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https://www.readbyqxmd.com/read/28330294/immuno-hybrid-algorithm-a-novel-hybrid-approach-for-grn-reconstruction
#1
A S Jereesh, V K Govindan
Bio-inspired algorithms are widely used to optimize the model parameters of GRN. In this paper, focus is given to develop improvised versions of bio-inspired algorithm for the specific problem of reconstruction of gene regulatory network. The approach is applied to the data set that was developed by the DNA microarray technology through biological experiments in the lab. This paper introduced a novel hybrid method, which combines the clonal selection algorithm and BFGS Quasi-Newton algorithm. The proposed approach implemented for real world E...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330283/multiplex-pcr-for-simultaneous-identification-of-e-coli-o157-h7-salmonella-spp-and-l-monocytogenes-in-food
#2
Thuy Trang Nguyen, Vo Van Giau, Tuong Kha Vo
The rapid detection of pathogens in food is becoming increasingly critical for ensuring the safety of consumers, since the majority of food-borne illnesses and deaths are caused by pathogenic bacteria. Hence, rapid, sensitive, inexpensive and convenient approaches to detect food-borne pathogenic bacteria is essential in controlling food safety. In this study, a multiplex PCR assay for the rapid and simultaneous detection of Escherichia coli O157:H7, Salmonella spp. and Listeria monocytogenes was established...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330282/in-vitro-cytotoxicity-and-antibacterial-activity-of-silver-coated-electrospun-polycaprolactone-gelatine-nanofibrous-scaffolds
#3
Mim Mim Lim, Naznin Sultana
The development of nano-sized scaffolds with antibacterial properties that mimic the architecture of tissue is one of the challenges in tissue engineering. In this study, polycaprolactone (PCL) and PCL/gelatine (Ge) (70:30) nanofibrous scaffolds were fabricated using a less toxic and common solvent, formic acid and an electrospinning technique. Nanofibrous scaffolds were coated with silver (Ag) in different concentrations of silver nitrate (AgNO3) aqueous solution (1.25, 2.5, 5, and 10 %) by using dipping method, drying and followed by ultraviolet (UV) photoreduction...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330270/expression-and-purification-of-a-gene-encoding-a-9-7%C3%A2-kda-pe-protein-of-mycobacterium-avium-subsp-paratuberculosis
#4
S Chandra Sekar, P P Goswami, R Deb
Mycobacterium avium subsp. paratuberculosis (Map) contains PE family antigens which are Proline and glutamic acid rich and may play important role as T-cell antigens. In the present study, the Map 1507 ORF encoding 9.7 kDa PE protein was amplified by polymerase chain reaction and cloned into E. coli vector pQE30 UA. The recombinant plasmid designated as pQ PE was transformed into E. coli M15 cells and induced with IPTG revealed the high level expression of 11.9 kDa His-fusion protein as estimated by migration in 15 % sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE)...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330248/photo-inactivation-of-escherichia-coli-and-enterococcus-hirae-using-methylene-blue-and-sodium-anthraquinone-2-sulphonate-effect-of-process-parameters
#5
Madhavi Singh, Kannan Pakshirajan, Vishal Trivedi
In this study, effect of different parameters, viz. concentration of photosensitizer (PS), pH of the bacterial cell suspension and initial cell count, on photo-inactivation of Escherichia coli and Enterococcus hirae bacteria using methylene blue (MB) and sodium anthraquinone-2-sulphonate (SAQS) was investigated employing the statistically valid full factorial design of experiments. The inactivation efficiency of E. hirae using MB ranges between 10.81 and 48.55 %, whereas in the case of E. coli it ranges between 10...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330241/purification-characterization-gene-cloning-and-expression-of-gh-10-xylanase-penicillium-citrinum-isolate-hzn13
#6
Zabin K Bagewadi, Sikandar I Mulla, Harichandra Z Ninnekar
An extracellular thermostable xylanase (Xyl-IIb) produced by Penicillium citrinum isolate HZN13 was purified to homogeneity using DEAE-Sepharose, Sephadex G-100 and Bio-Gel P-60 chromatography with specific activity of 6272.7 U/mg and 19.6-fold purification. The purification revealed the occurrence of multiple forms of xylanases (Xyl-I, Xyl-IIa, Xyl-IIb and Xyl-III). The molecular mass of highly purified Xyl-IIb was ~31 kDa with SDS-PAGE. The enzyme was cellulase-free, thermostable (55-75 °C) and acidophilic (3...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330118/cloning-expression-purification-and-characterization-of-lipase-from-bacillus-licheniformis-isolated-from-hot-spring-of-himachal-pradesh-india
#7
Gagandeep Kaur, Amninder Singh, Rohit Sharma, Vinay Sharma, Swati Verma, Pushpender K Sharma
In the present investigation, a gene encoding extracellular lipase was cloned from a Bacillus licheniformis. The recombinant protein containing His-tag was expressed as inclusion bodies in Esherichia coli BL21DE3 cells, using pET-23a as expression vector. Expressed protein purified from the inclusion bodies demonstrated ~22 kDa protein band on 12 % SDS-PAGE. It exhibited specific activity of 0.49 U mg(-1) and % yield of 8.58. Interestingly, the lipase displayed activity at wide range of pH and temperature, i...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330113/protein-fusion-tags-for-efficient-expression-and-purification-of-recombinant-proteins-in-the-periplasmic-space-of-e-coli
#8
REVIEW
Ajamaluddin Malik
Disulfide bonds occurred in majority of secreted protein. Formation of correct disulfide bonds are must for achieving native conformation, solubility and activity. Production of recombinant proteins containing disulfide bond for therapeutic, diagnostic and various other purposes is a challenging task of research. Production of such proteins in the reducing cytosolic compartment of E. coli usually ends up in inclusion bodies formation. Refolding of inclusion bodies can be difficult, time and labor consuming and uneconomical...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330075/a-novel-multiplex-pcr-method-for-the-detection-of-virulence-associated-genes-of-escherichia-coli-o157-h7-in-food
#9
Vo Van Giau, Thuy Trang Nguyen, Thi Kim Oanh Nguyen, Thi Thuy Hang Le, Tien Dung Nguyen
Shiga toxin-producing Escherichia coli O157:H7 (E. coli O157:H7) strains are foodborne infectious agents that cause a number of life-threatening diseases, including hemorrhagic colitis (HC) and hemolytic uremic syndrome (HUS). Shiga toxin 1 (stx1), shiga toxin 2 (stx2), or a combination of both are responsible for most clinical symptoms of these diseases. Hence, various diagnostic methods have been developed so far to detect shiga toxins such as cell culture, ELISA, Rapid Latex Agglutination (RPLA) and hybridization, but due to high costs and labor time in addition to low sensitivity, they have not received much attention...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28330072/molecular-dynamic-simulations-of-escherichia-coli-l-asparaginase-to-illuminate-its-role-in-deamination-of-asparagine-and-glutamine-residues
#10
Rajeswara Reddy Erva, Satish Babu Rajulapati, Chandrasai Potla Durthi, Mayuri Bhatia, Madhuri Pola
Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. L-Asparagine (L-Asn) and L-Glutamine (L-Gln) deamination play a crucial role in ALL treatment. Role of Elspar(®) (L-asparaginase from Escherichia coli) in regulation of L-Asn and L-Gln has been confirmed by the other researchers through experimental studies. Therapeutic research against ALL remained elusive with the lack of information on molecular interactions of Elspar(®) with amino acid substrates. In the present study, using different docking tools binding cavities, key residues in binding and ligand binding mechanisms were identified...
June 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329448/a-novel-nhad-type-na-h-antiporter-from-the-moderate-halophile-and-alkaliphile-halomonas-alkaliphila
#11
Yanhong Wang, Na Song, Lina Yang, Heba Abdel-Motaal, Rui Zhang, Zhenglai Zhang, Fankui Meng, Juquan Jiang
In this study, a NhaD-type Na+/H+ antiporter gene designated Ha-nhaD was obtained by selection of genomic DNA from the moderate halophile and alkaliphile Halomonas alkaliphila in Escherichia coli KNabc lacking three major Na+/H+ antiporters. The presence of Ha-NhaD conferred tolerance of E. coli KNabc to up to 0.6 M NaCl and 0.2 M LiCl and an alkaline pH. pH-dependent Na+(Li+)/H+ antiport activity was detected from everted membrane vesicles prepared from E. coli KNabc/pUC-nhaD but not those from KNabc/pUC18...
March 22, 2017: Canadian Journal of Microbiology
https://www.readbyqxmd.com/read/28329394/intermediate-follow-up-of-pediatric-patients-with-hemolytic-uremic-syndrome-during-the-2011-outbreak-caused-by-e-coli-o104-h4
#12
Sebastian Loos, Wiebke Aulbert, Bernd Hoppe, Thurid Ahlenstiel-Grunow, Birgitta Kranz, Charlotte Wahl, Hagen Staude, Alexander Humberg, Kerstin Benz, Martin Krause, Martin Pohl, Max C Liebau, Raphael Schild, Johanna Lemke, Ortraud Beringer, Dominik Müller, Christoph Härtel, Marianne Wigger, Udo Vester, Martin Konrad, Dieter Haffner, Lars Pape, Jun Oh, Markus J Kemper
Background.: In 2011 Escherichia coli O104:H4 caused an outbreak with over 800 cases of hemolytic uremic syndrome (HUS) in Germany, including 90 children. Data on the intermediate outcome in children after HUS due to E. coli O104:H4 have been lacking. Methods.: Follow-up data were gathered retrospectively from the medical records of patients who had been included in the German Pediatric HUS Registry during the 2011 outbreak. Results.: A total of 72/89 (81%) of the patients was included after a median follow-up of 3...
March 13, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/28328989/quorum-sensing-network-in-clinical-strains-of-a-baumannii-aida-is-a-new-quorum-quenching-enzyme
#13
María López, Celia Mayer, Laura Fernández-García, Lucía Blasco, Andrea Muras, Federico Martín Ruiz, German Bou, Ana Otero, María Tomás
Acinetobacter baumannii is an important pathogen that causes nosocomial infections generally associated with high mortality and morbidity in Intensive Care Units (ICUs). Currently, little is known about the Quorum Sensing (QS)/Quorum Quenching (QQ) systems of this pathogen. We analyzed these mechanisms in seven clinical isolates of A. baumannii. Microarray analysis of one of these clinical isolates, Ab1 (A. baumannii ST-2_clon_2010), previously cultured in the presence of 3-oxo-C12-HSL (a QS signalling molecule) revealed a putative QQ enzyme (α/ß hydrolase gene, AidA)...
2017: PloS One
https://www.readbyqxmd.com/read/28327560/revised-domain-structure-of-ulvan-lyase-and-characterization-of-the-first-ulvan-binding-domain
#14
Rebecca L J Melcher, Marten Neumann, Juan Pablo Fuenzalida Werner, Franziska Gröhn, Bruno M Moerschbacher
Biomass waste products from green algae have recently been given new life, as these polysaccharides have potential applications in industry, agriculture, and medicine. One such polysaccharide group called ulvans displays many different, potentially useful properties that arise from their structural versatility. Hence, performing structural analyses on ulvan is crucial for future applications. However, chemical reaction-based analysis methods cannot fully characterize ulvan and tend to alter its structure. Thus, better methods require well-characterized ulvan-degrading enzymes...
March 22, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28327423/characterization-of-an-extracellular-protein-rv1076-from-m-tuberculosis-with-a-potential-role-in-humoral-response
#15
Gurkamaljit Kaur, Bandana Kumari, Jagdeep Kaur
Many mycobacterial proteins involved in lipid metabolism are reported to be essential for survival and pathogenesis of M. tuberculosis. Rv1076 of M. tuberculosis has been annotated as a putative esterase/lipase based on the consensus sequence 'GXSXG'. It is conserved in all the mycobacterial species. Therefore, in the present study we have characterized Rv1076 gene product in detail. The gene rv1076 was expressed in E. coli and purified from inclusion bodies with approx. 40% yield. The protein showed high specific activity with pNP- butyrate as preferred substrate...
March 19, 2017: International Journal of Biological Macromolecules
https://www.readbyqxmd.com/read/28327306/design-synthesis-antibacterial-activity-and-docking-study-of-some-new-trimethoprim-derivatives
#16
Umer Rashid, Waqas Ahmad, Syed Fahad Hassan, Naveeda Akhtar Qureshi, Basit Niaz, Bakhtiar Muhammad, Sameera Imdad, Muhammad Sajid
In present study, nineteen novel trimethoprim (TMP) derivatives were designed, synthesized and evaluated for their antibacterial potential. Hydroxy trimethoprim 2 (HTMP) was synthesized by following the demethylation of 4-methoxy group at trimethoxy benzyl ring of TMP. Structure-activity relationship (SAR) studies were explored on HTMP by incorporating various substituents leading to the identification of some new compounds with improved antibacterial activities. The results revealed that the introduction of benzyloxy (4a-e) and phenyl ethanone (5a-e) group at 4-position of dimethoxy benzyl ring leads to overall increase in the antibacterial activity...
December 1, 2016: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28326812/evaluation-of-reticulated-gelatin-hibiscus-propolis-against-intestinal-commensal-species-commonly-associated-with-urinary-tract-infections
#17
Maïwenn Olier, Soraya Sekkal, Cherryl Harkat, Hélène Eutamene, Vassilia Theodorou
AIM: Reticulated gelatin (RG), hibiscus and propolis (RGHP) is a medical device that can reduce the bacterial adherence to epithelial cultured cells and invasion by enteropathogens, thus gathering relevant properties to decrease the risk of urinary tract infections (UTIs). We aimed at evaluating in Wistar rats the efficacy of RGHP, RG and vehicle against intestinal commensals commonly involved in UTIs. METHODS: Animals received orally (with supplemental Na2CO3): RGHP 1540 mg/day/rat; RG 500 mg/day/rat or vehicle...
March 3, 2017: Future Microbiology
https://www.readbyqxmd.com/read/28326614/recombinant-expression-of-porcine-spermadhesin-awn-and-its-phospholipid-interaction-indication-for-a-novel-lipid-binding-property
#18
F Schröter, K Müller, P Müller, E Krause, B C Braun
AWN is a porcine (Sus scrofa domestica) seminal plasma protein and has been linked to a variety of processes related to fertilization. To acquire the protein in sufficient amount and purity for functional studies, we established its recombinant expression in E. coli and a three-step purification protocol based on different chromatographies. The test for AWN-phospholipid interaction revealed phosphatidic acid and cardiolipin as potential binding partners. As phosphatidic acid is surmised to play a role in cation-induced membrane destabilization and fusion events, we propose a membrane protective function of the presented binding affinity...
March 21, 2017: Reproduction in Domestic Animals, Zuchthygiene
https://www.readbyqxmd.com/read/28326449/functional-analysis-of-the-minimal-twin-arginine-translocation-system-components-from-streptococcus-thermophilus-cgmcc-7-179-in-escherichia-coli-de3
#19
Chenchen Zhang, Tingting Guo, Yongping Xin, Susu Zhang, Xudong Ouyang, Ruixia Gu, Jian Kong
The twin-arginine translocation (Tat) system, which is used for folded protein secretion, is rare in lactic acid bacteria (LAB). Previously, a Tat system composed of TatAS and TatCS subunits (the subscript S denotes a Streptococcus thermophilus origin) was identified in S. thermophilus CGMCC 7.179. In the present study, the tatA S and tatC S genes were cloned and functionally analyzed in Escherichia coli DE3 tat-deficient mutants. The E. coli tatABCDE-deficient mutant complemented with tatC S A S exhibited shortened cellular chains, but its ability to grow in the presence of sodium dodecyl sulfate (SDS) was not restored, suggesting that the S...
March 22, 2017: Current Microbiology
https://www.readbyqxmd.com/read/28326322/a-comparison-of-tissue-engineering-scaffolds-incorporated-with-manuka-honey-of-varying-umf
#20
Katherine R Hixon, Tracy Lu, Sarah H McBride-Gagyi, Blythe E Janowiak, Scott A Sell
Purpose. Manuka honey (MH) is an antibacterial agent specific to the islands of New Zealand containing both hydrogen peroxide and a Unique Manuka Factor (UMF). Although the antibacterial properties of MH have been studied, the effect of varying UMF of MH incorporated into tissue engineered scaffolds have not. Therefore, this study was designed to compare silk fibroin cryogels and electrospun scaffolds incorporated with a 5% MH concentration of various UMF. Methods. Characteristics such as porosity, bacterial clearance and adhesion, and cytotoxicity were compared...
2017: BioMed Research International
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