journal
MENU ▼
Read by QxMD icon Read
search

Biological Procedures Online

journal
https://www.readbyqxmd.com/read/28596713/performances-of-different-fragment-sizes-for-reduced-representation-bisulfite-sequencing-in-pigs
#1
Xiao-Long Yuan, Zhe Zhang, Rong-Yang Pan, Ning Gao, Xi Deng, Bin Li, Hao Zhang, Per Torp Sangild, Jia-Qi Li
BACKGROUND: Reduced representation bisulfite sequencing (RRBS) has been widely used to profile genome-scale DNA methylation in mammalian genomes. However, the applications and technical performances of RRBS with different fragment sizes have not been systematically reported in pigs, which serve as one of the important biomedical models for humans. The aims of this study were to evaluate capacities of RRBS libraries with different fragment sizes to characterize the porcine genome. RESULTS: We found that the MspI-digested segments between 40 and 220 bp harbored a high distribution peak at 74 bp, which were highly overlapped with the repetitive elements and might reduce the unique mapping alignment...
2017: Biological Procedures Online
https://www.readbyqxmd.com/read/28490975/comparison-of-transepithelial-resistance-measurement-techniques-chopsticks-vs-endohm
#2
Rebecca A Sheller, Maria E Cuevas, Maria C Todd
BACKGROUND: TER measurements across confluent cellular monolayers provide a useful indication of TJ strength between epithelial and endothelial cells in culture. Having a reliable and accurate method of measuring cell-to-cell adhesion is critical to studies in pathophysiology and cancer metastasis. However, the use of different technical approaches to measure TER has reportedly yielded inconsistent measurements within the same cell lines. METHODS: In the current study, we compared the peak TER values for the MDCK (canine kidney) and MCF-7 (human breast cancer) epithelial cell lines using two common approaches (Chopstick and Endohm) and two types of polymer inserts (PC and PET)...
2017: Biological Procedures Online
https://www.readbyqxmd.com/read/28465674/lncrnas-and-immunity-watchdogs-for-host-pathogen-interactions
#3
REVIEW
Peerzada Tajamul Mumtaz, Shakil Ahmad Bhat, Syed Mudasir Ahmad, Mashooq Ahmad Dar, Raashid Ahmed, Uneeb Urwat, Aadil Ayaz, Divya Shrivastava, Riaz Ahmad Shah, Nazir Ahmad Ganai
Immune responses combat various infectious agents by inducing inflammatory responses, antimicrobial pathways and adaptive immunity. The polygenic responses to these external stimuli are temporally and coordinately regulated. Specific lncRNAs are induced to modulate innate and adaptive immune responses which can function through various target interactions like RNA-DNA, RNA-RNA, and RNA-protein interaction and hence affect the immunogenic regulation at various stages of gene expression. LncRNA are found to be present in various immune cells like monocytes, macrophages, dendritic cells, neutrophils, T cells and B cells...
2017: Biological Procedures Online
https://www.readbyqxmd.com/read/28331435/methylated-dna-rna-in-body-fluids-as-biomarkers-for-lung-cancer
#4
REVIEW
Yan Lu, Shulin/Sl Li, Shiguo/Sg Zhu, Yabin/Yb Gong, Jun/J Shi, Ling/L Xu
DNA/RNA methylation plays an important role in lung cancer initiation and progression. Liquid biopsy makes use of cells, nucleotides and proteins released from tumor cells into body fluids to help with cancer diagnosis and prognosis. Methylation of circulating tumor DNA (ctDNA) has gained increasing attention as biomarkers for lung cancer. Here we briefly introduce the biological basis and detection method of ctDNA methylation, and review various applications of methylated DNA in body fluids in lung cancer screening, diagnosis, prognosis, monitoring and treatment prediction...
2017: Biological Procedures Online
https://www.readbyqxmd.com/read/28100961/auxin-extraction-and-purification-based-on-recombinant-aux-iaa-proteins
#5
Yi Su, Weigui Luo, Xiaofei Chen, Huizhen Liu, Yueqing Hu, Wanhuang Lin, Langtao Xiao
BACKGROUND: Indole-3-acetic acid (IAA) extraction and purification are of great importance in auxin research, which is a hot topic in the plant growth and development field. Solid-phase extraction (SPE) is frequently used for IAA extraction and purification. However, no IAA-specific SPE columns are commercially available at the moment. Therefore, the development of IAA-specific recognition materials and IAA extraction and purification methods will help researchers meet the need for more precise analytical methods for research on phytohormones...
2017: Biological Procedures Online
https://www.readbyqxmd.com/read/27895534/an-automated-perifusion-system-for-modifying-cell-culture-conditions-over-time
#6
Nicholas B Whitticar, Elisha W Strahler, Parthiban Rajan, Savas Kaya, Craig S Nunemaker
BACKGROUND: Cells are continuously exposed to changes in their environment. Endocrine systems, in particular, communicate by rhythms and feedback loops. In this study, we developed an automated system to produce such conditions for cultured cells in a precisely timed manner. We utilized a programmable pair of syringe pumps for inflow and a peristaltic pump for outflow to create rhythmic pulses at 5-min intervals in solutions that mimic the endogenous patterns of insulin produced by pancreatic islets as a test case...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/27807400/aqueous-two-phase-system-atps-an-overview-and-advances-in-its-applications
#7
REVIEW
Mujahid Iqbal, Yanfei Tao, Shuyu Xie, Yufei Zhu, Dongmei Chen, Xu Wang, Lingli Huang, Dapeng Peng, Adeel Sattar, Muhammad Abu Bakr Shabbir, Hafiz Iftikhar Hussain, Saeed Ahmed, Zonghui Yuan
Aqueous two-phase system (ATPS) is a liquid-liquid fractionation technique and has gained an interest because of great potential for the extraction, separation, purification and enrichment of proteins, membranes, viruses, enzymes, nucleic acids and other biomolecules both in industry and academia. Although, the partition behavior involved in the method is complex and difficult to predict. Current research shows that it has also been successfully used in the detection of veterinary drug residues in food, separation of precious metals, sewage treatment and a variety of other purposes...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/27528826/fluorescence-immunoprecipitation-flip-a-novel-assay-for-high-throughput-ip
#8
Paolo Mita, Tenzin Lhakhang, Donghui Li, Daniel J Eichinger, David Fenyo, Jef D Boeke
BACKGROUND: The immunoprecipitation (IP) assay is a valuable molecular biology tool applied across a breadth of fields. The standard assay couples IP to immunoblotting (IP/IB), a procedure severely limited as it is not easily scaled for high-throughput analysis. RESULTS: Here we describe and characterize a new methodology for fast and reliable evaluation of an immunoprecipitation reaction. FLIP (FLuorescence IP) relies on the expression of the target protein as a chromophore-tagged protein and couples IP with the measurement of fluorescent signal coating agarose beads...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/27524942/isolation-expansion-and-characterization-of-porcine-urinary-bladder-smooth-muscle-cells-for-tissue-engineering
#9
Marta Pokrywczynska, Daria Balcerczyk, Arkadiusz Jundzill, Maciej Gagat, Monika Czapiewska, Tomasz Kloskowski, Maciej Nowacki, Agata M Gastecka, Magdalena Bodnar, Alina Grzanka, Andrzej Marszalek, Tomasz Drewa
BACKGROUND: A key requirements for therapy utilizing the tissue engineering methodologies is use of techniques which have the capability to yield a high number of cells, from small tissue biopsy in a relatively short time. Up to date there was no optimal methods of isolation and expansion of urinary bladder smooth muscle cells (UB-SMCs). The aim of this study was to compare isolation and expansion techniques of UB-SMCs to select the most repeatable and efficient one. METHOD: Five protocols of porcine UB- SMCs isolation including enzymatic and explant techniques and three expansion techniques were compared...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/27445641/an-optimised-method-for-the-proteomic-profiling-of-full-thickness-human-skin
#10
Emily Bliss, Wendy E Heywood, Malika Benatti, Neil J Sebire, Kevin Mills
BACKGROUND: The skin is the largest organ of the human body and is the first line barrier defence against trauma, microbial infiltration and radiation. Skin diseases can be a result of multi-systemic disease or an isolated condition. Due to its proteolysis resistant properties there are relatively few human skin proteomic datasets published compared with other human organs or body fluids. Skin is a challenging tissue to analyse using traditional proteomic techniques due to its high lipid content, insolubility and extensive cross-linking of proteins...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/27403084/an-optimized-protocol-for-packaging-pseudotyped-integrase-defective-lentivirus
#11
Ranjita Sengupta, Chandreyee Mukherjee, Nandita Sarkar, Zhihong Sun, Jacob Lesnik, Joseph Huang, Biao Lu
BACKGROUND: A number of integrase defective lentiviral (IDLV) packaging systems have been developed to produce integration deficient lentiviruses for gene delivery and epichromosomal expression. However, despite their growing demand, a comparative study to systemically evaluate the performance efficiency of different mutants on virus packaging and gene expression has not been done. RESULTS: Site-directed mutagenesis was used to generate five integrasedeficient mutants for non-integrative lentiviral packaging (NILVP)...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/27330413/reliable-fasp-based-procedures-for-optimal-quantitative-proteomic-and-phosphoproteomic-analysis-on-samples-from-acute-myeloid-leukemia-patients
#12
Maria Hernandez-Valladares, Elise Aasebø, Olav Mjaavatten, Marc Vaudel, Øystein Bruserud, Frode Berven, Frode Selheim
BACKGROUND: Satisfactory sample preparation for mass spectrometry-based analysis is a critical step in the proteomics workflow. The quality and reproducibility of sample preparation can determine the coverage and confidence of proteomics results. Up to date, several methodologies have been described to produce suitable peptides for mass spectrometry analysis, followed by strategies for enrichment of post-translational modified peptides, if desired. Among them, the filter-aided sample preparation (FASP) has been introduced as a method to allow for removal of denaturants, reductants, alkylators, lipids and nucleic acids prior to trypsin digestion...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/27293384/expression-of-concern-the-functional-role-of-long-non-coding-rnas-and-epigenetics
#13
Shulin Li
No abstract text is available yet for this article.
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/27168732/extracting-functional-trends-from-whole-genome-duplication-events-using-comparative-genomics
#14
REVIEW
Russell A Hermansen, Torgeir R Hvidsten, Simen Rød Sandve, David A Liberles
BACKGROUND: The number of species with completed genomes, including those with evidence for recent whole genome duplication events has exploded. The recently sequenced Atlantic salmon genome has been through two rounds of whole genome duplication since the divergence of teleost fish from the lineage that led to amniotes. This quadrupoling of the number of potential genes has led to complex patterns of retention and loss among gene families. RESULTS: Methods have been developed to characterize the interplay of duplicate gene retention processes across both whole genome duplication events and additional smaller scale duplication events...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/27127420/endothelial-mesenchymal-transition-comparative-analysis-of-different-induction-methods
#15
Mariana T Pinto, Dimas T Covas, Simone Kashima, Claudia O Rodrigues
BACKGROUND: Endothelial-Mesenchymal-Transition (EndMT) plays an essential role in cardiovascular development, and recently became an attractive therapeutic target based on evidence supporting its involvement in fibrosis and cancer. Important questions that remain to be answered are related to the molecular mechanisms that control EndMT in different organs and distinct pathological conditions. The lack of a detailed protocol for induction of EndMT and the assumption that TGF-β isoforms play similar roles on different types of endothelial cells, limit progress in the field...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/26997919/a-modified-coupled-spectrophotometric-method-to-detect-2-5-oligoadenylate-synthetase-activity-in-prostate-cell-lines
#16
Sushma M Bhosle, Aisha Hunt, Jaideep Chaudhary
BACKGROUND: 2'-5' oligoadenylate synthetases (OAS) are interferon inducible enzymes that polymerizes ATP to 2'-5'-linked oligomers of adenylate (2-5As). As part of the innate immune response, these enzymes are activated by viral double stranded RNA or mRNAs with significant double stranded structure. The 2-5As in turn activate RNaseL that degrade single stranded RNAs. Three distinct forms of OAS exist in human cells (OAS1, 2 and 3) with each form having multiple spliced variants. The OAS enzymes and their spliced variants have different enzyme activities...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/26966421/microrna-biogenesis-and-their-functions-in-regulating-stem-cell-potency-and-differentiation
#17
REVIEW
Shaomian Yao
Stem cells are unspecialized/undifferentiated cells that exist in embryos and adult tissues or can be converted from somatic differentiated cells. Use of stem cells for tissue regeneration and tissue engineering has been a cornerstone of the regenerative medicine. Stem cells are also believed to exist in cancer tissues, namely cancer stem cells (CSCs). Growing evidence suggests that CSCs are the culprit of cancer dormancy, progression and recurrence, and thus have recently received great attention. MicroRNAs (miRNAs) are a group of short, non-coding RNAs that regulate expression of a wide range of genes at a post-transcriptional manner...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/26880869/characterising-protein-detergent-complexes-by-triple-detection-size-exclusion-chromatography
#18
Katharina Gimpl, Jessica Klement, Sandro Keller
BACKGROUND: In vitro investigations of membrane proteins usually depend on detergents for protein solubilisation and stabilisation. The amount of detergent bound to a membrane protein is relevant to successful experiment design and data analysis but is often unknown. Triple-detection size-exclusion chromatography enables simultaneous separation of protein/detergent complexes and protein-free detergent micelles and determination of their molar masses in a straightforward and absolute manner...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/26877712/a-biobrick%C3%A2-compatible-vector-for-allelic-replacement-using-the-xyle-gene-as-selection-marker
#19
Michela Casanova, Lorenzo Pasotti, Susanna Zucca, Nicolò Politi, Ilaria Massaiu, Cinzia Calvio, Maria Gabriella Cusella De Angelis, Paolo Magni
BACKGROUND: Circular plasmid-mediated homologous recombination is commonly used for marker-less allelic replacement, exploiting the endogenous recombination machinery of the host. Common limitations of existing methods include high false positive rates due to mutations in counter-selection genes, and limited applicability to specific strains or growth media. Finally, solutions compatible with physical standards, such as the BioBrick™, are not currently available, although they proved to be successful in the design of other replicative or integrative plasmids...
2016: Biological Procedures Online
https://www.readbyqxmd.com/read/26843851/lambda-red-mediated-recombineering-in-the-attaching-and-effacing-pathogen-escherichia-albertii
#20
Marisa Egan, Jasmine Ramirez, Christian Xander, Chirag Upreti, Shantanu Bhatt
BACKGROUND: The ability to introduce site-specific mutations in bacterial pathogens is essential towards understanding their molecular mechanisms of pathogenicity. This has been greatly facilitated by the genetic engineering technique of recombineering. In recombineering, linear double- or single-stranded DNA molecules with two terminal homology arms are electroporated into hyperrecombinogenic bacteria that express a phage-encoded recombinase. The recombinase catalyzes the replacement of the endogenous allele with the exogenous allele to generate selectable or screenable recombinants...
2016: Biological Procedures Online
journal
journal
35161
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"