Articles

Method for improving the quality of genomic DNA obtained from minute quantities of tissue and blood samples using Chelex 100 resin

Although genomic DNA isolation using the Chelex 100 resin is rapid and inexpensive, the DNA obtained by this method has a low concentration in solution and contains suspended impurities. The presence of debris...

Authors: Utkarsha A. Singh, Mukta Kumari and Soumya Iyengar

Blockade of ITGA2 Induces Apoptosis and Inhibits Cell Migration in Gastric Cancer

Gastric cancer is currently the fourth leading cause of cancer-related death worldwide. Gastric cancer is often diagnosed at advanced stages and the outcome of the treatment is often poor. Therefore, identifyi...

Authors: Yu-Chang Chuang, Hsin-Yi Wu, Yu-Ling Lin, Shey-Cherng Tzou, Cheng-Hsun Chuang, Ting-Yan Jian, Pin-Rong Chen, Yuan-Ching Chang, Chi-Hsin Lin, Tse-Hung Huang, Chao-Ching Wang, Yi-Lin Chan and Kuang-Wen Liao

Use of RNA Immunoprecipitation Method for Determining Sinorhizobium meliloti RNA-Hfq Protein Associations In Vivo

Soil bacterium Sinorhizobium meliloti (S. meliloti) forms an endosymbiotic partnership with Medicago truncatula (M. truncatula) roots which results in root nodules. The bacteria live within root nodules where the...

Authors: Mengsheng Gao, Anne Benge, Julia M. Mesa, Regina Javier and Feng-Xia Liu

Treatment of Advanced Non-small-Cell Lung Cancer with Qi-Nourishing Essence-Replenishing Chinese Herbal Medicine Combined with Chemotherapy

To evaluate the effect of qi-nourishing essence-replenishing Chinese herbal medicine combined with chemotherapy in survival of advanced non-small-cell lung cancer(NSCLC) patients with essence and qi deficiency.

Authors: Yabin Gong, Zhenye Xu, Changjuan Jin, Haibin Deng, Zhongqi Wang, Weidong Zhou, Ming Zhang, Xiaozhen Zhao and Lifang Wang

DNA Area and NETosis Analysis (DANA): a High-Throughput Method to Quantify Neutrophil Extracellular Traps in Fluorescent Microscope Images

Neutrophil extracellular traps (NETs), extracellular structures composed of decondensed chromatin and antimicrobial molecules, are released in a process called NETosis. NETs, which are part of normal host defe...

Authors: Ryan Rebernick, Lauren Fahmy, Christopher Glover, Mandar Bawadekar, Daeun Shim, Caitlyn L. Holmes, Nicole Rademacher, Hemanth Potluri, Christie M. Bartels and Miriam A. Shelef

High-Sensitivity and High-Resolution In Situ Hybridization of Coding and Long Non-coding RNAs in Vertebrate Ovaries and Testes

Subcellular localization of coding and non-coding RNAs has emerged as major regulatory mechanisms of gene expression in various cell types and many organisms. However, techniques that enable detection of the s...

Authors: Natsumi Takei, Takuma Nakamura, Shohei Kawamura, Yuki Takada, Yui Satoh, Atsushi P. Kimura and Tomoya Kotani

Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results

Hierarchical Sample clustering (HSC) is widely performed to examine associations within expression data obtained from microarrays and RNA sequencing (RNA-seq). Researchers have investigated the HSC results wit...

Authors: Shitao Zhao, Jianqiang Sun, Kentaro Shimizu and Koji Kadota

Antitumor Efficacy of Human Monocyte-Derived Dendritic Cells: Comparing Effects of two Monocyte Isolation Methods

Dendritic cells (DCs), which can be used as anti-cancer vaccines, are generally obtained in vitro from isolated CD14⁺ monocytes (MoDCs). This generates high cell numbers and allows instructing DCs to guarantee ef...

Authors: Graça S Marques, Zélia Silva and Paula A. Videira

Visualisation of Multiple Tight Junctional Complexes in Human Airway Epithelial Cells

Apically located tight junctions in airway epithelium perform a fundamental role in controlling macromolecule migration through paracellular spaces. Alterations in their expression may lead to disruptions in b...

Authors: Alysia G. Buckley, Kevin Looi, Thomas Iosifidis, Kak-Ming Ling, Erika N. Sutanto, Kelly M. Martinovich, Elizabeth Kicic-Starcevich, Luke W. Garratt, Nicole C. Shaw, Francis J. Lannigan, Alexander N. Larcombe, Graeme Zosky, Darryl A. Knight, Paul J. Rigby, Anthony Kicic and Stephen M. Stick

Gibson Deletion: a novel application of isothermal in vitro recombination

Recombinant DNA technology is today a fundamental tool for virtually all biological research fields. Among the many techniques available for the construction of a “custom DNA” molecule, the isothermal in vitro...

Authors: Swara Kalva, Jef D. Boeke and Paolo Mita

Cancer chemoprevention and therapy using chinese herbal medicine

Traditional Chinese medicine (TCM) plays an indispensable role in cancer prevention and treatment. Chinese herbal medicine (CHM) is a key component of TCM and has been practiced for thousands of years. A numbe...

Authors: Lijing Jiao, Ling Bi, Yan Lu, Qin Wang, Yabin Gong, Jun Shi and Ling Xu

Maintaining RNA Integrity for Transcriptomic Profiling of Ex Vivo Cultured Limbal Epithelial Stem Cells after Fluorescence-Activated Cell Sorting (FACS)

Transcriptomic profiling of ex vivo cultured human limbal epithelial stem cells (hLESCs) will foster better understanding of corneal physiology and novel treatment paradigms to limbal stem cell deficiency (LSC...

Authors: Lei Liu, Frederik Mølgaard Nielsen, Simone Elkjær Riis, Jeppe Emmersen, Trine Fink, Jesper Østergaard Hjortdal, Chris Bath and Vladimir Zachar

Production of Monoclonal Antibodies against Human Trefoil Factor 3 and Development of a Modified-Sandwich ELISA for Detection of Trefoil Factor 3 Homodimer in Saliva

Human trefoil factor (TFF) peptides consist of three members: TFF1, TFF2 and TFF3. TFF3 is the most abundant TFF peptide in saliva. TFF3 homodimer was suggested to be involved in apoptosis inhibition and malig...

Authors: Saichit Khummuang, Waraporn Phanphrom, Witida Laopajon, Watchara Kasinrerk, Ponlatham Chaiyarit and Supansa Pata

SV40 Large T Antigen Disrupts Embryogenesis of Canine and Porcine Somatic Cell Nuclear Transfer Embryo

Somatic cell nuclear transfer (SCNT) is a useful biotechnological tool for transgenic animal production using genetically modified somatic cells (GMSCs). However, there are several limitations preventing succe...

Authors: Kiyoung Eun, Seon-Ung Hwang, Yeon Woo Jeong, Sunyoung Seo, Seon Yong Lee, Woo Suk Hwang, Sang-Hwan Hyun and Hyunggee Kim

Enhanced Mutant Screening in One-step PCR-based Multiple Site-directed Plasmid Mutagenesis by Introduction of Silent Restriction Sites for Structural and Functional Study of Proteins

Site-directed mutagenesis (SDM) has been widely used for studying the structure and function of proteins. A one-step polymerase chain reaction (PCR)-based multiple site-directed plasmid mutagenesis method with...

Authors: Ting-Yu Kuo, Chung-Che Tsai and Hua-Wen Fu

Efficient and inexpensive transient expression of multispecific multivalent antibodies in Expi293 cells

Immunotherapy is a very fast expanding field within drug discovery and, hence, rapid and inexpensive expression of antibodies would be extremely valuable. Antibodies are, however, difficult to express. Multifu...

Authors: Xiaotian T. Fang, Dag Sehlin, Lars Lannfelt, Stina Syvänen and Greta Hultqvist

An Assessment of Fixed and Native Chromatin Preparation Methods to Study Histone Post-Translational Modifications at a Whole Genome Scale in Skeletal Muscle Tissue

Genomic loci associated with histone marks are typically analyzed by immunoprecipitation of the chromatin followed by quantitative-PCR (ChIP-qPCR) or high throughput sequencing (ChIP-seq). Chromatin can be eit...

Authors: Sarah-Anne David, Benoît Piégu, Christelle Hennequet-Antier, Maëlle Pannetier, Tiphaine Aguirre-Lavin, Sabine Crochet, Thierry Bordeau, Nathalie Couroussé, Aurélien Brionne, Yves Bigot, Anne Collin and Vincent Coustham

An Initial Investigation of an Alternative Model to Study rat Primordial Germ Cell Epigenetic Reprogramming

Primordial germ cells (PGC) are the precursors of the gametes. During pre-natal development, PGC undergo an epigenetic reprogramming when bulk DNA demethylation occurs and is followed by sex-specific de novo m...

Authors: Isabelle Hernandez Cantão, Renato Borges Tesser and Taiza Stumpp

Cell Counting and Viability Assessment of 2D and 3D Cell Cultures: Expected Reliability of the Trypan Blue Assay

Whatever the target of an experiment in cell biology, cell counting and viability assessment are always computed. The Trypan Blue (TB) assay was proposed about a century ago and is still the most widely used m...

Authors: Filippo Piccinini, Anna Tesei, Chiara Arienti and Alessandro Bevilacqua

3D Printer Generated Tissue iMolds for Cleared Tissue Using Single- and Multi-Photon Microscopy for Deep Tissue Evaluation

Pathological analyses and methodology has recently undergone a dramatic revolution. With the creation of tissue clearing methods such as CLARITY and CUBIC, groups can now achieve complete transparency in tissu...

Authors: Sean J. Miller and Jeffrey D. Rothstein

Pre-Microporation Improves Outcome of Pancreatic Islet Labelling for Optical and ¹⁹F MR Imaging

In vitro labelling of cells and small cell structures is a necessary step before in vivo monitoring of grafts. We modified and optimised a procedure for pancreatic islet labelling using bimodal positively char...

Authors: Vít Herynek, Andrea Gálisová, Mangala Srinivas, Eric A. W. van Dinther, Lucie Kosinová, Jiri Ruzicka, Markéta Jirátová, Jan Kriz and Daniel Jirák

Performances of Different Fragment Sizes for Reduced Representation Bisulfite Sequencing in Pigs

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...

Authors: Xiao-Long Yuan, Zhe Zhang, Rong-Yang Pan, Ning Gao, Xi Deng, Bin Li, Hao Zhang, Per Torp Sangild and Jia-Qi Li

Comparison of transepithelial resistance measurement techniques: Chopsticks vs. Endohm

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-...

Authors: Rebecca A. Sheller, Maria E. Cuevas and Maria C. Todd

LncRNAs and immunity: watchdogs for host pathogen interactions

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 coordina...

Authors: Peerzada Tajamul Mumtaz, Shakil Ahmad Bhat, Syed Mudasir Ahmad, Mashooq Ahmad Dar, Raashid Ahmed, Uneeb Urwat, Aadil Ayaz, Divya Shrivastava, Riaz Ahmad Shah and Nazir Ahmad Ganai

Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer

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 ...

Authors: Yan Lu, Shulin/SL Li, Shiguo/SG Zhu, Yabin/YB Gong, Jun/J Shi and Ling/ L Xu

Auxin Extraction and Purification Based on Recombinant Aux/IAA Proteins

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...

Authors: Yi Su, Weigui Luo, Xiaofei Chen, Huizhen Liu, Yueqing Hu, Wanhuang Lin and Langtao Xiao

An Automated Perifusion System for Modifying Cell Culture Conditions over Time

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 cond...

Authors: Nicholas B. Whitticar, Elisha W. Strahler, Parthiban Rajan, Savas Kaya and Craig S. Nunemaker

Aqueous two-phase system (ATPS): an overview and advances in its applications

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, membran...

Authors: 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 and Zonghui Yuan

Fluorescence ImmunoPrecipitation (FLIP): a Novel Assay for High-Throughput IP

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 ea...

Authors: Paolo Mita, Tenzin Lhakhang, Donghui Li, Daniel J. Eichinger, David Fenyo and Jef D. Boeke

Isolation, expansion and characterization of porcine urinary bladder smooth muscle cells for tissue engineering

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...

Authors: Marta Pokrywczynska, Daria Balcerczyk, Arkadiusz Jundzill, Maciej Gagat, Monika Czapiewska, Tomasz Kloskowski, Maciej Nowacki, Agata M. Gastecka, Magdalena Bodnar, Alina Grzanka, Andrzej Marszalek and Tomasz Drewa

An optimised method for the proteomic profiling of full thickness human skin

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 isolate...

Authors: Emily Bliss, Wendy E. Heywood, Malika Benatti, Neil J. Sebire and Kevin Mills

An Optimized Protocol for Packaging Pseudotyped Integrase Defective Lentivirus

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 gro...

Authors: Ranjita Sengupta, Chandreyee Mukherjee, Nandita Sarkar, Zhihong Sun, Jacob Lesnik, Joseph Huang and Biao Lu

Reliable FASP-based procedures for optimal quantitative proteomic and phosphoproteomic analysis on samples from acute myeloid leukemia patients

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 confiden...

Authors: Maria Hernandez-Valladares, Elise Aasebø, Olav Mjaavatten, Marc Vaudel, Øystein Bruserud, Frode Berven and Frode Selheim

Expression of Concern: The functional role of long non-coding RNAs and epigenetics

Authors: Shulin Li

Extracting functional trends from whole genome duplication events using comparative genomics

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...

Authors: Russell A. Hermansen, Torgeir R. Hvidsten, Simen Rød Sandve and David A. Liberles

Endothelial Mesenchymal Transition: Comparative Analysis of Different Induction Methods

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 a...

Authors: Mariana T. Pinto, Dimas T. Covas, Simone Kashima and Claudia O. Rodrigues

A Modified Coupled Spectrophotometric Method to Detect 2-5 Oligoadenylate Synthetase Activity in Prostate Cell Lines

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 b...

Authors: Sushma M. Bhosle, Aisha Hunt and Jaideep Chaudhary

MicroRNA biogenesis and their functions in regulating stem cell potency and differentiation

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 engineeri...

Authors: Shaomian Yao

Thanks to all those who reviewed for Biological Procedures Online in 2015

A peer-reviewed journal would not survive without the generous time and insightful comments of the reviewers, whose efforts often go unrecognized. Although final decisions are always editorial, they are greatl...

Authors: Shulin Li

Characterising protein/detergent complexes by triple-detection size-exclusion chromatography

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 ...

Authors: Katharina Gimpl, Jessica Klement and Sandro Keller

A BioBrick™-Compatible Vector for Allelic Replacement Using the XylE Gene as Selection Marker

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 in...

Authors: Michela Casanova, Lorenzo Pasotti, Susanna Zucca, Nicolò Politi, Ilaria Massaiu, Cinzia Calvio, Maria Gabriella Cusella De Angelis and Paolo Magni

Lambda Red-mediated Recombineering in the Attaching and Effacing Pathogen Escherichia albertii

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 engineer...

Authors: Marisa Egan, Jasmine Ramirez, Christian Xander, Chirag Upreti and Shantanu Bhatt

Vectors for Genetically-Encoded Tags for Electron Microscopy Contrast in Drosophila

One of the most notable recent advances in electron microscopy (EM) was the development of genetically-encoded EM tags, including the fluorescent flavoprotein Mini-SOG (Mini-Singlet Oxygen Generator). Mini-SOG...

Authors: Marco Man Kin Tsui, Anri Itoh, Mohamed Amgad, Shao-Fang Wang and Toshio Sasaki

Lipase catalysis in organic solvents: advantages and applications

Lipases are industrial biocatalysts, which are involved in several novel reactions, occurring in aqueous medium as well as non-aqueous medium. Furthermore, they are well-known for their remarkable ability to c...

Authors: Ashok Kumar, Kartik Dhar, Shamsher Singh Kanwar and Pankaj Kumar Arora

Evaluation of local trace element status and 8-Iso-prostaglandin F_2α concentrations in patients with Tinea pedis

Tinea pedis (TP) is an infection of the feet caused by fungi. The infectious diseases caused by dermatophytes are mainly related to the enzymes produced by these fungi. Up to the now, the local 8-iso-prostagla...

Authors: Meral Miraloglu, Ergul Belge Kurutas, Perihan Ozturk and Ozer Arican

Predicting Crystallization Propensity of Proteins from Arabidopsis Thaliana

Many studies have correlated characteristics of amino acids with crystallization propensity, as part of the effort to determine the factors that affect the propensity of protein crystallization. However, these...

Authors: Shaomin Yan and Guang Wu

A Medium-Throughput Single Cell CRISPR-Cas9 Assay to Assess Gene Essentiality

Target selection for oncology is a crucial step in the successful development of therapeutics. Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 editing of specific loci offers an alterna...

Authors: A. R. Grassian, T. M. E. Scales, S. K. Knutson, K. W. Kuntz, N. J. McCarthy, C. E. Lowe, J. D. Moore, R. A. Copeland, H. Keilhack, J. J. Smith, J. A. Wickenden and S. Ribich

Detection of genetic variation using dual-labeled peptide nucleic acid (PNA) probe-based melting point analysis

Thermal denaturation of probe-target hybrid is highly reproducible, and which makes probe melting point analysis reliable in the detection of mutations, polymorphisms and epigenetic differences in DNA. To impr...

Authors: Deokhwe Hur, Myoung Sug Kim, Minsik Song, Jinwook Jung and Heekyung Park

Mitogen Activated Protein Kinase (MPK) Interacts With Auxin Influx Carrier (OsAux/LAX1) Involved in Auxin Signaling in Plant

Mitogen activated protein kinases (MPKs) are serine/threonine protein kinases that contain characteristic T-x-Y motif in the activation loop region. MPKs are important signaling molecules involved in diverse s...

Authors: Tapan Kumar Mohanta, Nibedita Mohanta, Pratap Parida and Hanhong Bae

A High-Throughput Assay for Screening of Natural Products that Enhanced Tumoricidal Activity of NK Cells

Recently, immunotherapy has shown a lot of promise in cancer treatment and different immune cell types are involved in this endeavor. Among different immune cell populations, NK cells are also an important com...

Authors: Chenyuan Gong, Zhongya Ni, Chao Yao, Xiaowen Zhu, Lulu Ni, Lixin Wang and Shiguo Zhu