Search results for: blaOXA-like genes

Authors: M. Suwaibah, S. W. Tan, I. Aiini, K. Yusoff, A. R. Omar

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Respiratory diseases are the most important infectious diseases affecting poultry worldwide. One of the avian respiratory virus of global importance causing significant economic losses is Infectious Bronchitis Virus (IBV). The virus causes a wide spectrum disease known as Infectious Bronchitis (IB), affecting not only the respiratory system but also the kidney and the reproductive system, depending on its strain. IB and Newcastle disease are two of the most prevalent diseases affecting poultry in Malaysia. However, a study on the molecular characterization of Malaysian IBV is lacking. In this study, an IBV strain IBS130 which was isolated in 2015 was fully sequenced using next-gene sequencing approach. Sequence analysis of IBS130 based on the complete genome, polyprotein 1ab and S1 genes were compared with other IBV sequences available in Genbank, National Center for Biotechnology Information (NCBI). IBV strain IBS130 is characterised as QX-like strain based on whole genome and S1 gene sequence analysis. Comparisons of the virus with other IBV strains showed that the nucleotide identity ranged from 67% to 99.2%, depending on the region analysed. The similarity in whole genome nucleotide ranging from 84.9% to 90.7% with the least similar was from Singapore strains (84.9%) and highly similar with China QX-like strains. Meanwhile, the similarity in polyprotein 1ab ranging from 85.3% to 89.9% with the least similar to Singapore strains (85.3%) and highly similar with Mass strains from USA.

Keywords: infectious bronchitis virus, phylogenetic analysis, chicken, Malaysia

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Authors: Sadhana Shukla, Pushplata Singh, Nidhi Didwania

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Arbuscular mycorrhizal (AM) fungi are a highly advantageous and versatile group of fungi that significantly contribute to the formation of soil organic matter by creating a demand for plant carbon (C) and distributing it through below-ground hyphal biomass, regardless of their substantial contribution in enhancing net primary productivity and accumulating additional photosynthetic fixed C in the soil. The genetic role of AM fungi in carbon cycling is largely unexplored. In our study, we propose that AM fungi significantly interact with the soil, particularly: the provision of photosynthates by plants. We have studied the expression of AM fungi genes involved in CO₂ sequestration during host-plant interaction was investigated by qPCR studies. We selected Rhizophagus proliferus (AM fungi) and Oryza sativa (Rice) (inoculated with or without 200ppg AMF inoculums per plant) and investigated the effect of AM fungi on soil organic carbon (SOC) and rice growth under field conditions. Results thus provided faster SOC turnover, 35% increased nutrient uptake in plants and pronounced hyphal biomass of AM fungi which enhanced soil carbon storage by 15% in comparison to uninoculated plants. This study will offer a foundation for delving into various carbon-soil studies while also advancing our comprehension of the relationship between AM fungi and the sustainability of agricultural ecosystems.

Keywords: arbuscular mycorrhizal (AM) fungi, carbon sequestration, gene expression, soil health, plant development.

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Authors: Mai M. Farid, Ximeng Yang, Tomoharu Kuboyama, Yuna Inada, Chihiro Tohda

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Intro: Trigonella foenum-graecum (Fenugreek), from Fabaceae family is a well-known plant traditionally used as food and medicine. Many pharmacological effects of Trigonella foenum- graecum seeds extract (TF extract) were evaluated such as anti-diabetic, anti-tumor and anti-dementia effects using in vivo models. Regarding the anti-dementia effects of TF extract, diabetic rats, aluminum chloride-induced amnesia rats and scopolamine-injected mice were used previously for evaluation, which are not well established as Alzheimer’s disease models. In addition, those previous studies, active constituents in TF extract for memory function were not identified. Method: This study aimed to clarify the effect of TF extract on Alzheimer’s disease model, 5XFAD mouse that overexpresses mutated APP and PS1 genes and determine the major active constituent in the brain after oral intake of TF extract. Results: Trigonelline was detected in the cerebral cortex of 5XFAD mice after 24 hours of oral administration of TF extract by LC-MS/MS. Oral administration of TF extract for 17 days improved object location memory in 5XFAD mice. Conclusion: These results suggest that TF extract and its active constituents could be an expected therapeutic candidate for Alzheimer’s disease.

Keywords: Alzheimer's disease, LC-MS/MS, memory recovery, Trigonella foenum-graecum Seeds, 5XFAD mice

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Authors: Adewole Tomiwa Adetunji, Francis Bayo Lewu, Richard Mundembe

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Plants require nitrogen (N) to support desired production levels. There is a need for better understanding of N transport mechanism in order to improve N assimilation by plant root. Nitrogen is available to plants in the form of nitrate or ammonium, which are transported into the cell with the aid of various transport proteins. Ammonium transporters (AMTs) play a role in the uptake of ammonium, the form in which N is preferentially absorbed by plants. Solanum tuberosum AMT1 (StAMT1) was amplified, sequenced and characterized using molecular biology and bioinformatics methods. Nucleotide database sequences were used to design 976 base pairs AMT1-specific primers which include forward primer 5’- GCCATCGCCGCCGCCGG-3’ and reverse primer 5’-GGGTCAGATCCATACCCGC-3’. These primers were used to amplify the Solanum tuberosum AMT1 internal regions. Nucleotide sequencing, alignment and phylogenetic analysis assigned StAMT1 to the AMT1 family due to the clade and high similarity it shared with other plant AMT1 genes. The deduced amino acid sequences showed that StAMT1 is 92%, 83% and 76% similar to Solanum lycopersicum LeAMT1.1, Lotus japonicus LjAMT1.1, and Solanum lycopersicum LeAMT1.2 respectively. StAMT1 fragments were shown to correspond to the 5th-10th trans-membrane domains. Residue StAMT1 D15 is predicted to be essential for ammonium transport, while mutations of StAMT1 S76A may further enhance ammonium transport.

Keywords: ammonium transporter, bioinformatics, nitrogen, primers, Solanum tuberosum

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Authors: S. Salah, S. A. El-Masry, H. F. Sheba, R. A. El-Banna, W. Saad

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Background: Familial Mediterranean fever (FMF) has episodic or subclinical inflammation that may lead to a decrease in bone mineral density (BMD). Objective: To assess BMD in Egyptian children with FMF on genetic basis. Subjects and Methods: A cross sectional study included 45 FMF patients and 25 control children of both sexes, with age range between 3-16 years old. The patients were reclassified into 2 groups: Group I (A) 23 cases used colchicines for 1 month or less, and Group I (B) 22 cases used colchicines for more than 6 months. For both patients and control, MEFV mutations were defined using molecular genetics technique and BMD was measured by DXA at 2 sites: proximal femur and the lumber spines. Results: four frequent gene mutations were found in the patient group: E148Q (35.6%), V726A (33.3%), M680I (28.9.0%) and M694V (2.2%). There were also 4 heterozygous gene mutations in 40% of control children. Patients received colchicines treatment for less than 1 month had highly significant lower values of BMD at femur and lumber spines than control children (p<0.05). Patients received colchicines treatment for more than 6 months had improved values of BMD at femur compared to control, but there were still significant differences between them at lumbar spine (p>0.05). There are insignificant effect of type of gene mutation on BMD and the risk of osteopenia among the patients. Conclusion: FMF had significant effect on BMD. However, regular use of colchicines treatment improves this effect mainly at femur.

Keywords: familial mediterranean fever, bone mineral density, genes, children

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Authors: Ananthakrishna L. R., Ramesh D., Kumar Wodeyar, Kotresh A. M., Gururaj P. M.

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Malnad Gidda is the indigenous recognized cattle breed of Shivamogga District of Karnataka state, India is known for its disease resistance to many of the infectious diseases. There are 25 LRR (Leucine Rich Repeats) identified in bovine (Bos indicus) TLR9. The amino acid sequence of LRR is deduced to nucleotide sequence in BLASTx bioinformatic online tools. LRR2 to LRR10 are involved in pathogen recognition and binding in human TLR9 which showed a higher degree of nucleotide variations with respect to disease resistance to various pathogens. Hence, primers were designed to amplify the flanking sequences of LRR2 to LRR10, to discover the nucleotide variations if any, in Malnad Gidda breed of Cattle which is associated with disease resistance. The DNA isolated from peripheral blood mononuclear cells of ten Malnad Gidda cattle. A desired and specific amplification product of 0.8 kb was obtained at an annealing temperature of 56.6ᵒC. All the PCR products were sequenced on both sides by gene-specific primers. The sequences were compared with TLR9 sequence of cross breed cattle obtained from NCBI data bank. The sequence analysis between Malnad Gidda and crossbreed cattle revealed no nucleotide variations in the region LRR2 to LRR9 which shows the conserved in pathogen binding domain (LRR) of TLR9.

Keywords: leucine rich repeats, Malnad Gidda, cross breed, TLR9

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Authors: Zuzana Chaloupková, Zdeňka Marková, Václav Ranc, Radek Zbořil

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Prostate cancer is now one of the most serious oncological diseases in men with an incidence higher than that of all other solid tumors combined. Diagnosis of prostate cancer usually involves detection of related genes or detection of marker proteins, such as PSA. One of the new potential markers is PSMA (prostate specific membrane antigen). PSMA is a unique membrane bound glycoprotein, which is considerably overexpressed on prostate cancer as well as neovasculature of most of the solid tumors. Commonly applied methods for a detection of proteins include techniques based on immunochemical approaches, including ELISA and RIA. Magnetically assisted surface enhanced Raman spectroscopy (MA-SERS) can be considered as an interesting alternative to generally accepted approaches. This work describes a utilization of MA-SERS in a detection of PSMA in human blood. This analytical platform is based on magnetic nanocomposites Fe3O4@Ag, functionalized by a low-molecular selector labeled as JB303. The system allows isolating the marker from the complex sample using application of magnetic force. Detection of PSMA is than performed by SERS effect given by a presence of silver nanoparticles. This system allowed us to analyze PSMA in clinical samples with limits of detection lower than 1 ng/mL.

Keywords: diagnosis, cancer, PSMA, MA-SERS, Ag nanoparticles

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Authors: Chao Sima, Shanaz Ghandhi, Sally A. Amundson, Michael L. Bittner, David J. Brenner

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In a large-scale radiologic emergency, potentially affected population need to be triaged efficiently using various biomarkers where personal dosimeters are not likely worn by the individuals. It has long been established that radiation injury can be estimated effectively using panels of genetic biomarkers. Furthermore, the rate of radiation, in addition to dose of radiation, plays a major role in determining biological responses. Therefore, a better and more accurate triage involves estimating both the dose level of the exposure and the length of time of that exposure. To that end, a large in vivo study was carried out on mice with internal emitter caesium-137 (¹³⁷Cs). Four different injection doses of ¹³⁷Cs were used: 157.5 μCi, 191 μCi, 214.5μCi, and 259 μCi. Cohorts of 6~7 mice from the control arm and each of the dose levels were sacrificed, and blood was collected 2, 3, 5, 7 and 14 days after injection for microarray RNA gene expression analysis. Using a generalized linear model with penalized maximum likelihood, a panel of 244 genes was established and both the doses of injection and the number of days after injection were accurately predicted for all 155 subjects using this panel. This has proven that microarray gene expression can be used effectively in radiation biodosimetry in predicting both the dose levels and the length of exposure time, which provides a more holistic view on radiation exposure and helps improving radiation damage assessment and treatment.

Keywords: caesium-137, gene expression microarray, multivariate responses prediction, radiation biodosimetry

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Authors: Shubham Dwivedi, Raghavender Medishetti, Rita Rani, Aarti Sevilimedu, Pushkar Kulkarni, Yogeeswari Perumal

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Autism Spectrum Disorder (ASD) is a complex neurodevelopmental disorder of early onset, characterized by impaired sociability, cognitive function and stereotypies. There is a significant urge to develop and establish new animal models with ASD-like characteristics for better understanding of underlying mechanisms. The aim of the present study was to develop a cost and time effective zebrafish model with quantifiable parameters to facilitate mechanistic studies as well as high-throughput screening of new molecules for autism. Zebrafish embryos were treated with valproic acid and a battery of behavioral tests (anxiety, inattentive behavior, irritability and social impairment) was performed on larvae at 7th day post fertilization, followed by study of molecular markers of autism. This model shows a significant behavioural impairment in valproic acid treated larvae in comparison to control which was again supported by alteration in few marker genes and proteins of autism. The model also shows a rescue of behavioural despair with positive control drugs. The model shows robust parameters to study behavior, molecular mechanism and drug screening approach in a single frame. Thus we postulate that our 7 days zebrafish larval model for autism can help in high throughput screening of new molecules on autism.

Keywords: autism, zebrafish, valproic acid, neurodevelopment, behavioral assay

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Authors: Shirin Jalili, Sadegh Hasannia, Hadi Shirzad, Afshin Khara

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Morphine is one of the most medicinally important analgesics and narcotics. Structurally, it is classified as an alkaloid because of the presence of nitrogen. Its structure is similar to that of codeine, thebaine, and heroin. An immunoassay to accurately discriminate between these analogous alkaloids would be highly beneficial. A key factor for such an assay is specificity with high sensitivity, which is totally dependent on the antibody employed. However, most antibodies against haptens are polyclonal serum antibodies that exhibit significant cross-reactivities with closely related compounds. The camel-derived single-chain antibody fragments (VHH) are the smallest molecules with antigen-binding capacity, possessing unique properties compared to other conventional antibodies. In this study, a library containing the VHH genes of a camel immunized with with morphine conjugated BSA following phage display technology was generated. By screening the camel-derived variable region of the heavy chain cDNA phage display library with the ability to bind the desired hapten, we obtained some nanobodies that recognize this hapten. Phage display expression of the Nbs from this library and pannings against this hapten resulted in a clear enrichment of four distinct Nb-displaying phages with specificity for morphine that could be a potential target site for the development of new strategies for the development of a biosensor for detecting illicit drug.

Keywords: phage display, nanobody, Morphine-3, glucuronide, ELISA, biosensor

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Authors: Sonam Kumari

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Tuberculosis is the deadliest disease worldwide. Millions of people lose their lives every year due to this disease. It has turned lethal due to the erratic nature of its causative organism, Mycobacterium tuberculosis (Mtb). Mtb tends to enter into an inactive, dormant state and emerge to replicating state upon encountering favorable conditions. The mechanism by which Mtb switches from the dormant state to the replicative form is still poorly characterized. Proteome studies have given us an insight into the role of certain proteins in giving stupendous virulence to Mtb, but numerous dotsremain unconnected and unaccounted. The WhiB family of proteins is one such protein that is associated with developmental processes in actinomycetes. Mtb has seven such proteins (WhiB1 to WhiB7). WhiB proteins are transcriptional regulators; they regulate various essential genes of Mtbby binding to their promoter DNA. Biophysical parameters of the effect of DNA binding on WhiB proteins has not yet been appropriately characterized. Interaction with DNA induces conformational changes in the WhiB proteins, confirmed by steady-state fluorescence and circular dichroism spectroscopy. ITC has deduced thermodynamic parameters and the binding affinity of the interaction. Since these transcription factors are highly unstable in vitro, their stability and solubility were enhanced by the co-expression of molecular chaperones. The present study findings help determine the conditions under which the WhiB proteins interact with their interacting partner and the factors that influence their binding affinity. This is crucial in understanding their role in regulating gene expression in Mtbandin targeting WhiB proteins as a drug target to cure TB.

Keywords: mycobacterium tuberculosis, TB, whiB proteins, ITC

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Authors: Zia Ullah, Muhammad Asim, Shi Sujuan, Rayyan Khan, Aaqib Shaheen, LIU Haobao

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The plant-specific auxin efflux proteins PIN-FORMED (PIN) have been well depicted in many plant species for their essential roles in regulating the transport of auxins in several phases of plant growth. Little is known about the various functions of the PIN family genes in the Nicotiana tabacum (N. tabacum) species during plant growth. To define the expression pattern of the NtPIN1a gene under abiotic stresses and hormone treatment, transgenic tobacco with promoterNtPIN1a::GUS construct was employed. Comprehensive computational analyses of the NtPIN1a promoter confirmed the existence of common core promoter elements including CAAT-box, TATA-box, hormone, and abiotic stress-responsive elements such as ABRE, P-box, MYC, MYB, ARE, and GC-motifs. The transgenic plants with the promoter of NtPIN1a displayed a promising expression of β-glucuronidase (GUS) in germinating seeds, root tips, shoot-apex, and developing leaves under optimal conditions. While the differential expression of GUS in moderate salt, drought, low potassium stresses, and externally high auxin level at two different time points, suggested NtPIN1a played a key role in growth processes and the plants’ response to abiotic stresses. This analysis provides a foundation for more in-depth discoveries of the biological functions of NtPIN1a in Nicotiana species and this promoter may be employed in genetic engineering of other crops for enhanced stress tolerance.

Keywords: tobacco, nicotiana tabacum, pin, promoter, GUS, abiotic stresses, auxin

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Authors: Siti Aishah Hasbullah

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Studies on identification of pork content in food have grown rapidly to meet the Halal food standard in Malaysia. The used mitochondria DNA (mtDNA) approaches for the identification of pig species is thought to be the most precise marker due to the mtDNA genes are present in thousands of copies per cell, the large variability of mtDNA. The standard method commonly used for DNA detection is based on polymerase chain reaction (PCR) method combined with gel electrophoresis but has major drawback. Its major drawbacks are laborious, need longer time and toxic to handle. Therefore, the need for simplicity and fast assay of DNA is vital and has triggered us to develop DNA biosensors for porcine DNA detection. Therefore, the aim of this project is to develop electrochemical DNA biosensor based on ruthenium (II) complex, [Ru(bpy)2(p-PIP)]2+ as DNA hybridization label. The interaction of DNA and [Ru(bpy)2(p-HPIP)]2+ will be studied by electrochemical transduction using Gold Screen-Printed Electrode (GSPE) modified with gold nanoparticles (AuNPs) and succinimide acrylic microspheres. The electrochemical detection by redox active ruthenium (II) complex was measured by cyclic voltammetry (CV) and differential pulse voltammetry (DPV). The results indicate that the interaction of [Ru(bpy)2(PIP)]2+ with hybridization complementary DNA has higher response compared to single-stranded and mismatch complementary DNA. Under optimized condition, this porcine DNA biosensor incorporated modified GSPE shows good linear range towards porcine DNA.

Keywords: gold, screen printed electrode, ruthenium, porcine DNA

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Authors: Navkiran Kaur, Apoorva Mathur, Abhishree Agarwal, Sakshi Gupta, Tuhin Rashmi

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Aim: Breast cancer is the most common cancer in women worldwide, and resistance to the current therapeutics, often concurrently, is an increasing clinical challenge. Glycosylation of proteins is one of the most important post-translational modifications. It is widely known that aberrant glycosylation has been implicated in many different diseases due to changes associated with biological function and protein folding. Alterations in cell surface glycosylation, can promote invasive behavior of tumor cells that ultimately lead to the progression of cancer. In breast cancer, there is an increasing evidence pertaining to the role of glycosylation in tumor formation and metastasis. In the present study, an attempt has been made to study the disease associated sialoglycoproteins in breast cancer by using bioinformatics tools. The sequence will be retrieved from UniProt database. A database in the form of a word document was made by a collection of FASTA sequences of breast cancer gene sequence. Glycosylation was studied using yinOyang tool on ExPASy and Differential genes expression and protein analysis was done in context of breast cancer metastasis. The number of residues predicted O-glc NAc threshold containing 50 aberrant glycosylation sites or more was detected and recorded for individual sequence. We found that the there is a significant change in the expression profiling of glycosylation patterns of various proteins associated with breast cancer. Differential aberrant glycosylated proteins in breast cancer cells with respect to non-neoplastic cells are an important factor for the overall progression and development of cancer.

Keywords: breast cancer, bioinformatics, cancer, metastasis, glycosylation

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Authors: Sadaf Ilyas, Saba Riaz

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The extensive use of antibiotics has led to increases emergence of antibiotic-resistant organisms. Pseudomonas is a notorious opportunistic pathogen involoved in nosocomial infections and exhibit innate resistance to many antibiotics. The present study was conducted to assess the prevalence, levels of antimicrobial susceptibility and resistance mechanisms of Pseudomonas. A total of thirty clinical strains of Pseudomonas were isolated from different clinical sites of infection. All clinical specimens were collected from Chughtais Lahore Lab. Jail road, during 8-07-2010 to 11-01-2011. Biochemical characterization was done using routine biochemical tests. Antimicrobial susceptibility was determined by Kirby-Baeur method. The plasmids were isolated from all the strains and digested with restriction enzyme PstI and EcoRI. Transfer of Multi-resistance plasmid was checked via transformation and conjugation to confirm the plasmid mediated resistance to antibiotics. The prevalence of Pseudomonas in clinical specimens was found out to be 14% of all bacterial infections. IPM has shown to be the most effective drug against Pseudomonas followed by CES, PTB and meropenem, wheareas most of the Pseudomonas strains have developed significant resistance against Penicillins and some Cephalasporins. Antibiotic resistance determinants were carried by plasmids, as they conferred resistance to transformed K1 strains. The isolates readily undergo conjugation, transferring the resistant genes to other strains, illustrating the high rates of cross infection and nosocomial infection in the immunocompromised patients.

Keywords: pseudomonas, antibiotics, drug resistance, horizontal gene transfer

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Authors: Yan-Shiang Chiou, Yi-Huang Hsueh

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Bacillus cereus is a foodborne pathogen that causes two types of foodborne illness, the emetic and diarrheal syndromes. B. cereus consistently ranks among the top three among bacterial foodborne outbreaks in the ten years of 2001 to 2010 in Taiwan. Foodborne outbreak caused by B. cereus has been increased, and recently it ranks second foodborne pathogen after Vibrio parahaemolyticus. This pathogen is difficult to control due to its ubiquitousness in the environment, the psychrotrophic nature of many strains, and the heat resistance of their spores. Because complete elimination of biofilms is difficult, a better understanding of the molecular mechanisms of biofilm formation by B. cereus will help to develop better strategies to control this pathogen. Surface translocation can be an important factor in biofilm formation. In B. cereus, NprR is a quorum sensor, and its apo NprR is a dimer and changes to a tetramer in the presence of NprX. The small peptide NprX may induce conformational change allowing the apo dimer to switch to an active tetramer specifically recognizing target DNA sequences. Our result showed that mutation of nprRX causes surface spreading deficiency. Mutation of flagella, pili and surfactant genes (flgAB, bcpAB, krsABC), did not abolish spreading motility. Under nprRX mutant, mutation of spo0A restored the spreading deficiency. This suggests that spreading motility is not related surfactant, pili and flagella but other unknown mechanism and Spo0A, a sporulation initiation protein, inhibits spreading motility.

Keywords: Bacillus cereus, nprRX, spo0A, spreading motility

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Authors: Manaphol Kulpraneet, Anirut Limtrakul, Surangrat Srisurapanon, Piyatida Tangteerawatana

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Tuberculosis (TB) remains a global health care disease world-wide. Control of the global TB epidemic has been impaired by the lack of an effective vaccine, by the emergence of drug resistant forms of Mycobacterium tuberculosis and by lack of sensitive and rapid diagnostics. Cytokines play a major role in defense against M. tuberculosis infection. Polymorphisms in the genes encoding various cytokines have been associated with tuberculosis susceptibility. Polymorphisms of the regulatory cytokine gene, the interleukin (IL)-10 is associated with the risk of tuberculosis (TB) in different populations. However, IL-10 gene polymorphism and susceptibility to TB in Thai is still unknown. The purpose of this study was to evaluate whether the common IL-10 promoter gene polymorphisms are associated with TB in Thai population. Forty eight patients with newly diagnosed pulmonary tuberculosis were studied. DNA samples were extracted from leukocytes and used to investigate -1087A/G, -819C/T, -252C/A (rs1800896, rs1800871, rs1800872) in IL-10 gene using restriction fragment length polymorphism (PCR-RFLP) methods. In this study, the genotype and allele frequencies of IL-10-1087A/G, -819C/T, -252C/A polymorphism did not significantly different between TB patients and healthy controls ((genotype: p=0.38, p=0.92, p=1; allele: p=0.57, p=0.77, p=0.89, respectively). The lack of association between common IL-10 promoter polymorphisms and TB susceptibility in this study may provide clue for better understanding of IL-10-1087A/G, -819C/T, -252C/A polymorphism and TB susceptibility in Thai population, which might facilitate the rationale design of vaccines. However, further studies in large scales population are required for confirmation.

Keywords: IL-10, cytokines, single nucleotide polymorphism (SNP), tuberculosis

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Authors: Rohit Singh Dangi, Ravi Kant Pal, Monica Sundd

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Acyl-CoA binding protein (ACBP) is a housekeeping protein which functions as an intracellular carrier of acyl-CoA esters. Given the fact that the amastigote stage (blood stage) of Leishmania depends largely on fatty acids as the energy source, of which a large part is derived from its host, these proteins might have an important role in its survival. In Leishmania major, genome sequencing suggests the presence of six ACBPs, whose function remains largely unknown. For functional and structural characterization, one of the ACBP genes was cloned, and the protein was expressed and purified heterologously. Acyl-CoA ester binding and stoichiometry were analyzed by isothermal titration calorimetry and Dynamic light scattering. Our results shed light on high affinity of ACBP towards longer acyl-CoA esters, such as myristoyl-CoA to arachidonoyl-CoA with single binding site. To understand the binding mechanism & dynamics, Nuclear magnetic resonance assignments of this protein are being done. The protein's crystal structure was determined at 1.5Å resolution and revealed a classical topology for ACBP, containing four alpha-helical bundles. In the binding pocket, the loop between the first and the second helix (16 – 26AA) is four residues longer from other extensively studied ACBPs (PfACBP) and it curls upwards towards the pantothenate moiety of CoA to provide a large tunnel space for long acyl chain insertion.

Keywords: acyl-coa binding protein (ACBP), acyl-coa esters, crystal structure, isothermal titration, calorimetry, Leishmania

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Authors: Lauren M. McKinnon, Justin B. Miller, Michael F. Whiting, John S. K. Kauwe, Perry G. Ridge

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Background: Ramp sequences increase translational speed and accuracy when rare, slowly-translated codons are found at the beginnings of genes. Here, the results of the first analysis of ramp sequences in a phylogenetic construct are presented. Methods: Ramp sequences were compared from 211 vertebrates (110 Mammalian and 101 non-mammalian). The presence and absence of ramp sequences were analyzed as a binary character in a parsimony and maximum likelihood framework. Additionally, ramp sequences were mapped to the Open Tree of Life taxonomy to determine the number of parallelisms and reversals that occurred, and these results were compared to what would be expected due to random chance. Lastly, aligned nucleotides in ramp sequences were compared to the rest of the sequence in order to examine possible differences in phylogenetic signal between these regions of the gene. Results: Parsimony and maximum likelihood analyses of the presence/absence of ramp sequences recovered phylogenies that are highly congruent with established phylogenies. Additionally, the retention index of ramp sequences is significantly higher than would be expected due to random chance (p-value = 0). A chi-square analysis of completely orthologous ramp sequences resulted in a p-value of approximately zero as compared to random chance. Discussion: Ramp sequences recover comparable phylogenies as other phylogenomic methods. Although not all ramp sequences appear to have a phylogenetic signal, more ramp sequences track speciation than expected by random chance. Therefore, ramp sequences may be used in conjunction with other phylogenomic approaches.

Keywords: codon usage bias, phylogenetics, phylogenomics, ramp sequence

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Authors: Donatella Cimini, Sergio D’ambrosio, Saba Sadiq, Chiara Schiraldi

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Chondroitin sulfate (CS), as well as modified CS, and unsulfated chondroitin, are largely applied in research today. CS is a linear glycosaminoglycan normally present in cartilage-rich tissues and bones in the form of proteoglycans decorated with sulfate groups in different positions. CS is used as an effective non-pharmacological alternative for the treatment of osteoarthritis, and other potential applications in the biomedical field are being investigated. Some bacteria, such as E. coli K4, produce a polysaccharide that is a precursor of CS (unsulfated chondroitin). This work focused on the construction of integrative E. coli K4 recombinant strains overexpressing genes (kfoA, kfoF, pgm and galU in different combinations) involved in the biosynthesis of the nucleotide sugars necessary for polysaccharide synthesis. Strain growth and polymer production were evaluated using renewable waste materials as substrates in shake flasks and small-scale batch fermentation processes. Results demonstrated the potential to replace pure sugars with cheaper medium components to establish environmentally sustainable and cost-effective production routes for potential industrial development. In fact, although excellent fermentation results have been described so far by employing strains that naturally produce chondroitin-like polysaccharides on semi-defined media, there is still the need to reduce manufacturing costs by providing a cost-effective biotechnological alternative to currently used animal-based extraction procedures.

Keywords: E. coli K4, chondroitin, microbial cell factories, glycosaminoglycans, renewable resources

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Authors: Abu Salim Mustafa

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Water plays a major role in maintaining life on earth, but it can also serve as a matrix for pathogenic organisms, posing substantial health threats to humans. Although, outbreaks of diseases attributable to drinking water may not be common in industrialized countries, they still occur and can lead to serious acute, chronic, or sometimes fatal health consequences. The analysis of drinking water samples from different regions of Kuwait was performed in this study for bacterial and viral contaminations. Drinking tap water samples were collected from 15 different locations of the six Kuwait governorates. All samples were analyzed by confocal microscopy for the presence of bacteria. The samples were cultured in vitro to detect cultivable organisms. DNA was isolated from the cultured organisms and the identity of the bacteria was determined by sequencing the bacterial 16S rRNA genes, followed by BLAST analysis in the database of NCBI, USA. RNA was extracted from water samples and analyzed by real-time PCR for the detection of viruses with potential health risks, i.e. Astrovirus, Enterovirus, Norovirus, Rotavirus, and Hepatitis A. Confocal microscopy showed the presence of bacteria in some water samples. The 16S rRNA gene sequencing of culture grown organisms, followed by BLAST analysis, identified the presence of several non-pathogenic bacterial species. However, one sample had Acinetobacter baumannii, which often causes opportunistic infections in immunocompromised people, but none of the studied viruses could be detected in the drinking water samples analyzed. The results indicate that drinking water samples analyzed from various locations in Kuwait are relatively safe for drinking and do not contain many harmful pathogens.

Keywords: drinking water, microbial contaminant, 16S rDNA, Kuwait

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Authors: Andrew Thayer, Courtney Rondeau, Paraskevi Papadopoulou

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The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) gene-editing technologies have generated considerable discussion about the applications and ethics of their use. However, no consistent guidelines for using CRISPR technologies have been developed -nor common legislation passed related to gene editing, especially as it is connected to genetically modified organisms (GMOs) in the European Union. The recent announcement that the first babies with CRISPR-edited genes were born, along with new studies exploring CRISPR’s applications in treating thalassemia, sickle-cell anemia, cancer, and certain forms of blindness, have demonstrated that the technology is developing faster than the policies needed to control it. Therefore, it can be seen that a reasonable and coherent regulatory framework for the use of CRISPR in human somatic and germline cells is necessary to ensure the ethical use of the technology in future years. The European Union serves as a unique region of interconnected countries without a standard set of regulations or legislation for CRISPR gene-editing. We posit that the EU would serve as a suitable model in comparing the legislations of its affiliated countries in order to understand the practicality and effectiveness of adopting majority-approved practices. Additionally, we present a proposed set of guidelines which could serve as a basis in developing a consistent regulatory framework for the EU countries to implement but also act as a good example for other countries to adhere to. Finally, an additional, multidimensional framework of smart solutions is proposed with which all stakeholders are engaged to become better-informed citizens.

Keywords: CRISPR, ethics, regulatory framework, European legislation

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Authors: Ngoc Tu Truong, Nuong T. Bui, Ben Rao, Ya L. Shen

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Quorum sensing is a phenomenon present in many gram-negative bacteria that allows bacterial communication and controlled expression of a large suite of genes through quorum sensing signals - N-acyl homoserine lactones (AHLs). In order to investigate the ability of the rhlR/rhlI quorum sensing system in Pseudomonas aeruginosa to express the ß-Galactosidase reporter gene, an engineered E. coli strain EpHL02, was genetically engineered. This engineered E. coli strain EpHL02 responded to the presence of the N-butanoyl homoserine lactone and N-hexanoyl homoserine lactone to express the ß-Galactosidase reporter gene at a concentration limit of 5x10⁻⁸ M. This was also found to be comparable to AHLs extraction from Serratia marcescens H31. Moreover, we examined this ability of this engineered E. coli strain for respond of AHLs from extractions of Pseudomonas aeruginosa ATCC9027. The results demonstrated that the rhlR/rhlI quorum sensing system can express the ß-Galactosidase reporter gene by using the N-butanoyl homoserine lactone, N-hexanoyl homoserine lactone and AHLs from extractions of Serratia marcescens H31 and Pseudomonas aeruginosa ATCC9027 in the engineered E. coli strain EpHL02.

Keywords: N-butanoyl homoserine lactone, C4-HSL, N-hexanoyl homoserine lactone, C6-HSL, Pseudomonas aeruginosa, quorum sensing, Serratia marcescens, ß-galactosidase reporter gene

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Authors: Nunthawan Nowwarote, Waleerat Sukarawan, Prasit Pavasant, Thanaphum Osathanon

Abstract:

Interleukin 6 (IL-6) is a multifunctional cytokine, regulating various biological responses in several tissues. A Recent study shows that IL-6 plays a role in stemness maintenance in stem cells isolated from human exfoliated deciduous teeth (SHEDs). However, the role of IL-6 on cell differentiation in SHEDs remains unknown. The present study investigated the effect of IL-6 on SHEDs differentiation. Cells were isolated from dental pulp tissues of human deciduous teeth. Flow cytometry was used to determined mesenchymal stem cell marker expression, and the multipotential differentiation (osteogenic, adipogenic and neurogenic lineage ) was also determined. The mRNA was determined using real-time quantitative polymerase chain reaction, and the phenotypes were confirmed by chemical and immunofluorescence staining. Results demonstrated that SHEDs expressed CD44, CD73, CD90, CD105 but not CD45. Further, the up-regulation of osteogenic, adipogenic and neurogenic marker genes was observed upon maintaining cells in osteogenic, adipogenic and neurogenic induction medium, respectively. The addition of IL-6 induced osteogenic by up-regulated osteogenic marker gene also increased in vitro mineralization. Under neurogenic medium supplement with IL-6, up-regulated neurogenic marker. Whereas, an addition of IL-6 attenuated adipogenic differentiation by SHEDs. In conclusion, this evidence implies that IL-6 may participate in cells differentiation ability of SHEDs.

Keywords: SHEDs, IL-6, cell differentiations, dental pulp

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Authors: Akeem Akinboro, Bala Alhaj Kegun

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Haemoglobinopathy is a genetic disorder that has the potentiality to cause death of individuals in whom both the alpha (α) and beta (β) globin chains of the haemoglobin molecule are defective due to mutations in their genes. The haemoglobin genotype variants among some residents of Niger state, Nigeria, were determined using the secondary data available at Bida, Minna and Kotangora general hospitals of the state. A total of 1,639 data, representing 434, 655 and 550, collected from the outside patients who visited the medical laboratory units of the three general hospitals, respectively, over five years period (2015-2020) were analyzed into gene frequency, sex and age to determine their haemoglobin genotypes status. More males (51.6 – 58.7%) than females (41.3 – 48.4%) visited the three hospitals during the period covered and most of the patients were between 11 - 20 years old. The frequency of HbA allele in the human population was 0.72, 0.65, 0.68 for Bida, Minna and Kotangora, respectively, while it was 0.25, 0.29 and 0.28 for HbS allele. The HbC allele was prevalent at 0.03, 0.06 and 0.05 among the human population in Bida, Minna and Kotangora cities of Niger state. In overall, the prevalence of HbA, HbS and HbC alleles in Niger state of Nigeria was 0.68, 0.28 and 0.05. Minna being the capital city of Niger state and the most populous among the three cities in the state seems to have influx of more people who are carriers of abnormal haemoglobin genotypes which has resulted to higher frequency of HbS and HbC than those of the other two cities in this study. These results show that the pattern of haemoglobin genotypes frequency of Kontagora could be a prediction for the whole of Niger state. It is therefore necessary and important to take screening of blood for haemoglobin genotype serious among intending couples to prevent and reduce the possibility of having increase in the number of people with abnormal haemoglobin genotypes in the state.

Keywords: haemoglobin, genotype, niger state, gene frequency, general hospitals

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Authors: Don Buddika Oshadi Malaweera, Lora Harris, Bruce Rathgeber, Chibuike C. Udenigwe, Kirsti Rouvinen-Watt

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Fatty liver disease is among the three most severe health concerns for mink and believed to occur through the same mechanism as nursing sickness. In North America, nursing sickness affects about 45% of mink farms and in Canada, approximately 50,000 mink females is affected annually. Orotic acid (OA) plays a critical role in lipid metabolism and can increase hepatic lipids by enhancing Sterol regulatory element binding protein-1c expression and decreasing Carnitine palmitoyl transferase I activity. This study was conducted to identify particular pathways and regulatory control points involved in fatty liver development, and evaluate the effectiveness of arginine and bioactive peptides for prevention and treatment of fatty liver disease in mink. A total of 45 mink were used in 9 treatments. The experimental diets consisted of 1% OA, 2% L-arginine and 5% of whey protein hydrolysates. At the end of 10 days of experimental period, the mink were anaesthetized, sampled for blood and euthanized, samples were obtained for histological, biochemical and molecular assays. The blood samples will be analyzed for clinical chemistry and triacylglycerol. The liver samples will be analyzed for total lipid content and analyzed for 6 genes of interest involved in adipogenic transformation, ER stress, and liver inflammation.

Keywords: fatty liver, L-arginine, mink, orotic acid, whey protein hydrolysates

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Authors: Piotr J. Balwierz, Mikhail Pachkov, Phil Arnold, Andreas J. Gruber, Mihaela Zavolan, Erik van Nimwegen

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Understanding the key players and interactions in the regulatory networks that control gene expression and chromatin state across different cell types and tissues in metazoans remains one of the central challenges in systems biology. Our laboratory has pioneered a number of methods for automatically inferring core gene regulatory networks directly from high-throughput data by modeling gene expression (RNA-seq) and chromatin state (ChIP-seq) measurements in terms of genome-wide computational predictions of regulatory sites for hundreds of transcription factors and micro-RNAs. These methods have now been completely automated in an integrated webserver called ISMARA that allows researchers to analyze their own data by simply uploading RNA-seq or ChIP-seq data sets and provides results in an integrated web interface as well as in downloadable flat form. For any data set, ISMARA infers the key regulators in the system, their activities across the input samples, the genes and pathways they target, and the core interactions between the regulators. We believe that by empowering experimental researchers to apply cutting-edge computational systems biology tools to their data in a completely automated manner, ISMARA can play an important role in developing our understanding of regulatory networks across metazoans.

Keywords: gene expression analysis, high-throughput sequencing analysis, transcription factor activity, transcription regulation

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Authors: Peter John, Zainab Ali, Attya Bhatti

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Rheumatoid Arthritis (RA) is a systemic autoimmune inflammatory disease that primarily affects the joints. RA is caused in many cases by the interaction between genes and environmental factors, including tobacco, that primarily involves synovial joints. It typically starts in small peripheral joints, is usually symmetric, and progresses to involve proximal joints if left untreated. The prevalence of rheumatoid arthritis varies substantially around the globe, ranging from 0·25% to 1%.3. Rheumatoid arthritis can affect individuals of any age, with an increased incidence in people older than 40 years. Women are affected two to three times more frequently than men. The present work involved evaluating the toxicity and therapeutic potential of Dodonaea viscosa in a collagen-induced arthritic mouse model. Chemical analysis exhibited that Dodonaea viscosa has high levels of beneficial compounds, including phenols, flavonoids, and other phytochemicals. The Dodonaea viscosa showed significant antioxidant, anti-inflammatory, and anti-arthritic potential without toxic effects. Arthritic mice treated with Dodonaea viscosa showed reduced levels of rheumatoid factor and paw edema, while no significant effects on spleen indices and radiological examination of paws were found compared to control untreated arthritic mice. In summary, the Dodonaea viscosa treatment results in improvement in Arthritic Mice Model for which further studies are required.

Keywords: rheumatoid arthritis, dodonaea viscisa, anti-inflammatory, anti-rheumatic

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Authors: Meenakshi Srivastava, A. K. Mishra

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This study characterizes the metabolic versatility of denitrifying bacterial communities residing in the paddy soil using the GC-MS based Phospholipid Fatty Acid (PLFA) analyses simultaneously with nosZ gene based PCR-DGGE (Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis) and real time Q-PCR analysis. We have analyzed the abundance of nitrous oxide reductase (nosZ) genes, which was subsequently related to soil PLFA profile and DGGE based denitrifier community structure. Soil denitrifying bacterial community comprised majority or dominance of Ochrobactrum sp. following Cupriavidus and uncultured bacteria strains in paddy soil of selected sites. Initially, we have analyzed the abundance of the nitrous oxide reductase gene (nosZ), which was found to be related with PLFA based lipid profile. Chandauli of Eastern UP, India represented greater amount of lipid content (C18-C20) and denitrifier’s diversity. This study suggests the positive co-relation between soil PLFA profiles, DGGE, and Q-PCR data. Thus, a close networking among metabolic abilities and taxonomic composition of soil microbial communities existed, and subsequently, such work at greater extent could be helpful in managing nutrient dynamics as well as microbial dynamics of paddy soil ecosystem.

Keywords: denaturing gradient gel electrophoresis, DGGE, nitrifying and denitrifying bacteria, PLFA, Q-PCR

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Authors: Mehrnoosh Azimi Sanavi, Hamed Ghazvini, Mehryar Zargari, Hossein Ghalehnoei, Zahra Hosseini-khah

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Objectives: Calcium Voltage-Gated Channel Subunit Alpha1 C (CACNA1C) is one of the most important genes associated with schizophrenia. Methods: 45 male Wistar rats were divided into 5 groups: saline, control, ketamine, clozapine, and risperidone. Animals in ketamine, risperidone, and clozapine groups received ketamine (30 mg/ kg-i.p.) for 10 days. After the last injection of ketamine, we started injecting clozapine (7.5 mg/kg-i.p.) risperidone (1 mg/kg-i.p.) for up to 28 days. Twenty-four hours after the last injection, open field, social interaction, and elevated plus-maze tests, and gene expression in the hippocampus were performed. Results: The results of the social interaction test revealed a significant decrease in cumulative time with ketamine compared with the saline group and an increase with clozapine and risperidone compared with the ketamine group. Moreover, results from the elevated plus-maze test demonstrated a critical decrease in open-arm time and an increase in close-arm time with ketamine compared with saline, as well as an increase in open-arm time with risperidone compared with ketamine. Further results revealed a significant increase in rearing and grooming with ketamine compared to saline, as well as a decrease with risperidone and clozapine compared to ketamine. There were no significant differences in CACNA1C gene expression between groups in the rat hippocampus. In brief, the results of this study indicated that clozapine and risperidone could partially improve cognitive impairments in the rat. However, our findings demonstrated that this treatment is not related to CACNA1C gene expression.

Keywords: schizophrenia, ketamine, clozapine, risperidone

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