331 results match your criteria Biological procedures online[Journal]


Bimodal Whole-Mount Imaging of Tendon Using Confocal Microscopy and X-ray Micro-Computed Tomography.

Biol Proced Online 2020 1;22:13. Epub 2020 Jul 1.

Comparative Biomedical Sciences, Royal Veterinary College, Royal College Street, London, UK.

Background: Three-dimensional imaging modalities for optically dense connective tissues such as tendons are limited and typically have a single imaging methodological endpoint. Here, we have developed a bimodal procedure utilising fluorescence-based confocal microscopy and x-ray micro-computed tomography for the imaging of adult tendons to visualise and analyse extracellular sub-structure and cellular composition in small and large animal species.

Results: Using fluorescent immunolabelling and optical clearing, we visualised the expression of the novel cross-species marker of tendon basement membrane, laminin-α4 in 3D throughout whole rat Achilles tendons and equine superficial digital flexor tendon 5 mm segments. Read More

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http://dx.doi.org/10.1186/s12575-020-00126-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7329428PMC

Combination of Size-Exclusion Chromatography and Ultracentrifugation Improves the Proteomic Profiling of Plasma-Derived Small Extracellular Vesicles.

Biol Proced Online 2020 23;22:12. Epub 2020 Jun 23.

Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, National Clinical Research Center for Digestive Disease, Beijing Digestive Disease Center, Beijing Key Laboratory for Precancerous Lesion of Digestive Disease, Beijing, 100050 P. R. China.

Background: Circulating small extracellular vesicles (sEVs) and its associated proteins are of great interest in the early detection of many diseases. However, there is no gold standard for plasma sEVs isolation, especially for proteomic profiling which could be largely affected by contamination such as lipoproteins and plasma proteins. Previous studies suggested combinations of different sEVs isolation methods could improve the yield and purity of the isolated fractions. Read More

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http://dx.doi.org/10.1186/s12575-020-00125-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7313174PMC

Application of System Biology to Explore the Association of Neprilysin, Angiotensin-Converting Enzyme 2 (ACE2), and Carbonic Anhydrase (CA) in Pathogenesis of SARS-CoV-2.

Biol Proced Online 2020 19;22:11. Epub 2020 Jun 19.

Department of Biochemistry, Faculty of Medicine, Iran University of Medical Sciences, Tehran, Iran.

Background: Coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) appears with common symptoms including fever, dry cough, and fatigue, as well as some less common sysmptoms such as loss of taste and smell, diarrhea, skin rashes and discoloration of fingers. COVID-19 patients may also suffer from serious symptoms including shortness of breathing, chest pressure and pain, as well as loss of daily routine habits, pointing out to a sever reduction in the quality of life. COVID-19 has afftected almost all countries, however, the United States contains the highest number of infection (> 1,595,000 cases) and deaths cases (> 95,000 deaths) in the world until May 21, 2020. Read More

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http://dx.doi.org/10.1186/s12575-020-00124-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7302923PMC

Deep Insights in Circular RNAs: from biogenesis to therapeutics.

Biol Proced Online 2020 15;22:10. Epub 2020 May 15.

1Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry Shuhama, Sher-e- Kashmir University of Agricultural Sciences and Technology, Kashmir, 19006 India.

Abstract: Circular RNAs (circRNAs) have emerged as a universal novel class of eukaryotic non-coding RNA (ncRNA) molecules and are becoming a new research hotspot in RNA biology. They form a covalent loop without 5' cap and 3' tail, unlike their linear counterparts. Endogenous circRNAs in mammalian cells are abundantly conserved and discovered so far. Read More

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http://dx.doi.org/10.1186/s12575-020-00122-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7227217PMC

Reverse Genetics Assembly of Newcastle Disease Virus Genome Template Using Asis-Sal-Pac BioBrick Strategy.

Biol Proced Online 2020 1;22. Epub 2020 May 1.

1Division of Biotechnology, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran.

Background: The BioBrick construction as an approach in synthetic biology provides the ability to assemble various gene fragments. To date, different BioBrick strategies have been exploited for assembly and cloning of a variety of gene fragments. We present a new BioBrick strategy, here referred as Asis-Sal-Pac BioBrick, which we used for the assembly of NDV as a candidate for single-stranded non-segmented, negative-sense RNA genome viruses. Read More

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http://dx.doi.org/10.1186/s12575-020-00119-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7193399PMC

Combination of Biodata Mining and Computational Modelling in Identification and Characterization of ORF1ab Polyprotein of SARS-CoV-2 Isolated from Oronasopharynx of an Iranian Patient.

Biol Proced Online 2020 21;22. Epub 2020 Apr 21.

3Nanobiotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.

Background: Coronavirus disease 2019 (COVID-19) is an emerging zoonotic viral infection, which was started in Wuhan, China, in December 2019 and transmitted to other countries worldwide as a pandemic outbreak. Iran is one of the top ranked countries in the tables of COVID-19-infected and -mortality cases that make the Iranian patients as the potential targets for diversity of studies including epidemiology, biomedical, biodata, and viral proteins computational modelling studies.

Results: In this study, we applied bioinformatic biodata mining methods to detect CDS and protein sequences of ORF1ab polyprotein of SARS-CoV-2 isolated from oronasopharynx of an Iranian patient. Read More

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http://dx.doi.org/10.1186/s12575-020-00121-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7171442PMC

Caco-2 Cells for Measuring Intestinal Cholesterol Transport - Possibilities and Limitations.

Biol Proced Online 2020 11;22. Epub 2020 Apr 11.

1Department of Pharmacognosy, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria.

Background: The human Caco-2 cell line is a common in vitro model of the intestinal epithelial barrier. As the intestine is a major interface in cholesterol turnover and represents a non-biliary pathway for cholesterol excretion, Caco-2 cells are also a valuable model for studying cholesterol homeostasis, including cholesterol uptake and efflux. Currently available protocols are, however, either sketchy or not consistent among different laboratories. Read More

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http://dx.doi.org/10.1186/s12575-020-00120-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7149936PMC

High-Resolution Confocal Fluorescence Imaging of Serine Hydrolase Activity in Cryosections - Application to Glioma Brain Unveils Activity Hotspots Originating from Tumor-Associated Neutrophils.

Biol Proced Online 2020 15;22. Epub 2020 Mar 15.

1Institute of Biomedicine, University of Eastern Finland (UEF), POB 1627, FI-70211 Kuopio, Finland.

Background: Serine hydrolases (SHs) are a functionally diverse family of enzymes playing pivotal roles in health and disease and have emerged as important therapeutic targets in many clinical conditions. Activity-based protein profiling (ABPP) using fluorophosphonate (FP) probes has been a powerful chemoproteomic approach in studies unveiling roles of SHs in various biological systems. ABPP utilizes cell/tissue proteomes and features the FP-warhead, linked to a fluorescent reporter for in-gel fluorescence imaging or a biotin tag for streptavidin enrichment and LC-MS/MS-based target identification. Read More

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http://dx.doi.org/10.1186/s12575-020-00118-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7073015PMC

Adjuvant Chemotherapy with Chinese Herbal Medicine Formulas Versus Placebo in Patients with Lung Adenocarcinoma after Radical Surgery: a Multicenter, Randomized, Double-Blind, Placebo-Controlled Trial.

Biol Proced Online 2020 1;22. Epub 2020 Mar 1.

1Department of Oncology, Yueyang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine, Shanghai, China.

Background: The toxicity and side effects caused by adjuvant chemotherapy (ACT) after radical surgery for lung adenocarcinoma (LAC) lead to early termination frequently. This study was conducted to provide an objective basis for the effect of Chinese herbal medicine formulas (CHMFs) combined with chemotherapy in reducing toxicity and enhancing efficacy of ACT.

Method: From February 17th, 2012 to March 20th, 2015, 233 patients from 7 hospitals diagnosed with LAC in IB~IIIA stage were randomly assigned into ACT + CHMF group (116 patients) and ACT + placebo group (117 patients). Read More

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http://dx.doi.org/10.1186/s12575-020-00117-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7049384PMC

Exploring G Protein-Coupled Receptor Signaling in Primary Pancreatic Islets.

Biol Proced Online 2020 15;22. Epub 2020 Feb 15.

1Rudolf Schönheimer Institute of Biochemistry, Medical Faculty, University of Leipzig, Leipzig, Germany.

Background: Targeting G protein-coupled receptors (GPCRs) in pancreatic cells is feasible to modulate glucose-induced insulin secretion. Because pancreatic islets consist of several cell types and GPCRs can couple to more than one G-protein family, results obtained in pancreatic cell lines do not always match the response in primary cells or intact islets. Therefore, we set out to establish a protocol to analyze second messenger activation in mouse pancreatic islets. Read More

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http://dx.doi.org/10.1186/s12575-019-0116-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7023723PMC
February 2020

A microcarrier-based spheroid 3D invasion assay to monitor dynamic cell movement in extracellular matrix.

Biol Proced Online 2020 1;22. Epub 2020 Feb 1.

1Laboratory of Experimental Oncology, Department of Pathology, Erasmus Medical Center, Rotterdam, the Netherlands.

Background: Cell invasion through extracellular matrix (ECM) is a critical step in tumor metastasis. To study cell invasion in vitro, the internal microenvironment can be simulated via the application of 3D models.

Results: This study presents a method for 3D invasion examination using microcarrier-based spheroids. Read More

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http://dx.doi.org/10.1186/s12575-019-0114-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6995242PMC
February 2020

Analytical Validation of Telomere Analysis Technology® for the High-Throughput Analysis of Multiple Telomere-Associated Variables.

Biol Proced Online 2020 15;22. Epub 2020 Jan 15.

Life Length SL, Miguel Ángel 11, 28010 Madrid, Spain.

Background: A large number of studies have suggested a correlation between the status of telomeres and disease risk. High-throughput quantitative fluorescence in situ hybridization (HT Q-FISH) is a highly accurate telomere measurement technique that can be applied to the study of large cell populations. Here we describe the analytical performance testing and validation of Telomere Analysis Technology (TAT®), a laboratory-developed HT Q-FISH-based methodology that includes HT imaging and software workflows that provide a highly detailed view of telomere populations. Read More

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https://link.springer.com/track/pdf/10.1186/s12575-019-0115-
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https://www.researchgate.net/publication/20812666_Telomeres_
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https://www.researchgate.net/publication/322521342_Compariso
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http://dx.doi.org/10.1186/s12575-019-0115-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6961256PMC
January 2020

Glycosaminoglycans from Co-Products of «»: Extraction and Purification in Reference to the European Pharmacopoeia Requirement.

Biol Proced Online 2020 2;22. Epub 2020 Jan 2.

1Blue Biotechnology & Aquatic Bioproducts Laboratory (B3Aqua)-Institut National des Sciences et technologies de la Mer (INSTM), 28, street March 2, 1934 -Salammbô, 2035 Tunis, Tunisia.

Background: Glycosaminoglycans (GAGs), including hyaluronic acid (HA), dermatan sulfate (DS) and chondroitin sulfate (CS) are essential components of the bone and cartilage tissues. CS isolated from the cartilage tissue of various animals has found application in pharmaceuticals, cosmetics and food industries. In the first part of the present work, three methods were used and compared to extract and purify glycosaminoglycans (GAGs) from the cartilage powder of a local cartilaginous marine species «». Read More

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http://dx.doi.org/10.1186/s12575-019-0113-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6939328PMC
January 2020

Bone Marrow-Derived Mesenchymal Stem Cells Modified with Akt1 Ameliorates Acute Liver GVHD.

Biol Proced Online 2019 16;21:24. Epub 2019 Dec 16.

1State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, 288 Nanjing Road, Tianjin, China.

Background: Liver injury associated with acute graft-versus-host disease (aGVHD) is a frequent and severe complication of hematopoietic stem cell transplantation and remains a major cause of transplant-related mortality. Bone marrow-derived mesenchymal stem cells (BM-MSCs) has been proposed as a potential therapeutic approach for aGVHD. However, the therapeutic effects are not always achieved. Read More

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http://dx.doi.org/10.1186/s12575-019-0112-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6913026PMC
December 2019

Application of a New Multiplexed Array for Rapid, Sensitive, Simultaneous and Quantitative Assessment of Spliced and Unspliced XBP1.

Biol Proced Online 2019 15;21:22. Epub 2019 Nov 15.

Randox Teoranta, Meenmore, Dungloe, Co. Donegal Ireland.

Background: IRE1α-mediated unconventional splicing of XBP1 is emerging as a biomarker in several disease states and is indicative of activation of the unfolded protein response sensor IRE1. Splicing of mRNA results in the translation of two distinct XBP1 protein isoforms (XBP1s and XBP1u) which, due to post-translational regulation, do not correlate with mRNA levels. As both XBP1 isoforms are implicated in pathogenic or disease progression mechanisms there is a need for a reliable, clinically applicable method to detect them. Read More

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http://dx.doi.org/10.1186/s12575-019-0111-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6857227PMC
November 2019

Cell-Wide Survey of Amide-Bonded Lysine Modifications by Using Deacetylase CobB.

Biol Proced Online 2019 1;21:23. Epub 2019 Dec 1.

1Institutes of Biomedical Sciences, Obstetrics & Gynecology Hospital of Fudan University, State Key Lab of Genetic Engineering and School of Life Sciences, Shanghai, People's Republic of China.

Background: Lysine post-translational modifications are important regulators of protein function. Proteomic and biochemical approaches have resulted in identification of several lysine modifications, including acetylation, crotonylation, and succinylation. Here, we developed an approach for surveying amide-bonded lysine modifications in the proteome of human tissues/cells based on the observation that many lysine modifications are amide-bonded and that the deacetylase, CobB, is an amidase. Read More

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http://dx.doi.org/10.1186/s12575-019-0109-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6885319PMC
December 2019

Manipulating Expression by Promoter to Regulate Plant Architecture and Yield Traits both in Seasonal and Ratooning Rice.

Biol Proced Online 2019 4;21:21. Epub 2019 Nov 4.

1Hunan Provincial Key Laboratory of Phytohormones and Growth Development, Hunan Agricultural University, Changsha, 410128 China.

Background: Rice ( L.) feeds more than half of the world's population. Ratooning rice is an economical alternative to the second seasonal rice, thus increasing the yield of ratooning rice is highly important. Read More

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http://dx.doi.org/10.1186/s12575-019-0110-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6827258PMC
November 2019
1.792 Impact Factor

Comprehensive Transcriptomic Analysis of Mouse Gonadal Development Involving Sexual Differentiation, Meiosis and Gametogenesis.

Biol Proced Online 2019 15;21:20. Epub 2019 Oct 15.

1Renji Hospital, Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200032 China.

Background: Mammalian gonadal development is crucial for fertility. Sexual differentiation, meiosis and gametogenesis are critical events in the process of gonadal development. Abnormalities in any of these events may cause infertility. Read More

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http://dx.doi.org/10.1186/s12575-019-0108-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6794783PMC
October 2019
1 Read

DNA Methylation Validation Methods: a Coherent Review with Practical Comparison.

Biol Proced Online 2019 1;21:19. Epub 2019 Oct 1.

2Institute of Hematology and Blood Transfusion, Prague, Czech Republic.

Here, we present a practical overview of four commonly used validation methods for DNA methylation assessment: methylation specific restriction endonucleases (MSRE) analysis, pyrosequencing, methylation specific high-resolution DNA melting (MS-HRM) and quantitative methylation specific polymerase chain reaction (qMSP). Using these methods, we measured DNA methylation levels of three loci in human genome among which one was highly methylated, one intermediately methylated and one unmethylated. We compared the methods in terms of primer design demands, methods' feasibility, accuracy, time and money consumption, and usability for clinical diagnostics. Read More

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http://dx.doi.org/10.1186/s12575-019-0107-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6771119PMC
October 2019
1 Read

MBEC Versus MBIC: the Lack of Differentiation between Biofilm Reducing and Inhibitory Effects as a Current Problem in Biofilm Methodology.

Biol Proced Online 2019 13;21:18. Epub 2019 Sep 13.

1Institute for Infectious Diseases and Infection Control, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany.

Background: Biofilms are communities of aggregated, matrix-embedded microbial cells showing a high tolerance to an in principle adequate antibiotic therapy, often resulting in treatment failure. A major challenge in the management of biofilm-associated infections is the development of adequate, standardized biofilm susceptibility testing assays that are clinically meaningful, i.e. Read More

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http://dx.doi.org/10.1186/s12575-019-0106-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6743098PMC
September 2019
1 Read

Development and Validation of Quantitative Real-Time PCR for the Detection of Residual CHO Host Cell DNA and Optimization of Sample Pretreatment Method in Biopharmaceutical Products.

Biol Proced Online 2019 1;21:17. Epub 2019 Sep 1.

The fourth research department, Lanzhou Institute of Biological Products Co., Ltd, No.888 Yanchang Road, Chengguan District, Lanzhou City, Gansu Province China.

Background: The presence of residual DNA carried by biological products in the body may lead to an increased oncogenicity, infectivity, and immunomodulatory risk. Therefore, current agencies including WHO, EU, and the FDA limited the accepted amounts of residual DNA (less than 10 ng or 100 pg/dose). Among the methods of detecting residual DNA, qPCR is considered to be the most practical for residual DNA quantitation due to its sensitivity, accuracy, precision, and time-saving. Read More

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https://biologicalproceduresonline.biomedcentral.com/article
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http://dx.doi.org/10.1186/s12575-019-0105-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6717637PMC
September 2019
5 Reads

Genetic Manipulation of MicroRNAs in the Silk Gland of Silkworm, .

Biol Proced Online 2019 15;21:16. Epub 2019 Aug 15.

1State Key Laboratory of Silkworm Genome Biology,Biological Science Research Center, Southwest University, Chongqing, 400715 People's Republic of China.

Background: MicroRNAs (miRNAs) are a class of non-coding RNAs with important post-transcriptional regulatory functions. To reveal the function of miRNAs , the critical step is to change their expression levels in the tissues or organs. In this work, we explored the application of several important genetic techniques in altering the expression of silk gland-specific miR-274 of silkworm (). Read More

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http://dx.doi.org/10.1186/s12575-019-0102-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6694536PMC
August 2019
1 Read

Immunostick Test for Detecting ζ-Globin Chains and Screening of the Southeast Asian α-Thalassemia 1 Deletion.

Biol Proced Online 2019 1;21:15. Epub 2019 Aug 1.

1Division of Clinical Immunology, Department of Medical Technology, Faculty of Associated Medical Sciences, Chiang Mai University, Chiang Mai, 50200 Thailand.

Background: Couples who carry α-thalassemia-1 deletion are at 25% risk of having a fetus with hemoglobin Bart's hydrops fetalis. Southeast Asian deletion (--(SEA)) is the most common type of α-thalassemia 1 among Southeast Asian populations. Thus, identification of the (--(SEA)) α-thalassemia 1 carrier is necessary for controlling severe α-thalassemia in Southeast Asian countries. Read More

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http://dx.doi.org/10.1186/s12575-019-0104-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6670165PMC
August 2019
5 Reads

Exploiting Differential Gene Expression to Discover Ionic and Osmotic-Associated Transcripts in the Halophyte Grass .

Biol Proced Online 2019 15;21:14. Epub 2019 Jul 15.

3Department of Agronomy and Plant Breeding, Faculty of Agriculture, Bu-Ali Sina University, Hamedan, Iran.

Background: Salinity as a most significant environmental challenges affects the growth and productivity of plants worldwide. In this study, the ionic and iso-osmotic effects of salt stress were investigated in L., a halophyte grass species from Poaceae family, by cDNA-amplified fragment length polymorphism (cDNA-AFLP) technique. Read More

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http://dx.doi.org/10.1186/s12575-019-0103-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628506PMC
July 2019
1 Read

Automated macrophage counting in DLBCL tissue samples: a ROF filter based approach.

Biol Proced Online 2019 1;21:13. Epub 2019 Jul 1.

Department of Pathology, Hematopathology Section and Lymph Node Registry, University of Kiel/University Hospital Schleswig-Holstein, Arnold-Heller-Str. 3, Haus 14, Kiel, 24105 Germany.

Background: For analysis of the tumor microenvironment in diffuse large B-cell lymphoma (DLBCL) tissue samples, it is desirable to obtain information about counts and distribution of different macrophage subtypes. Until now, macrophage counts are mostly inferred from gene expression analysis of whole tissue sections, providing only indirect information. Direct analysis of immunohistochemically (IHC) fluorescence stained tissue samples is confronted with several difficulties, e. Read More

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http://dx.doi.org/10.1186/s12575-019-0098-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6600891PMC
July 2019
2 Reads

Establishment and Morphological Characterization of Patient-Derived Organoids from Breast Cancer.

Biol Proced Online 2019 15;21:12. Epub 2019 Jun 15.

1Nanomedicine Laboratory, Department of Biomedical and Clinical Sciences "Luigi Sacco", University of Milan, via G. B. Grassi, 74, 20157 Milan, Italy.

Background: Patient-derived organoids (PDO) technology represents an emerging tool for the study of tumor biology and drug responsiveness, thus being useful to design personalized medicine approaches. Despite several studies and clinical trials are ongoing using PDO from colorectal and pancreatic cancer, only few research papers have been published exploiting PDO from breast cancer. Here, we have developed a new protocol to establish PDO from surgical and biopsy samples. Read More

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http://dx.doi.org/10.1186/s12575-019-0099-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6570967PMC
June 2019
5 Reads

Correlations between quantitative parameters of contrast-enhanced ultrasound and vasculogenic mimicry in murine tumor model: a novel noninvasive technique for assessment?

Biol Proced Online 2019 11;21:11. Epub 2019 Jun 11.

1Wuxi Medical School, Jiangnan University, Wuxi, 214122 Jiangsu Province, People's Republic of China.

Objective: Vasculogenic mimicry (VM) is a novel mechanism of tumor blood supply distinct from endothelial vessel (EV). VM is associated with malignancy, invasion, metastasis, and poor prognosis. Hitherto a noninvasive method for the assessment of VM in vivo has been lacking. Read More

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http://dx.doi.org/10.1186/s12575-019-0101-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6560886PMC
June 2019
19 Reads

Correction to: Three-Dimensional Quantification of Spheroid Degradation-Dependent Invasion and Invadopodia Formation.

Biol Proced Online 2019 21;21:10. Epub 2019 May 21.

1Cancer Invasion and Metastasis Laboratory, Faculty of Dentistry, University of Toronto, Toronto, Canada.

[This corrects the article DOI: 10.1186/s12575-018-0085-6.]. Read More

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http://dx.doi.org/10.1186/s12575-019-0100-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6530126PMC
May 2019
1 Read

An Alternative Model of Laser-Induced Stroke in the Motor Cortex of Rats.

Biol Proced Online 2019 16;21. Epub 2019 May 16.

1Division of Anesthesiology and Critical Care, Soroka University Medical Center and the Faculty of Health Sciences, Ben-Gurion University of the Negev, 84101 Beer-Sheva, Israel.

Background: A common experimental rodent model for stroke includes induction by a technique in which middle cerebral artery is transiently (MCAO-t) or permanently (MCAO-p) occluded by catheterization. However, this model has prominent disadvantages which consist of the high variability of localization and size of the ischemic area, cases of intracranial hemorrhage and high mortality. Furthermore, the duration of a single MCAO operation takes about thirty minutes and requires highly trained staff. Read More

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http://dx.doi.org/10.1186/s12575-019-0097-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524336PMC
May 2019
3 Reads

Use of Plasmid pVMG to Make Transcriptional ß-Glucuronidase Reporter Gene Fusions in the Genome for Monitoring the Expression of Rhizobial Genes In Vivo.

Biol Proced Online 2019 3;21. Epub 2019 May 3.

Soil and Water Sciences Department, Cancer and Genetics Research Complex, University of Florida-Institute of Food and Agricultural Sciences, Room 330E, Gainesville, 32610 USA.

Background: The soil bacterium and its allies are important nitrogen-fixing bacterial symbionts that cause N-fixing nodules on the roots of legumes. Chromosomal ß-glucuronidase gene ( transcriptional fusions are frequently used to monitor the expression of bacterial genes during the symbiosis. However, the construction of the fusions is laborious. Read More

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http://dx.doi.org/10.1186/s12575-019-0096-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6498626PMC

An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data.

Biol Proced Online 2019 24;21. Epub 2019 Apr 24.

1Department of Electrical Engineering and Computer Science, University of Missouri, Columbia, MO 65211 USA.

Over the past decade, methods for predicting three-dimensional (3-D) chromosome and genome structures have proliferated. This has been primarily due to the development of high-throughput, next-generation chromosome conformation capture (3C) technologies, which have provided next-generation sequencing data about chromosome conformations in order to map the 3-D genome structure. The introduction of the Hi-C technique-a variant of the 3C method-has allowed researchers to extract the interaction frequency (IF) for all loci of a genome at high-throughput and at a genome-wide scale. Read More

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http://dx.doi.org/10.1186/s12575-019-0094-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6482566PMC
April 2019
1 Read
1.792 Impact Factor

A Cautionary Tale: Endogenous Biotinylated Proteins and Exogenously-Introduced Protein A Cause Antibody-Independent Artefacts in Western Blot Studies of Brain-Derived Proteins.

Biol Proced Online 2019 18;21. Epub 2019 Apr 18.

1Departments of Neurology, University of Minnesota, Minneapolis, MN 55455 USA.

Antibodies are commonly used to detect or isolate proteins from biological samples. Much attention has been paid to the potential for poorly-characterized antibodies to lead to misleading results, but artefacts may also occur. Here, we recount two examples of antibody-independent artefacts that have confounded the interpretation of results in our search for molecular entities associated with memory loss in Alzheimer's disease (AD). Read More

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http://dx.doi.org/10.1186/s12575-019-0095-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6474067PMC
April 2019
2 Reads

Development of Effective Therapeutics Targeting HER3 for Cancer Treatment.

Biol Proced Online 2019 19;21. Epub 2019 Mar 19.

2Department of Genetics, Stanley S. Scott Cancer Center, School of Medicine, Louisiana State University Health Sciences Center, New Orleans, LA USA.

HER3 is the third member of the human epidermal growth factor receptor (HER/EGFR) family, and unlike its other family members, is unique due to its minimal intrinsic kinase activity. As a result, HER3 has to interact with another receptor tyrosine kinase (RTK), such as EGFR or HER2, in order to activate the PI-3 K/Akt, MEK/MAPK, Jak/Stat pathways, as well as Src kinase. Over-expression of HER3 in various human cancers promotes tumor progression by increasing metastatic potential and acting as a major cause of treatment failure. Read More

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http://dx.doi.org/10.1186/s12575-019-0093-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6425631PMC
March 2019
3 Reads

Effective Visualization and Easy Tracking of Extracellular Vesicles in Glioma Cells.

Biol Proced Online 2019 15;21. Epub 2019 Mar 15.

National Centre for Cell Science (NCCS), Savitribai Phule Pune University Campus, Pune, India.

Extracellular vesicles (EVs) are nano-sized, membrane-bound structures secreted by cells and play critical roles in mediating intercellular signaling. EVs based on their size as well as mechanisms of biosynthesis are categorized as either microvesicles (200-1000 nm) or exosomes (30-200 nm). The EVs carry several biomolecules like proteins, DNAs, RNAs, and lipids into other cells and modulate several cellular functions. Read More

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http://dx.doi.org/10.1186/s12575-019-0092-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6419365PMC
March 2019
2 Reads

A simple and reliable protocol for long-term culture of murine bone marrow stromal (mesenchymal) stem cells that retained their in vitro and in vivo stemness in long-term culture.

Biol Proced Online 2019 1;21. Epub 2019 Feb 1.

2Endocrine Research (KMEB), Department of Endocrinology, Odense University Hospital and University of Southern Denmark, Odense, Denmark.

Background: Bone marrow derived stromal stem cells (BMSCs) are a clonogenic cell population that is characterized by self-renewal capacity and differentiation potential into osteoblasts, and other mesenchymal cell types. Mouse BMSCs (mBMSCs) are difficult to be cultured and propagated in vitro due to their replicative senescent phenotype, heterogeneity and high contamination with plastic adherent hematopoietic progenitors (HPCs). In this study, we described long-term culture of homogenous population of mBMSCs using simple and highly reproducible approach based on frequent subculturing (FS) at fixed split ratio in the presence of basic fibroblast growth factor (bFGF). Read More

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http://dx.doi.org/10.1186/s12575-019-0091-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357407PMC
February 2019
6 Reads
1.792 Impact Factor

Regeneration of TiO Nanotube Arrays after Long-Term Cell and Tissue Culture for Multiple Use - an Environmental Scanning Electron Microscopy (ESEM) Survey of Adult Pig Retina and beyond.

Biol Proced Online 2019 29;21. Epub 2019 Jan 29.

1Leibniz-Institut für Oberflächenmodifizierung e.V. (IOM), Permoserstr. 15, 04318 Leipzig, Germany.

Long-term organotypic culture of adult tissues not only open up possibilities for studying complex structures of explants in vitro, but also can be employed e.g. to investigate pathological changes, their fingerprints on tissue mechanics, as well as the effectiveness of drugs. Read More

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http://dx.doi.org/10.1186/s12575-019-0090-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6350358PMC
January 2019

Circular Estimate Method (CEM) - a Simple Method to Estimate Culture Densities in Liquid Medium.

Biol Proced Online 2019 15;21. Epub 2019 Jan 15.

1Instituto de Ciências Biológicas (ICB), Universidade Federal do Rio Grande - FURG, Av. Itália km 8, Rio Grande, RS 96203-900 Brazil.

Background: Nematodes are used in many different fields of science, including environmental and biomedical research. Counting and/or estimating nematode numbers is required during research. Although being one of the most common procedures, this apparently simple task is a time-consuming process, prone to errors and concerns regarding procedure, reliability, and accuracy. Read More

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http://dx.doi.org/10.1186/s12575-018-0089-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6334471PMC
January 2019
2 Reads

Performance evaluation for MOTIFSIM.

Biol Proced Online 2018 18;20:23. Epub 2018 Dec 18.

Department of Computer Science and Engineering, University of Connecticut, Storrs, CT 06269 USA.

Background: Previous studies show various results obtained from different motif finders for an identical dataset. This is largely due to the fact that these tools use different strategies and possess unique features for discovering the motifs. Hence, using multiple tools and methods has been suggested because the motifs commonly reported by them are more likely to be biologically significant. Read More

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http://dx.doi.org/10.1186/s12575-018-0088-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6299673PMC
December 2018
1 Read

Anti-inflammatory Activity of Tocotrienols in Age-related Pathologies: A SASPected Involvement of Cellular Senescence.

Biol Proced Online 2018 20;20:22. Epub 2018 Nov 20.

Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, via Birarelli 8, 60121 Ancona, Italy.

Tocotrienols (T3) have been shown to represent a very important part of the vitamin E family since they have opened new opportunities to prevent or treat a multitude of age-related chronic diseases. The beneficial effects of T3 include the amelioration of lipid profile, the promotion of Nrf2 mediated cytoprotective activity and the suppression of inflammation. All these effects may be the consequence of the ability of T3 to target multiple pathways. Read More

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http://dx.doi.org/10.1186/s12575-018-0087-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6247629PMC
November 2018
1 Read
1.792 Impact Factor

CRISPR/Cas9 Knockout Strategies to Ablate lncRNA Gene in Cancer Cells.

Biol Proced Online 2018 1;20:21. Epub 2018 Nov 1.

1Department of Basic Sciences, Faculty of Veterinary Medicine, Ferdowsi University of Mashhad, Azadi Square, Mashhad, Iran.

Background: With the increasing discovery of long noncoding RNAs (lncRNAs), the application of functional techniques that could have very specific, efficient, and robust effects and readouts is necessary. Here, we have applied and analyzed three gene knockout (KO) strategies to ablate the gene in different colorectal adenocarcinoma cell lines. We refer to these strategies as "CRISPR excision", "CRISPR HDR", and "CRISPR du-HITI". Read More

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http://dx.doi.org/10.1186/s12575-018-0086-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6211572PMC
November 2018
24 Reads

Three-Dimensional Quantification of Spheroid Degradation-Dependent Invasion and Invadopodia Formation.

Biol Proced Online 2018 15;20:20. Epub 2018 Oct 15.

1Cancer Invasion and Metastasis Laboratory, Faculty of Dentistry, University of Toronto, Toronto, Canada.

Invadopodia are actin-rich, proteolytic structures that enable cancer cell to invade into the surrounding tissues. Several in vitro invasion assays have been used in the literature ranging from directional quantitative assays to complex three-dimensional (3D) analyses. One of the main limitations of these assays is the lack of quantifiable degradation-dependent invasion in a three-dimensional (3D) environment that mimics the tumor microenvironment. Read More

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http://dx.doi.org/10.1186/s12575-018-0085-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6190556PMC
October 2018
2 Reads

Modified SureSelect Target Enrichment Protocol for Illumina Multiplexed Sequencing of FFPE Samples.

Biol Proced Online 2018 12;20:19. Epub 2018 Oct 12.

1CIBER-ONC, Instituto de Salud Carlos III, Madrid, Spain.

Background: Personalised medicine is nowadays a major objective in oncology. Molecular characterization of tumours through NGS offers the possibility to find possible therapeutic targets in a time- and cost-effective way. However, the low quality and complexity of FFPE DNA samples bring a series of disadvantages for massive parallel sequencing techniques compared to high-quality DNA samples (from blood cells, cell cultures, etc. Read More

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http://dx.doi.org/10.1186/s12575-018-0084-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6182866PMC
October 2018
5 Reads

A New ELISA to Overcome the Pitfalls in Quantification of Recombinant Human Monoclonal Anti-HBs, GC1102, by Commercial Immunoassays.

Biol Proced Online 2018 27;20:18. Epub 2018 Sep 27.

4Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, 24641 Korea.

Several methods for the quantification of human anti-HBs, an antibody to hepatitis B surface antigen (HBsAg), have been developed based on enzyme reaction, chemiluminescence, fluorescence, and radioactivity for application to human serum or plasma. Commercial anti-HBs immunoassay kits use a sandwich method in which a bridge is formed by the anti-HBs between a HBsAg immobilized solid matrix and the labeled HBsAg. However, this direct sandwich enzyme-linked immunosorbent assay (ELISA) is insufficient to accurately evaluate the activity of the human monoclonal anti-HBs, GC1102. Read More

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https://www.researchgate.net/publication/327918351_A_New_ELI
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https://biologicalproceduresonline.biomedcentral.com/article
Publisher Site
http://dx.doi.org/10.1186/s12575-018-0083-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6158867PMC
September 2018
52 Reads

microRNA Regulation in Estrogen Receptor-Positive Breast Cancer and Endocrine Therapy.

Biol Proced Online 2018 11;20:17. Epub 2018 Sep 11.

Julius L. Chambers Biomedical/Biotechnology Research Institute, Department of Biological and Biomedical Sciences, North Carolina Central University, North Carolina Research Campus, 500 Laureate Way, NRI 4301, Kannapolis, North Carolina 28081 USA.

As de novo and acquired resistance to standard first line endocrine therapies is a growing clinical challenge for estrogen receptor-positive (ER) breast cancer patients, understanding the mechanisms of resistance is critical to develop novel therapeutic strategies to prevent therapeutic resistance and improve patient outcomes. The widespread post-transcriptional regulatory role that microRNAs (miRNAs) can have on various oncogenic pathways has been well-documented. In particular, several miRNAs are reported to suppress ERα expression via direct binding with the 3' UTR of mRNA, which can confer resistance to estrogen/ERα-targeted therapies. Read More

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http://dx.doi.org/10.1186/s12575-018-0082-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6134714PMC
September 2018
1 Read

Targeting of HER3 with Functional Cooperative miRNAs Enhances Therapeutic Activity in HER2-Overexpressing Breast Cancer Cells.

Biol Proced Online 2018 8;20:16. Epub 2018 Aug 8.

1Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, MS-8104, 12801 E. 17th Ave, Aurora, CO 80045 USA.

Background: The HER3 receptor functions as a major cause of drug resistance in cancer treatment. It is believed that therapeutic targeting of HER3 is required to improve patient outcomes. It is not clear whether a novel strategy with two functional cooperative miRNAs would effectively inhibit expression and potentiate the anti-proliferative/anti-survival effects of a HER2-targeted therapy (trastuzumab) and chemotherapy (paclitaxel) on HER2-overexpressing breast cancer cells. Read More

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http://dx.doi.org/10.1186/s12575-018-0081-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6081814PMC
August 2018
3 Reads

Real-Time Vital Mineralization Detection and Quantification during In Vitro Osteoblast Differentiation.

Biol Proced Online 2018 1;20:14. Epub 2018 Aug 1.

2Department of Clinical Science, University of Bergen, Po Box 7804, 5020, Bergen, Norway.

Background: In vitro studies of osteoblasts traditionally use Alizarin Red as a golden standard for the detection and quantification of mineralization, which is a marker of osteoblast differentiation. However, this method presents a number of drawbacks, including the need to fix cells, which prevents additional measurements. Years ago, Calcein Green was proposed as an alternative to Alizarin Red, with the advantage to be directly detectable in live cells. Read More

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http://dx.doi.org/10.1186/s12575-018-0079-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6069543PMC
August 2018
4 Reads

Optimization of Immunofluorescent Detection of Bone Marrow Disseminated Tumor Cells.

Biol Proced Online 2018 1;20:13. Epub 2018 Jul 1.

1The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, 600 North Wolfe St., Marburg Building Room 121, Baltimore, MD 21287 USA.

Background: Cancer metastasis is the primary cause of cancer-related deaths and remains incurable. Current clinical methods for predicting metastatic recurrence are not sensitive enough to detect individual cancer cells in the body; therefore, current efforts are directed toward liquid biopsy-based assays to capture circulating and disseminated tumor cells (CTCs and DTCs) in the blood and bone marrow, respectively. The most promising strategy is fluorescence-based immunostaining using cancer cell-specific markers. Read More

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http://dx.doi.org/10.1186/s12575-018-0078-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6026516PMC
July 2018
7 Reads

Icariin: a Potential Compound for the Recovery of Tibial Dyschondroplasia Affected Chicken Via Up-Regulating BMP-2 Expression.

Biol Proced Online 2018 1;20:15. Epub 2018 Jul 1.

1College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 People's Republic of China.

Background: Tibial dyschondroplasia (TD) is a skeletal disease of fast growing chicken and other avian species. It is characterized by an avascular and non-mineralized growth plate, which leads to a deformed tibial bone and lameness. Unfortunately, this disease is not only responsible for causing huge economic losses but also raises animal welfare concerns. Read More

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http://dx.doi.org/10.1186/s12575-018-0080-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6026509PMC
July 2018
3 Reads
1.792 Impact Factor

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

Biol Proced Online 2018 1;20:12. Epub 2018 Jun 1.

Division of Systems Neuroscience, National Brain Research Centre, Deemed University, Gurugram, Haryana India.

Background: 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 in the DNA solution may result in degradation of DNA on long term storage and inhibition of the polymerase chain reaction. In order to remove impurities and concentrate the DNA in solution, we have introduced modifications in the existing DNA isolation protocol using Chelex-100. Read More

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http://dx.doi.org/10.1186/s12575-018-0077-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984428PMC
June 2018
18 Reads

Isolation and Semi Quantitative PCR of Na/H Antiporter (SOS1 and NHX) Genes under Salinity Stress in .

Biol Proced Online 2018 1;20:11. Epub 2018 Jun 1.

2Agriculture and Biotechnology Research Institute, University of Zabol, Zabol, 98613-35856 Iran.

Background: is a dicotyledonous annual herb and belongs to the Amaranthaceae family. Genetic diversity and resistance to drought stress of this plant has made it widely scattered in different regions which contains highly genetic diversity and great potential as fodder and can grow on salty, drought affected areas. Since the soil salinity has become widely spread, environmental concern has sparked so many debates. Read More

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http://dx.doi.org/10.1186/s12575-018-0076-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5984343PMC
June 2018
5 Reads