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https://www.readbyqxmd.com/read/28416945/a-chip-seq-data-analysis-pipeline-based-on-bioconductor-packages
#1
Seung-Jin Park, Jong-Hwan Kim, Byung-Ha Yoon, Seon-Young Kim
Nowadays, huge volumes of chromatin immunoprecipitation-sequencing (ChIP-Seq) data are generated to increase the knowledge on DNA-protein interactions in the cell, and accordingly, many tools have been developed for ChIP-Seq analysis. Here, we provide an example of a streamlined workflow for ChIP-Seq data analysis composed of only four packages in Bioconductor: dada2, QuasR, mosaics, and ChIPseeker. 'dada2' performs trimming of the high-throughput sequencing data. 'QuasR' and 'mosaics' perform quality control and mapping of the input reads to the reference genome and peak calling, respectively...
March 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/28407026/streptococcal-adhesin-p-sadp-contributes-to-streptococcus-suis-adhesion-to-the-human-intestinal-epithelium
#2
Maria Laura Ferrando, Niels Willemse, Edoardo Zaccaria, Yvonne Pannekoek, Arie van der Ende, Constance Schultsz
BACKGROUND: Streptococcus suis is a zoonotic pathogen, causing meningitis and septicemia. We previously demonstrated that the gastrointestinal tract (GIT) is an entry site for zoonotic S. suis infection. Here we studied the contribution of Streptococcal adhesin Protein (SadP) to host-pathogen interaction at GIT level. METHODS: SadP expression in presence of Intestinal Epithelial Cells (IEC) was compared with expression of other virulence factors by measuring transcript levels using quantitative Real Time PCR (qRT-PCR)...
2017: PloS One
https://www.readbyqxmd.com/read/28377276/encapsulation-systems-for-the-delivery-of-hydrophilic-nutraceuticals-food-application
#3
REVIEW
N P Aditya, Yadira Gonzalez Espinosa, Ian T Norton
Increased health risk associated with the sedentary life style is forcing the food manufacturers to look for food products with specific or general health benefits e.g. beverages enriched with nutraceuticals like catechin, curcumin rutin. Compounds like polyphenols, flavonoids, vitamins are the good choice of bioactive compounds that can be used to fortify the food products to enhance their functionality. However due to low stability and bioavailability of these bioactives (both hydrophobic and hydrophilic) within the heterogeneous food microstructure and in the Gastro Intestinal Tract (GIT), it becomes extremely difficult to pass on the real health benefits to the consumers...
April 1, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28339527/microbial-community-mapping-in-intestinal-tract-of-broiler-chicken
#4
Yingping Xiao, Yun Xiang, Weidong Zhou, Jinggang Chen, Kaifeng Li, Hua Yang
Domestic chickens are valuable sources of protein associated with producing meat and eggs for humans. The gastrointestinal tract (GIT) houses a large microbial community, and these microbiota play an important role in growth and health of chickens, contributing to the enhancement of nutrient absorption and improvement of the birds' immune systems. To improve our understanding of the chicken intestinal microbial composition, microbiota inhabiting 5 different intestinal locations (duodenum, jejunum, ileum, cecum, and colon) of 42-day-old broiler chickens were detected based on 16S rRNA gene sequence analysis...
October 6, 2016: Poultry Science
https://www.readbyqxmd.com/read/28281573/formulation-for-oral-delivery-of-lactoferrin-based-on-bovine-serum-albumin-and-tannic-acid-multilayer-microcapsules
#5
Ece Kilic, Marina V Novoselova, Su Hui Lim, Nikolay A Pyataev, Sergey I Pinyaev, Oleg A Kulikov, Olga A Sindeeva, Oksana A Mayorova, Regan Murney, Maria N Antipina, Brendan Haigh, Gleb B Sukhorukov, Maxim V Kiryukhin
Lactoferrin (Lf) has considerable potential as a functional ingredient in food, cosmetic and pharmaceutical applications. However, the bioavailability of Lf is limited as it is susceptible to digestive enzymes in gastrointestinal tract. The shells comprising alternate layers of bovine serum albumin (BSA) and tannic acid (TA) were tested as Lf encapsulation system for oral administration. Lf absorption by freshly prepared porous 3 μm CaCO3 particles followed by Layer-by-Layer assembly of the BSA-TA shells and dissolution of the CaCO3 cores was suggested as the most efficient and harmless Lf loading method...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28276727/evaluation-of-prothrombin-induced-by-vitamin-k-absence-macrophage-migration-inhibitory-factor-and-golgi-protein-73-versus-alpha-fetoprotein-for-hepatocellular-carcinoma-diagnosis-and-surveillance
#6
Manar M Ismail, Heba K Morsi, Nahla A B Abdulateef, Maissa K Noaman, Ghada A Abou El-Ella
Hepatocellular carcinoma (HCC) represents a challenging malignancy of worldwide importance. It is the third most common cause of cancer-related death globally as most patients present with unresectable disease. Alpha-fetoprotein (AFP) is the widely and solely used biomarker for HCC diagnosis; yet, its usefulness is hampered by low sensitivity and specificity. We aimed to identify more sensitive biomarkers for HCC diagnosis and a surveillance algorithm that may facilitate early detection of HCC. A total of 305 Egyptian and Saudi participants grouped as healthy controls, cancer controls, benign hepatic lesions, chronic viral hepatitis and HCC were included...
May 2017: Scandinavian Journal of Clinical and Laboratory Investigation
https://www.readbyqxmd.com/read/28249113/fabrication-of-a-soybean-bowman-birk-inhibitor-bbi-nanodelivery-carrier-to-improve-bioavailability-of-curcumin
#7
Chun Liu, Fenfen Cheng, Xiaoquan Yang
Curcumin is a poorly water-soluble drug, and its oral bioavailability is very low. Here, a novel self-assembly nanoparticle delivery carrier has been successfully developed by using soybean Bowman-Birk inhibitor (BBI) to improve the solubility, bioaccessibility, and oral absorption of curcumin. BBI is a unique protein, which can be resistant to the pH range and proteolytic enzymes in the gastrointestinal tract (GIT), bioavailable, and not allergenic. The encapsulation efficiencies (EE) and the loading capacities (LC) of curcumin in the curcumin-loaded BBI nanoparticles (Cur-BBI-NPs, size = 90...
March 8, 2017: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/28214467/paxillin-a-crossroad-in-pathological-cell-migration
#8
REVIEW
Ana María López-Colomé, Irene Lee-Rivera, Regina Benavides-Hidalgo, Edith López
Paxilllin is a multifunctional and multidomain focal adhesion adapter protein which serves an important scaffolding role at focal adhesions by recruiting structural and signaling molecules involved in cell movement and migration, when phosphorylated on specific Tyr and Ser residues. Upon integrin engagement with extracellular matrix, paxillin is phosphorylated at Tyr31, Tyr118, Ser188, and Ser190, activating numerous signaling cascades which promote cell migration, indicating that the regulation of adhesion dynamics is under the control of a complex display of signaling mechanisms...
February 18, 2017: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/28201934/feeding-value-of-field-beans-vicia-faba-l-var-minor-with-and-without-enzyme-containing-tannase-pectinase-and-xylanase-activities-for-broilers
#9
Jalil Mahmwd Abdulla, Stephen Paul Rose, Alexander Mackay Mackenzie, Vasil Radoslavov Pirgozliev
Effects of field beans with various tannin content and exogenous enzyme mixture containing tannase, pectinase and xylanase activities on N-corrected dietary apparent metabolisable energy (AMEn), coefficients of dry matter (DMR) and nitrogen retention (NR), fat digestibility, gastrointestinal tract (GIT) development, jejunal villus morphometry, ileal digesta viscosity and sialic acid were examined. Birds' growth performance and energy conversion ratio (ECR) were also measured. Birds were fed one of eight mash diets...
April 2017: Archives of Animal Nutrition
https://www.readbyqxmd.com/read/28173798/spasmogenic-and-spasmolytic-activity-of-rind-of-punica-granatum-linn
#10
Niaz Ali, Ayesha Jamil, Syed Wadood Ali Shah, Ismail Shah, Ghayour Ahmed
BACKGROUND: Rind of Punica granatum is traditionally used in treatment of abdominal cramps and various GIT disorders. So far spasmolytic activity of rind of Punica granatum has been reported using in vitro model. However, its mode of action is not explored yet. Therefore, the current work describes the possible mode of action for spasmolytic activity of methanolic extract of rind of Punica granatum (Pg. Cr). Acute toxicity study is also performed to determine its safe dose range. METHODS: Rind of Punica granatum was subjected to shade drying...
February 7, 2017: BMC Complementary and Alternative Medicine
https://www.readbyqxmd.com/read/28135856/promoter-hypermethylation-and-its-impact-on-expression-of-mgmt-gene-in-the-git-malignant-patients-of-kashmiri-origin
#11
Arif Akbar Bhat, Hilal Ahmad Wani, Shiekh Ishaq, Ajaz Ahmad Waza, Rawoof Ahmad Malik, Iram Shabir, Showkat Jeelani, Showkat Kadla, Waseem Qureshie, Akbar Masood, Sabhiya Majid
Epigenetic alterations, in addition to multiple gene abnormalities, are involved in the genesis and progression of human cancers. Gastrointestinal tract (GIT) cancer is a major medical and economic burden worldwide. Aberrant methylation of CpG islands within promoter regions is associated with transcriptional inactivation of various tumor suppressor genes. Although a number of cancer-associated genes have been found to be hypermethylated in GIT cancer, valuable methylation markers for early diagnosis and prognostic evaluation of this cancer remain largely unknown...
February 7, 2017: Cancer Investigation
https://www.readbyqxmd.com/read/28113048/large-t-antigen-variants-of-human-polyomaviruses-9-and-12-and-seroreactivity-against-their-n-terminus
#12
Sarah-Verena Korup-Schulz, Claudia Lucke, Rosa Schmuck, Ugo Moens, Bernhard Ehlers
The tumor antigens (TAgs) of mammalian polyomaviruses (PyVs) are key proteins responsible for modulating the host cell cycle and involved in virus replication as well as cell transformation and tumor formation. Here we aimed at identifying mRNA sequences of known and novel TAgs encoded by the recently discovered human polyomaviruses 9 and 12 (HPyV9 and HPyV12) in cell culture. Synthetic viral genomes were transfected into human and animal cell lines. Gene expression occurred in most cell lines, as measured by qPCR of cDNA copies of mRNA encoding major structural protein VP1...
January 22, 2017: Journal of General Virology
https://www.readbyqxmd.com/read/28087515/h-blast-a-fast-protein-sequence-alignment-toolkit-on-heterogeneous-computers-with-gpus
#13
Weicai Ye, Ying Chen, Yongdong Zhang, Yuesheng Xu
Motivation: The sequence alignment is a fundamental problem in bioinformatics. BLAST is a routinely used tool for this purpose with over 118 000 citations in the past two decades. As the size of bio-sequence databases grows exponentially, the computational speed of alignment softwares must be improved. Results: We develop the heterogeneous BLAST (H-BLAST), a fast parallel search tool for a heterogeneous computer that couples CPUs and GPUs, to accelerate BLASTX and BLASTP-basic tools of NCBI-BLAST...
April 15, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28060926/comparison-of-tst-and-igra-in-diagnosis-of-latent-tuberculosis-infection-in-a-high-tb-burden-setting
#14
Surendra K Sharma, Richa Vashishtha, L S Chauhan, V Sreenivas, Divya Seth
BACKGROUND: There are currently two tests for diagnosing latent tuberculosis infection (LTBI); TST and IGRA. However, it is still unclear that which one of these tests performs better in high TB-burden settings. METHODS: 1511 household contacts of pulmonary TB patients were enrolled to compare the performance of TST and IGRA for LTBI. At baseline all participant underwent testing for IGRA [QuantiFERON-TB® Gold In-tube (QFT-GIT) assay] and TST [2 tuberculin unit (TU), purified protein derivative (PPD), RT23, Staten Serum Institute (SSI), Copenhagen, Denmark]...
2017: PloS One
https://www.readbyqxmd.com/read/28043588/characterization-of-the-cd4-and-cd8-t-cell-response-in-the-quantiferon-tb-gold-plus-kit
#15
Elisa Petruccioli, Teresa Chiacchio, Ilaria Pepponi, Valentina Vanini, Rocco Urso, Gilda Cuzzi, Lucia Barcellini, Fabrizio Palmieri, Daniela M Cirillo, Giuseppe Ippolito, Delia Goletti
OBJECTIVE/BACKGROUND: QuantiFERON-TB Gold In-Tube (QFT-GIT, Qiagen, Hilden, Germany) is an interferon-γ (IFN-γ) release assay designed to detect latent tuberculosis infection (LTBI). Although QFT-GIT has several advantages (mainly that it is not affected by the Bacille Calmette-Guérin vaccination), it has a poor sensitivity in immune-compromised individuals as it involves an immune response-based detection. Recently, QuantiFERON-TB Gold Plus (QFT-Plus) assay has been proposed as a new generation of QFT-GIT...
December 2016: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/27994031/flexible-model-based-clustering-of-mixed-binary-and-continuous-data-application-to-genetic-regulation-and-cancer
#16
Fatin N Zainul Abidin, David R Westhead
Clustering is used widely in 'omics' studies and is often tackled with standard methods, e.g. hierarchical clustering. However, the increasing need for integration of multiple data sets leads to a requirement for clustering methods applicable to mixed data types, where the straightforward application of standard methods is not necessarily the best approach. A particularly common problem involves clustering entities characterized by a mixture of binary data (e.g. presence/absence of mutations, binding, motifs and epigenetic marks) and continuous data (e...
April 20, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/27979220/controlling-the-potential-gastrointestinal-fate-of-%C3%AE-carotene-emulsions-using-interfacial-engineering-impact-of-coating-lipid-droplets-with-polyphenol-protein-carbohydrate-conjugate
#17
Fuguo Liu, Cuicui Ma, Ruojie Zhang, Yanxiang Gao, David Julian McClements
The impact of interfacial coatings comprised of polyphenol-protein-carbohydrate conjugates on the properties of nutraceutical-fortified lipid droplets during digestion was investigated. Surface-active chlorogenic acid-lactoferrin-polydextrose (CA-LF-PD) conjugate was synthesized as emulsifier to stabilize lipid droplets in β-carotene-enriched oil-in-water emulsions. Changes in droplet size, charge, and microstructure were monitored as β-carotene emulsions were passed through a simulated gastrointestinal tract model (mouth, stomach, small intestine)...
April 15, 2017: Food Chemistry
https://www.readbyqxmd.com/read/27976713/genetically-manipulated-phages-with-improved-ph-resistance-for-oral-administration-in-veterinary-medicine
#18
Franklin L Nobrega, Ana Rita Costa, José F Santos, Melvin F Siliakus, Jan W M van Lent, Servé W M Kengen, Joana Azeredo, Leon D Kluskens
Orally administered phages to control zoonotic pathogens face important challenges, mainly related to the hostile conditions found in the gastrointestinal tract (GIT). These include temperature, salinity and primarily pH, which is exceptionally low in certain compartments. Phage survival under these conditions can be jeopardized and undermine treatment. Strategies like encapsulation have been attempted with relative success, but are typically complex and require several optimization steps. Here we report a simple and efficient alternative, consisting in the genetic engineering of phages to display lipids on their surfaces...
December 15, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27852671/highly-multiplexed-proteomic-analysis-of-quantiferon-supernatants-to-identify-biomarkers-of-latent-tuberculosis-infection
#19
Mary Ann De Groote, Michael Higgins, Thomas Hraha, Kirsten Wall, Michael L Wilson, David G Sterling, Nebojsa Janjic, Randall Reves, Urs A Ochsner, Robert Belknap
The tests for diagnosing latent tuberculosis infection (LTBI) are limited by a poor predictive value for identifying people at the highest risk for progressing to active tuberculosis (TB) and have various sensitivities and specificities in different populations. Identifying a more robust signature for LTBI is important for TB prevention and elimination. A pilot study was conducted with samples from immigrants to the United States that were screened for LTBI by the three commercially approved tests, namely, the tuberculin skin test (TST), the Quantiferon-TB Gold in-tube (QFT-GIT), and the T-SPOT...
February 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/27847276/polyelectrolyte-complexes-as-prospective-carriers-for-the-oral-delivery-of-protein-therapeutics
#20
REVIEW
Vassilis Bourganis, Theodora Karamanidou, Olga Kammona, Costas Kiparissides
The oral administration of protein therapeutics is hindered by the multitude of barriers confronted by these molecules along the gastrointestinal tract (i.e., acidic environment, proteolytic degradation, mucosal barrier, etc.). Their unique properties (e.g., high molecular weight, hydrophilicity, charge, etc.) and labile structure are mainly responsible for their instability in the harsh conditions along the gastrointestinal tract (GIT) and dictate the employment of alternative routes for their administration (e...
February 2017: European Journal of Pharmaceutics and Biopharmaceutics
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