-A strain of CMV shared from 97.50 to 98.33% with those strains belonging to subgroup IA. The cluster analysis grouped the Egyptian isolate with strains Fny and Ri8 belonging sub-group IA. It appears that there occurs a high incidence of CMV infecting banana belonging to IA subgroup in most parts of Egypt.

Keywords: banana, CMV, transmission, CP gene, RT-PCR

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Authors: Ali Bayram, Burak Uz, Remzi Yiğiter

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The aim of the present study was to investigate the expression levels of homo sapiens nuclear factor of kappa light polypeptide gene enhancer in B-cells 1, transcript variant 1 (NFKB1*1) mRNA in the peripheral blood of patients with Parkinson to elucidate the role in the pathogenesis of Parkinson disease (PD). The study group comprised 50 patients with the diagnosis of PD who have applied to Gaziantep University Faculty of Medicine, and Department of Neurology. 50 healthy individuals without any neuro degenerative disease are included as controls. Ribonucleic acid (RNA) was obtained from blood samples of patient and control groups. Complementary deoxyribonucleic acid (cDNA) was obtained from RNA samples using reverse transcription polymerase chain reaction (RT-PCR) technique. The gene expression of NFKB1*1 in patient/control groups were observed to decrease significantly, and the differences between groups with the Mann-Whitney method within 95% confidence interval (p<0.05) were analyzed. This salient finding provide a clue for our hypothesis that reduced activity of NFKB1*1 gene might play a role, at least partly, in the pathophysiology of PD.

Keywords: Parkinson’s Disease, NFKB1, mRNA expression, RT-PCR

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Authors: Gowtham Kalkere Jayanna, Mohamad Nazri Husin

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Graph theory, chemistry, and technology are all combined in cheminformatics. The structure and physiochemical properties of organic substances are linked using some useful graph invariants and the corresponding molecular graph. In this paper, we study specific reverse topological indices such as the reverse sum-connectivity index, the reverse Zagreb index, the reverse arithmetic-geometric, and the geometric-arithmetic, the reverse Sombor, the reverse Nirmala indices for the bistar graphs B (n: m) and the corona product Kₘ∘Kₙ', where Kₙ' Represent the complement of a complete graph Kₙ.

Keywords: reverse topological indices, bistar graph, the corona product, graph

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Authors: Agnieszka Krzemińska, Katarzyna Świderek, Vicente Molinier, Piotr Paneth

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In order to understand in details the interactions between ligands and the enzyme isotope effects were studied between clinically used drugs that bind in the active site of Human Immunodeficiency Virus Reverse Transcriptase, HIV-1 RT, as well as triazole-based inhibitor that binds in the allosteric pocket of this enzyme. The magnitudes and origins of the resulting binding isotope effects were analyzed. Subsequently, binding isotope effect of the same triazole-based inhibitor bound in the active site were analyzed and compared. Together, these results show differences in binding origins in two sites of the enzyme and allow to analyze binding mode and place of newly synthesized inhibitors. Typical protocol is described below on the example of triazole ligand in the allosteric pocket. Triazole was docked into allosteric cavity of HIV-1 RT with Glide using extra-precision mode as implemented in Schroedinger software. The structure of HIV-1 RT was obtained from Protein Data Bank as structure of PDB ID 2RKI. The pKa for titratable amino acids was calculated using PROPKA software, and in order to neutralize the system 15 Cl- were added using tLEaP package implemented in AMBERTools ver.1.5. Also N-terminals and C-terminals were build using tLEaP. The system was placed in 144x160x144Å3 orthorhombic box of water molecules using NAMD program. Missing parameters for triazole were obtained at the AM1 level using Antechamber software implemented in AMBERTools. The energy minimizations were carried out by means of a conjugate gradient algorithm using NAMD. Then system was heated from 0 to 300 K with temperature increment 0.001 K. Subsequently 2 ns Langevin−Verlet (NVT) MM MD simulation with AMBER force field implemented in NAMD was carried out. Periodic Boundary Conditions and cut-offs for the nonbonding interactions, range radius from 14.5 to 16 Å, are used. After 2 ns relaxation 200 ps of QM/MM MD at 300 K were simulated. The triazole was treated quantum mechanically at the AM1 level, protein was described using AMBER and water molecules were described using TIP3P, as implemented in fDynamo library. Molecules 20 Å apart from the triazole were kept frozen, with cut-offs established on range radius from 14.5 to 16 Å. In order to describe interactions between triazole and RT free energy of binding using Free Energy Perturbation method was done. The change in frequencies from ligand in solution to ligand bounded in enzyme was used to calculate binding isotope effects.

Keywords: binding isotope effects, molecular dynamics, HIV, reverse transcriptase

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Authors: Sabine A. Zauchner-Studnicka

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As the term indicates, reverse-mentoring flips the classical roles of mentoring: In school, students take over the role of mentors for adults, i.e. teachers or parents. Originally reverse-mentoring stems from US enterprises, which implemented this innovative method in order to benefit from the resources of skilled younger employees for the enhancement of IT competences of senior colleagues. However, reverse-mentoring in schools worldwide is rare. Based on empirical studies and theoretical approaches, in this article an implementation model for reverse-mentoring is developed in order to bring the significant potential reverse-mentoring has for education into practice.

Keywords: reverse-mentoring, innovation in education, implementation model, school education

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Authors: Rawan Al-Nemari, Abdulrahman Al-Senaidy, Abdelhabib Semlali

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Background and objectives: The most common cause of death in women worldwide is breast cancer. Regarding all chemotherapy disadvantages and side effects, it’s becoming necessary to identify natural products that target cancer cells with lesser harmful side effects on non-targeted cells and biological environment. Different parts of A. squamosa L., commonly known as custard apple, show varied therapeutic effects. The objective of this study is to investigate in vitro and in vivo, the anti-cancer activity of A. squamosa leaves extract. Methods: The physiological responses using MTT, nucleus staining, and LDH assays were used to evaluate cell survival and proliferation in both ER+ and ER- cells when they were exposed to extract. Monolayer wound repair assay was used to investigate the effect of extracts on cell migration. Apoptotic gene’s expression was investigated by real-time polymerase chain reaction. To study the effect of the extract on the size of tumor, breast cancer induced rats were used. Results: A. squamosa leaves extract showed high anti-proliferative and cytotoxicity effects against different breast cancer cell lines with high concentration, 100 ug/ml. The extracts have reduced the cells wound closure. Polymerase chain reaction revealed downregulation of Bcl-2 and upregulation of Bax. In breast cancer model animal developed in our laboratory, after 4 weeks treatment, treated groups have shown smaller tumor size in comparison with control group (n=4). Conclusion: These results suggest that A. squamosa leaves extract has anti-cancer activity against breast cancer in both in vitro and in vivo, and it may be developed as a potential novel agent to treat breast cancer.

Keywords: apoptosis, breast cancer, migration, proliferation

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Authors: Manal Kamel, Sara Maher, Hanan El Baz, Faten Salah, Omar Sayyouh, Zeinab Demerdash

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In the recent COVID 19 pandemic, experts of public health have emphasized testing, tracking infected people, and tracing their contacts as an effective strategy to reduce the spread of the virus. Development of rapid and sensitive diagnostic assays to replace reverse transcription polymerase chain reaction (RT-PCR) is mandatory..Our innovative test strip relying on the application of nanoparticles conjugated to recombinant nanobodies for SARS-COV-2 spike protein (S1) & angiotensin-converting enzyme 2 (that is responsible for the virus entry into host cells) for rapid detection of SARS-COV-2 spike protein (S1) in saliva or sputum specimens. Comparative tests with RT-PCR will be held to estimate the significant effect of using COVID 19 nanobodies for the first time in the development of lateral flow test strip. The SARS-CoV-2 S1 (3 ng of recombinant proteins) was detected by our developed LFIA in saliva specimen of COVID-19 Patients No cross-reaction was detected with Middle East respiratory syndrome coronavirus (MERS-CoV) or SARS- CoV antigens..Our developed system revealed 96 % sensitivity and 100% specificity for saliva samples compared to 89 % and 100% sensitivity and specificity for nasopharyngeal swabs. providing a reliable alternative for the painful and uncomfortable nasopharyngeal swab process and the complexes, time consuming PCR test. An increase in testing compliances to be expected.

Keywords: COVID 19, diagnosis, LFIA, nanobodies, ACE2

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Authors: Abu Salim Mustafa

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Polymerase chain reaction (PCR) assays targeting genomic DNA segments have been established for the detection of Helicobacter pylori in clinical specimens. However, the data on comparative evaluations of various targets in detection of H. pylori are limited. Furthermore, the frequencies of vacA (s1 and s2) and cagA genotypes, which are suggested to be involved in the pathogenesis of H. pylori in other parts of the world, are not well studied in Kuwait. The aim of this study was to evaluate PCR assays for the detection and genotyping of H. pylori by targeting the amplification of DNA targets from four genomic segments. The genomic DNA were isolated from 72 clinical isolates of H. pylori and tested in PCR with four pairs of oligonucleotides primers, i.e. ECH-U/ECH-L, ET-5U/ET-5L, CagAF/CagAR and Vac1F/Vac1XR, which were expected to amplify targets of various sizes (471 bp, 230 bp, 183 bp and 176/203 bp, respectively) from the genomic DNA of H. pylori. The PCR-amplified DNA were analyzed by agarose gel electrophoresis. PCR products of expected size were obtained with all primer pairs by using genomic DNA isolated from H. pylori. DNA dilution experiments showed that the most sensitive PCR target was 471 bp DNA amplified by the primers ECH-U/ECH-L, followed by the targets of Vac1F/Vac1XR (176 bp/203 DNA), CagAF/CagAR (183 bp DNA) and ET-5U/ET-5L (230 bp DNA). However, when tested with undiluted genomic DNA isolated from single colonies of all isolates, the Vac1F/Vac1XR target provided the maximum positive results (71/72 (99% positives)), followed by ECH-U/ECH-L (69/72 (93% positives)), ET-5U/ET-5L (51/72 (71% positives)) and CagAF/CagAR (26/72 (46% positives)). The results of genotyping experiments showed that vacA s1 (46% positive) and vacA s2 (54% positive) genotypes were almost equally associated with VaCA+/CagA- isolates (P > 0.05), but with VacA+/CagA+ isolates, S1 genotype (92% positive) was more frequently detected than S2 genotype (8% positive) (P< 0.0001). In conclusion, among the primer pairs tested, Vac1F/Vac1XR provided the best results for detection of H. pylori. The genotyping experiments showed that vacA s1 and vacA s2 genotypes were almost equally associated with vaCA⁺/cagA^- isolates, but vacA s1 genotype had a significantly increased association with vacA⁺/cagA⁺ isolates.

Keywords: H. pylori, PCR, detection, genotyping

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Authors: Foteini Zagklavara, Peter Jimack, Nikil Kapur, Ozz Querin, Harvey Thompson

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The invention and development of the Polymerase Chain Reaction (PCR) technology have revolutionised molecular biology and molecular diagnostics. There is an urgent need to optimise their performance of those devices while reducing the total construction and operation costs. The present study proposes a CFD-enabled optimisation methodology for continuous flow (CF) PCR devices with serpentine-channel structure, which enables the trade-offs between competing objectives of DNA amplification efficiency and pressure drop to be explored. This is achieved by using a surrogate-enabled optimisation approach accounting for the geometrical features of a CF μPCR device by performing a series of simulations at a relatively small number of Design of Experiments (DoE) points, with the use of COMSOL Multiphysics 5.4. The values of the objectives are extracted from the CFD solutions, and response surfaces created using the polyharmonic splines and neural networks. After creating the respective response surfaces, genetic algorithm, and a multi-level coordinate search optimisation function are used to locate the optimum design parameters. Both optimisation methods produced similar results for both the neural network and the polyharmonic spline response surfaces. The results indicate that there is the possibility of improving the DNA efficiency by ∼2% in one PCR cycle when doubling the width of the microchannel to 400 μm while maintaining the height at the value of the original design (50μm). Moreover, the increase in the width of the serpentine microchannel is combined with a decrease in its total length in order to obtain the same residence times in all the simulations, resulting in a smaller total substrate volume (32.94% decrease). A multi-objective optimisation is also performed with the use of a Pareto Front plot. Such knowledge will enable designers to maximise the amount of DNA amplified or to minimise the time taken throughout thermal cycling in such devices.

Keywords: PCR, optimisation, microfluidics, COMSOL

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Authors: P. A. Broodryk, A. F. Van Der Merwe, H. W. J. P. Neomagus

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The production of the clear liquid fertilizer ammonium polyphosphate (APP) is best achieved by the pyrolysis of urea phosphate, as it produces a product that is free from any of the impurities present in the raw phosphoric acid it was made from. This is a multiphase, multi-step reaction that produces carbon dioxide and ammonia as gasses and ammonium polyphosphate as liquid products. The polyphosphate chain length affects the solubility and thus the applicability of the product as liquid fertiliser, thus proper control of the reaction conditions is thus required for the use of this reaction in the production of fertilisers. This study investigates the reaction kinetics of the aforementioned reaction, describing a mathematical model for the kinetics of the reaction along with the accompanying rate constants. The reaction is initially exothermic, producing only carbon dioxide as a gas product and ammonium diphosphate, at higher temperatures the reaction becomes endothermic, producing ammonia gas as an additional by-product and longer chain polyphosphates, which when condensed too far becomes highly water insoluble. The aim of this study was to (i) characterise the pyrolysis reaction of urea phosphate by determining the mechanisms and the associated kinetic constants, and (ii) to determine the optimum conditions for ammonium diphosphate production. A qualitative investigation was also done to find the rate of hydrolysis of APP as this provides an estimate of the shelf life of an APP clear liquid fertiliser solution.

Keywords: ammonium polyphosphate, kinetics, pyrolysis, urea phosphate

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Authors: Chao Li, Lei Zhou, Ruiqi Ren, Dan Li, Yali Wang, Daxin Ni, Zijian Feng, Qun Li

Abstract:

Background: In 2016, yellow fever had been first ever discovered in China, soon after the yellow fever epidemic occurred in Angola. After the discovery, China had promptly made the national protocol of control and prevention and strengthened the surveillance on passenger and vector. In this study, a descriptive analysis was conducted to summarize China’s experiences of response towards this import epidemic, in the hope of providing experiences on prevention and control of yellow fever and other similar imported infectious diseases in the future. Methods: The imported cases were discovered and reported by General Administration of Quality Supervision, Inspection and Quarantine (AQSIQ) and several hospitals. Each clinically diagnosed yellow fever case was confirmed by real-time reverse transcriptase polymerase chain reaction (RT–PCR). The data of the imported yellow fever cases were collected by local Centers for Disease Control and Prevention (CDC) through field investigations soon after they received the reports. Results: A total of 11 imported cases from Angola were reported in China, during Angola’s yellow fever outbreak. Six cases were discovered by the AQSIQ, among which two with mild symptom were initiative declarations at the time of entry. Except for one death, the remaining 10 cases all had recovered after timely and proper treatment. All cases are Chinese, and lived in Luanda, the capital of Angola. 73% were retailers (8/11) from Fuqing city in Fujian province, and the other three were labors send by companies. 10 cases had experiences of medical treatment in Luanda after onset, among which 8 cases visited the same local Chinese medicine hospital (China Railway four Bureau Hospital). Among the 11 cases, only one case had an effective vaccination. The result of emergency surveillance for mosquito density showed that only 14 containers of water were found positive around places of three cases, and the Breteau Index is 15. Conclusions: Effective response was taken to control and prevent the outbreak of yellow fever in China after discovering the imported cases. However, though the similar origin of Chinese in Angola has provided an easy access for disease detection, information sharing, health education and vaccination on yellow fever; these conveniences were overlooked during previous disease prevention methods. Besides, only one case having effective vaccination revealed the inadequate capacity of immunization service in China. These findings will provide suggestions to improve China’s capacity to deal with not only yellow fever but also other similar imported diseases in China.

Keywords: yellow fever, first import, China, suggestion

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Authors: Kayode O. Afolabi, Benson C. Iweriebor, Anthony I. Okoh, Larry C. Obi

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Porcine circovirus type 2 (PCV2) is the major etiological viral agent of porcine multisystemic wasting syndrome (PWMS) and other porcine circovirus-associated diseases (PCVAD) of great economic importance in pig industry globally. In an effort to determine the status of swine herds in the Province as regarding the ‘small but powerful’ viral pathogen; a total of 375 blood, faecal and nasal swab samples were obtained from seven pig farms (commercial and communal) in Amathole, O.R. Tambo and Chris-Hani District Municipalities of Eastern Cape Province between the year 2015 and 2016. Three hundred and thirty nine (339) samples out of the total sample were subjected to molecular screening using PCV2 specific primers by conventional polymerase chain reaction (PCR). Selected sequences were further analyzed and confirmed through genome sequencing and phylogenetic analyses. The data obtained revealed that 15.93% of the screened samples (54/339) from the swine herds of the studied areas were positive for PCV2; while the severity of occurrence of the viral pathogen as observed at farm level ranges from approximately 5.6% to 60% in the studied farms. The Majority, precisely 15 out of 17 (88%) analyzed sequences were found clustering with other PCV2b reference strains in the phylogenetic analysis. More interestingly, two other sequences obtained were also found clustering within PCV2d genogroup, which is presently another fast-spreading genotype with observable higher virulence in global swine herds. This finding confirmed the presence of this all-important viral pathogen in pigs of the region; which could result in a serious outbreak of PCVAD and huge economic loss at the instances of triggering factors if no appropriate measures are taken to curb its spread effectively.

Keywords: pigs, polymerase chain reaction, porcine circovirus type 2, South Africa

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Authors: Agumah N. B. Orji, M. U., Oru C. M., Ugbo, E. N., Onwuliri E. A Nwakaeze, E. A.,

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ERG11 gene has been reported to be one of the genes whose expression is responsible for resistance of Candida to various triazole drugs, which are first line treatment for candidiasis. This study was carried out to determine the prevalence of Triazole (Fluconazole and voriconazole) resistant Candida albicans expressing ERG11 gene from adult females in Abakaliki. Urine and vaginal swab samples were randomly collected from volunteers after obtaining their consent to participate in the study. A total of 565 adult females participated in the study. A total of 340 urine specimens and 288 vaginal swab specimens were collected. Direct wet mount technique, as well as culture in Trichomonas broth, were used to examine the urine and vaginal swab specimens for the presence of motile Trichomonads. The Trichomonas broth used was selective for both T. vaginalis and C. albicans. Broths that yielded budding yeast cells after microscopy were subcultured on to Sabouraud dextrose agar, after which Germ tube test was carried out to confirm the presence of C. albicans. Biochemical tests, including carbohydrate fermentation and urease utilization, were also performed. Antibiogram of C. albicans isolates obtained from this study was carried out using commercially available azole drugs. Fluconazole and voriconazole were selected as Triazole drugs used for this study. Nystatin was used as a tangential control. An MIC test was carried out with E-strips on some of the resistant C. albicans isolates A total of 6 isolates that resisted all the azole drugs were selected and screened for the presence of ERG11 gene using Reverse transcriptase polymerase chain reaction technique. The total prevalence recorded for C. albicans was 13.0%. Frequency was statistically higher in Pregnant (7.96%) than non pregnant (5.09%) volunteers (X2=0.94 at P=0.05). With respect to clinical samples, frequency was higher in vaginal swabs samples (7.96%) than Urine samples (5.09%) (X2=9.05 at P=0.05). Volunteers within the age group 26-30 years recorded the highest prevalence (4.46%), while those within the age group 36-40 years recorded the lowest at 1.27%(X2=4.34 at P=0.05). In pregnant female participants, the highest frequency was recorded with those in their 3rd trimester (4.14%), while lowest incidence was recorded for those in their first trimester (0.80%). Antibiogram results from this study showed that C. albicans isolates obtained from this study resisted Fluconazole (72%) more than Voriconazole (57%). Only one out of the six selected isolates yielded resistance in the MIC test. Results obtained from the RT-PCR showed that there was no expression of ERG11 gene among the fluconazole resistant isolates of C. albicans. Observed resistance may be due to other factors other than expression of ERG11 gene.

Keywords: candida, ERG11, triazole, nigeria

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Authors: Jianli Dong, Fangling Xu, Gengming Huang

Abstract:

Human endogenous retroviral elements (HERVs) comprise approximately 8% of the human genome. They are thought to be germline-integrated genetic remnants of retroviral infections. Although HERV sequences are highly defective, some, especially the K type (HERV-K), have been shown to be expressed and may have biological activities in the pathogenesis of cancer, chronic inflammation and autoimmune diseases. We found that HERV-K GAG and ENV proteins were strongly expressed in pleomorphic melanoma cells. We also detected a critical role of HERV-K ENV in mediating intercellular fusion and colony formation of melanoma cells. Interestingly, we found that levels of HERV-K GAG and ENV expression correlated with the activation of ERK and loss of p16INK4A in melanoma cells, and inhibition of MEK or CDK4, especially in combination, reduced HERV-K expression in melanoma cells. We also performed a reverse transcription-polymerase chain reaction (RT-PCR) assay using DNase I digestion to remove “contaminating” HERV-K genomic DNA and examined HERV-K RNA expression in plasma samples from HIV-1 infected individuals. We found a covariation between HERV-K RNA expression and CD4 cell counts in HIV-1 positive samples. Although a causal link between HERV-K activation and melanoma development, and between HERV-K activation, HIV-1 infection and CD4 cell count have yet to be determined, existing data support the further research efforts in HERV-K.

Keywords: CD4 cell, HERV-K, HIV-1, melanoma

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Authors: Olena Mayboroda, Angel Gonzalez Benito, Jonathan Sabate Del Rio, Marketa Svobodova, Sandra Julich, Herbert Tomaso, Ciara K. O'Sullivan, Ioanis Katakis

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DNA amplification is required for most molecular diagnostic applications but conventional PCR has disadvantages for field testing. Isothermal amplification techniques are being developed to respond to this problem. One of them is the Recombinase Polymerase Amplification (RPA) that operates at isothermal conditions without sacrificing specificity and sensitivity in easy-to-use formats. In this work RPA was used for the optical detection of solid-phase amplification of the potential biowarfare agent Yersinia pestis. Thiolated forward primers were immobilized on the surface of maleimide-activated microtitre plates for the quantitative detection of synthetic and genomic DNA, with elongation occurring only in the presence of the specific template DNA and solution phase reverse primers. Quantitative detection was achieved via the use of biotinylated reverse primers and post-amplification addition of streptavidin-HRP conjugate. The overall time of amplification and detection was less than 1 hour at a constant temperature of 37oC. Single-stranded and double-stranded DNA sequences were detected achieving detection limits of 4.04*10-13 M and 3.14*10-16 M, respectively. The system demonstrated high specificity with negligible responses to non-specific targets.

Keywords: recombinase polymerase amplification, Yersinia pestis, solid-phase detection, ELONA

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Authors: Vladimir Ryabov, Mikhail Baryshevs, Mikhail Voskresenskey, Boris Popov

Abstract:

The human prostate gland (PG) samples were obtained from patients who had undergone radical prostatectomy for prostate cancer (PC) and used to extract total RNA and prepare the prostate stromal cell cultures (PSCC) and patients-derived organoids (PDO). Growth of the cell cultures was accessed under microscopic evaluation in transmitted light and the marker expression by reverse polymerase chain reaction (RT-PCR), immunofluorescence, and immunoblotting. Some PCR products from prostate tissue, PSCC, and PDO were cloned and sequenced. We found that the cells of early and late passages of PSCC and corresponding PDO expressed luminal (androgen receptor, AR; cytokeratin 18, CK18) and basal (CK5, p63) epithelial markers, the production of which decreased or disappeared in late PSCC and PDO. The PSCC and PDO of early passages from cancer tissue additionally produced cancer markers AMACR, TMPRSS2-ERG, and Ezh2. The expression of TMPRSS2-ERG fusion transcripts was verified by cloning and sequencing the PCR products. The results obtained suggest that early passages of PSCC might be used as a pre-clinical model for the evaluation of early markers of prostate cancer.

Keywords: localized prostate cancer, prostate epithelial markers, prostate cancer markers, AMACR, TMPRSS2-ERG, prostate stromal cell cultures, PDO

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Authors: Kittipong Tissayakorn, Fumio Akagi, Yu Song

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Logistics is the integrated management of all of the activities required to move products through the supply chain. For a typical product, this supply chain extends from a raw material source through the production and distribution system to the point of consumption and the associated reverse logistics. The logistical activities are comprised of freight transport, storage, inventory management, materials handling and all related information processing. This paper analyzes the green management system of logistics enterprise for Thailand and advances the concept of Green Logistics, which should be held by the public. In addition, it proposes that the government should strengthen its supervision and support for green logistics, and companies should construct self-disciplined green logistics management systems and corresponding processes, a reverse logistics management system and a modern green logistics information collection and management system.

Keywords: logistics, green logistics, management system, ecological economics

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Authors: Yuli Hou, Jianping Sun, Mengdan Gao, Hui Liu, Ling Qin, Ang Li, Dongfu Li, Yonghong Zhang, Yan Zhao

Abstract:

Background and Aims: Interferon-induced transmembrane protein 3 (IFITM3) is a component of ISG (Interferon-Stimulated Gene) family. IFITM3 has been recognized as a key signal molecule regulating cell growth in some tumors. However, the function of IFITM3 rs12252-CC genotype in the hepatocellular carcinoma (HCC) remains unknown to author’s best knowledge. A cohort study was employed to clarify the relationship between IFITM3 rs12252-CC genotype and HCC progression, and cellular experiments were used to investigate the correlation of function of IFITM3 and the progress of HCC. Methods: 336 candidates were enrolled in study, including 156 with HBV related HCC and 180 with chronic Hepatitis B infections or liver cirrhosis. Polymerase chain reaction (PCR) was employed to determine the gene polymorphism of IFITM3. The functions of IFITM3 were detected in PLC/PRF/5 cell with different treated:LV-IFITM3 transfected with lentivirus to knockdown the expression of IFITM3 and LV-NC transfected with empty lentivirus as negative control. The IFITM3 expression, proliferation and migration were detected by Quantitative reverse transcription polymerase chain reaction (qRT-PCR), QuantiGene Plex 2.0 assay, western blotting, immunohistochemistry, Cell Counting Kit(CCK)-8 and wound healing respectively. Six samples (three infected with empty lentiviral as control; three infected with LV-IFITM3 vector lentiviral as experimental group ) of PLC/PRF/5 were sequenced at BGI (Beijing Genomics Institute, Shenzhen,China) using RNA-seq technology to identify the IFITM3-related signaling pathways and chose PI3K/AKT pathway as related signaling to verify. Results: The patients with HCC had a significantly higher proportion of IFITM3 rs12252-CC compared with the patients with chronic HBV infection or liver cirrhosis. The distribution of CC genotype in HCC patients with low differentiation was significantly higher than that in those with high differentiation. Patients with CC genotype found with bigger tumor size, higher percentage of vascular thrombosis, higher distribution of low differentiation and higher 5-year relapse rate than those with CT/TT genotypes. The expression of IFITM3 was higher in HCC tissues than adjacent normal tissues, and the level of IFITM3 was higher in HCC tissues with low differentiation and metastatic than high/medium differentiation and without metastatic. Higher RNA level of IFITM3 was found in CC genotype than TT genotype. In PLC/PRF/5 cell with knockdown, the ability of cell proliferation and migration was inhibited. Analysis RNA sequencing and verification of RT-PCR found out the phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin(PI3K/AKT/mTOR) pathway was associated with knockdown IFITM3.With the inhibition of IFITM3, the expression of PI3K/AKT/mTOR signaling pathway was blocked and the expression of vimentin was decreased. Conclusions: IFITM3 rs12252-CC with the higher expression plays a vital role in the progress of HCC by regulating HCC cell proliferation and migration. These effects are associated with PI3K/AKT/mTOR signaling pathway.

Keywords: IFITM3, interferon-induced transmembrane protein 3, HCC, hepatocellular carcinoma, PI3K/ AKT/mTOR, phosphatidylinositol 3-kinase/protein kinase B/mammalian target of rapamycin

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