Articles

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

CellProfiler: Novel Automated Image Segmentation Procedure for Super-Resolution Microscopy

Super resolution (SR) microscopy enabled cell biologists to visualize subcellular details up to 20 nm in resolution. This breakthrough in spatial resolution made image analysis a challenging procedure. Direct ...

Authors: Kareem Soliman

Chicken chorioallantoic membrane as a reliable model to evaluate osteosarcoma—an experimental approach using SaOS2 cell line

Osteosarcoma is the most common primary tumor that affects usually children. Due to its cellular complex and osteoid formation it is very difficult to understand the mechanism behind the progressiveness of ost...

Authors: Reji Manjunathan and Malathi Ragunathan

Erratum to: Model of Cation Transportation Mediated by High-Affinity Potassium Transporters (HKTs) in Higher Plants

Authors: Yi Su, Weigui Luo, Wanhuang Lin, Liying Ma and Mohammed Humayun Kabir

The diversity of fungal genome

The genome size of an organism varies from species to species. The C-value paradox enigma is a very complex puzzle with regards to vast diversity in genome sizes in eukaryotes. Here we reported the detailed ge...

Authors: Tapan Kumar Mohanta and Hanhong Bae

Evaluation of Epic® label-free technology to quantify functional recombinant hemagglutinin

Alternative methods are being sought to measure the potency of influenza vaccines. Label-free technologies that do not require the use of hemagglutinin (HA)-specific antisera are particularly attractive as the...

Authors: Lianlian Jiang and Maryna C Eichelberger

Recombinase-mediated cassette exchange (RMCE) system for functional genomics studies in Mycoplasma mycoides

We have previously established technologies enabling us to engineer the Mycoplasma mycoides genome while cloned in the yeast Saccharomyces cerevisiae, followed by genome transplantation into Mycoplasma capricolum

Authors: Vladimir N Noskov, Li Ma, Stephen Chen and Ray-Yuan Chuang

cDNA synthesis for BCR-ABL1 detection at the MMR level: the importance of using the appropriate kit

The synthesis of complementary DNA (cDNA) for use in the detection of BCR-ABL1 at the Major Molecular Response (MMR) level is a well-established method used by clinical laboratories world-wide. However, the quali...

Authors: Jianxiang Chi, Chryso Pierides, Andrie Mitsidou, Andri Miltiadou, Petroula Gerasimou and Paul Costeas

Evaluation of method performance for oxidative stress biomarkers in urine and biological variations in urine of patients with type 2 diabetes mellitus and diabetic nephropathy

Oxidative stress biomarkers such as superoxide dismutase (CuZnSOD), catalase (CAT) and malondialdehyde (MDA) play an important role in the pathogenesis or progression of numerous diseases. Data regarding the b...

Authors: Ergul Belge Kurutas, Yakup Gumusalan, Ali Cetinkaya and Ekrem Dogan

Thanks to all those who reviewed for Biological Procedures Online in 2014

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

Comparison of Vibratome and Compresstome sectioning of fresh primate lymphoid and genital tissues for in situ MHC-tetramer and immunofluorescence staining

For decades, the Vibratome served as a standard laboratory resource for sectioning fresh and fixed tissues. In skilled hands, high quality and consistent fresh unfixed tissue sections can be produced using a V...

Authors: Hadia M Abdelaal, Hyeon O Kim, Reece Wagstaff, Ryoko Sawahata, Peter J Southern and Pamela J Skinner

Model of Cation Transportation Mediated by High-Affinity Potassium Transporters (HKTs) in Higher Plants

Trk/Ktr/HKT transporters probably were evolved from simple K⁺ channels KcsA. HKT transporters, which mediate Na⁺-uniport or Na⁺/K⁺-symport, maintain K⁺/Na⁺ homeostasis and increase salinity tolerance, can be clas...

Authors: Yi Su, Weigui Luo, Wanhuang Lin, Liying Ma and Mohammed Hunayun Kabir

The functional role of long non-coding RNAs and epigenetics

Long non-coding RNAs (lncRNAs) are non-protein coding transcripts longer than 200 nucleotides. The post-transcriptional regulation is influenced by these lncRNAs by interfering with the microRNA pathways, invo...

Authors: Jinneng Cao

A novel model of appendicitis and appendectomy to investigate inflammatory bowel disease pathogenesis and remediation

The appendix contains copious lymphoid tissue and is constantly exposed to gut flora. Appendicitis and appendectomy (AA) has been shown to prevent or significantly ameliorate ulcerative colitis. In our novel m...

Authors: Rajkumar Cheluvappa

A convenient, optimized pipeline for isolation, fluorescence microscopy and molecular analysis of live single cells

Heterogeneity within cell populations is relevant to the onset and progression of disease, as well as development and maintenance of homeostasis. Analysis and understanding of the roles of heterogeneity in bio...

Authors: Jordan R Yaron, Colleen P Ziegler, Thai H Tran, Honor L Glenn and Deirdre R Meldrum

Integration of bioinformatics to biodegradation

Bioinformatics and biodegradation are two primary scientific fields in applied microbiology and biotechnology. The present review describes development of various bioinformatics tools that may be applied in th...

Authors: Pankaj Kumar Arora and Hanhong Bae

A novel recombinant baculovirus overexpressing a Bacillus thuringiensis Cry1Ab toxin enhances insecticidal activity

Baculoviruses have been genetically modified to express foreign genes under powerful promoters in order to accelerate their speed of killing. In this study a truncated form of cry1Ab gene derived from Bacillus th...

Authors: Wael El-Menofy, Gamal Osman, Abdulrahman Assaeedi and Mohamed Salama

Real-time vascular mechanosensation through ex vivo artery perfusion

Cell-based perfusion studies have provided great insight into fluid-sensing mechanisms, such as primary cilia in the renal and vascular systems. However, the intrinsic limitations of in vitro cell culture, such a...

Authors: Rahul M Prasad, Xingjian Jin, Wissam A AbouAlaiwi and Surya M Nauli

Detection and quantification of extracellular microRNAs in murine biofluids

MicroRNAs (miRNAs) are short RNA molecules which regulate gene expression in eukaryotic cells, and are abundant and stable in biofluids such as blood serum and plasma. As such, there has been heightened intere...

Authors: Thomas C Roberts, Anna M L Coenen-Stass, Corinne A Betts and Matthew J A Wood

Isolation of T cells from mouse oral tissues

Utilizing mouse models provides excellent immunological and experimental tools to study oral immune responses. However for functional assays, isolating T lymphocytes from the oral tissues has proved to be chal...

Authors: Pushpa Pandiyan, Natarajan Bhaskaran, Yifan Zhang and Aaron Weinberg