Establishment and Morphological Characterization of Patient-Derived Organoids from Breast Cancer.
Conclusions: Despite obtaining some organoids from a surgical or biopsy specimen is not a difficult procedure, the establishment of a stable organoid line able to grow and replicate, suitable for long-term biobank storage, is not so obvious. A novel, simple and quick procedure to obtain PDO from surgical and biopsy samples is here proposed to achieve high success rate . PMID: 31223292 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - June 23, 2019 Category: Molecular Biology Authors: Mazzucchelli S, Piccotti F, Allevi R, Truffi M, Sorrentino L, Russo L, Agozzino M, Signati L, Bonizzi A, Villani L, Corsi F Tags: Biol Proced Online Source Type: research

Correlations between quantitative parameters of contrast-enhanced ultrasound and vasculogenic mimicry in murine tumor model: a novel noninvasive technique for assessment?
Abstract 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. Methods: Contrast-enhanced ultrasound (CEUS) was performed to evaluate the quantitative parameters of tumors in mice. CD31 immunohistochemistry-Periodic Acid-Schiff double staining was conducted to identify the VM or EV in tumor tissues. Correlations between perfusion parameters and VM density was analyzed by Pearson correlation ...
Source: Biological Procedures Online - June 19, 2019 Category: Molecular Biology Authors: Zhou YT, Cai WW, Li Y, Jiang X, Feng L, Zhu QY, Liu YL, Chen YX, Li SS, Du B, Lang F, Wu PX, Qiu LY Tags: Biol Proced Online Source Type: research

Correction to: Three-Dimensional Quantification of Spheroid Degradation-Dependent Invasion and Invadopodia Formation.
Abstract [This corrects the article DOI: 10.1186/s12575-018-0085-6.]. PMID: 31139025 [PubMed - in process] (Source: Biological Procedures Online)
Source: Biological Procedures Online - May 31, 2019 Category: Molecular Biology Authors: Goertzen C, Eymael D, Magalhaes M Tags: Biol Proced Online Source Type: research

An Alternative Model of Laser-Induced Stroke in the Motor Cortex of Rats.
Conclusions: The data presented in this paper show that the model of laser irradiation can serve as an effective method of inducible brain cortical infarction and may lead to a better understanding of the pathophysiology of ischemic stroke and the future development of new drugs and other neuro-protective agents. PMID: 31130825 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - May 29, 2019 Category: Molecular Biology Authors: Boyko M, Kuts R, Gruenbaum BF, Tsenter P, Grinshpun J, Frank D, Zvenigorodsky V, Melamed I, Brotfain E, Zlotnik A Tags: Biol Proced Online Source Type: research

Use of Plasmid pVMG to Make Transcriptional ß-Glucuronidase Reporter Gene Fusions in the Rhizobium Genome for Monitoring the Expression of Rhizobial Genes In Vivo.
Conclusions: A simple, pVMG-based method for construction of chromosomal uidA transcriptional fusions has been successfully used in the model rhizobium S. meliloti. It is also applicable for other rhizobial strains. PMID: 31073281 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - May 11, 2019 Category: Molecular Biology Authors: Gao M, Benge A, Wu TJ, Javier R Tags: Biol Proced Online Source Type: research

An Overview of Methods for Reconstructing 3-D Chromosome and Genome Structures from Hi-C Data.
Abstract 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. In this review we describe, ...
Source: Biological Procedures Online - May 4, 2019 Category: Molecular Biology Authors: Oluwadare O, Highsmith M, Cheng J Tags: Biol Proced Online Source Type: research

A Cautionary Tale: Endogenous Biotinylated Proteins and Exogenously-Introduced Protein A Cause Antibody-Independent Artefacts in Western Blot Studies of Brain-Derived Proteins.
Abstract 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 antibody-independent 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). First, when using biotin-avidin systems for antibody detection, endogenous biotinylated proteins created spurious bands in Western blots of brain lysates f...
Source: Biological Procedures Online - April 27, 2019 Category: Molecular Biology Authors: Grant MKO, Shapiro SL, Ashe KH, Liu P, Zahs KR Tags: Biol Proced Online Source Type: research

Development of Effective Therapeutics Targeting HER3 for Cancer Treatment.
Abstract 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. Effective inhibition of HER3, and/or the key downstream mediators of HE...
Source: Biological Procedures Online - April 3, 2019 Category: Molecular Biology Authors: Liu X, Liu S, Lyu H, Riker AI, Zhang Y, Liu B Tags: Biol Proced Online Source Type: research

Effective Visualization and Easy Tracking of Extracellular Vesicles in Glioma Cells.
In conclusion, the method described here is a simple, sensitive and efficient immune-fluorescence based method for visualization of molecules within the EVs. PMID: 30918474 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - March 30, 2019 Category: Molecular Biology Authors: Mondal A, Ashiq KA, Phulpagar P, Singh DK, Shiras A Tags: Biol Proced Online Source Type: research

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.
Conclusions: Our data provide a simple and reliable protocol for generating long-term cultures of mBMSCs and OBs with retained high in vitro and in vivo osteoblast differentiation capacities for use in pre-clinical and molecular mechanism studies. PMID: 30733647 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - February 9, 2019 Category: Molecular Biology Authors: Abdallah BM, Alzahrani AM, Abdel-Moneim AM, Ditzel N, Kassem M Tags: Biol Proced Online Source Type: research

Regeneration of TiO2 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.
Abstract 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. While conventional culture methods do not allow for survival times of more than a few days, we have demonstrated recently that TiO2 nanotube arrays allow to maintain integrity of numerous tissues, including retina, brain, spline and tonsils, for as long as 2 weeks in vitro. A mystery in culturing has been the interaction of tissue w...
Source: Biological Procedures Online - February 7, 2019 Category: Molecular Biology Authors: Friebe S, Mayr SG Tags: Biol Proced Online Source Type: research

Circular Estimate Method (CEM) - a Simple Method to Estimate Caenorhabditis elegans Culture Densities in Liquid Medium.
Conclusion: The proposed method is accurate, facile and reproducible, requiring simple, inexpensive materials that make it an excellent alternative to the DM manual counting procedure. Although the DM is faster, its estimates are not as accurate or as precise as those of the new proposed method. PMID: 30675134 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - January 26, 2019 Category: Molecular Biology Authors: Josende ME, Nunes SM, Müller L, Ferreira-Cravo M, Monserrat JM, Ventura-Lima J Tags: Biol Proced Online Source Type: research

Performance evaluation for MOTIFSIM.
Conclusions: The pair-wise comparison results reveal that MOTIFSIM attains better performance than the un-gapped Smith-Waterman algorithm and four distance metrics. The clustering results also demonstrate that MOTIFSIM achieves similar or even better performance than RSAT Matrix-clustering. Furthermore, the findings indicate if the motif detection does not require a special tool for detecting a specific type of motif then using multiple motif finders and combining with MOTIFSIM for obtaining the common significant motifs, it improved the results for DNA motif detection. PMID: 30574025 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - December 24, 2018 Category: Molecular Biology Authors: Tran NTL, Huang CH Tags: Biol Proced Online Source Type: research

Anti-inflammatory Activity of Tocotrienols in Age-related Pathologies: A SASPected Involvement of Cellular Senescence.
Abstract 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. We here propose that these effects may be the result of a single target of T3, namely senescent cells. Indeed, T3 may act by a direct suppression of the senes...
Source: Biological Procedures Online - November 29, 2018 Category: Molecular Biology Authors: Malavolta M, Pierpaoli E, Giacconi R, Basso A, Cardelli M, Piacenza F, Provinciali M Tags: Biol Proced Online Source Type: research

CRISPR/Cas9 Knockout Strategies to Ablate CCAT1 lncRNA Gene in Cancer Cells.
Conclusions: The strategies applied and introduced in this study can be used for the generation of CCAT1 knockout cell lines and in principle can be applied to the deletion of other lncRNAs for the study of their function. PMID: 30410426 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - November 10, 2018 Category: Molecular Biology Authors: Zare K, Shademan M, Ghahramani Seno MM, Dehghani H Tags: Biol Proced Online Source Type: research

Three-Dimensional Quantification of Spheroid Degradation-Dependent Invasion and Invadopodia Formation.
Abstract 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. In this article, we describe a new invasion and degradation assay based on the currently available tumor spheroid model that allows long-term high-resolution i...
Source: Biological Procedures Online - October 27, 2018 Category: Molecular Biology Authors: Goertzen C, Eymael D, Magalhaes M Tags: Biol Proced Online Source Type: research

Modified SureSelectQXT Target Enrichment Protocol for Illumina Multiplexed Sequencing of FFPE Samples.
Conclusions: Our experiments allowed us to unveil the behaviour of low-quality FFPE DNA samples during the construction of SureSelectQXT libraries. Sequencing results showed that, using our modified SureSelectQXT protocol, the final percentage of usable reads for low-quality samples was increased more than three times allowing to reach median depth/million reads values of 76.35. This value is equivalent to ~ 0.9 and ~ 0.7 of the values obtained for good-quality FFPE and high-quality DNA respectively. PMID: 30337841 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - October 20, 2018 Category: Molecular Biology Authors: Rosa-Rosa JM, Caniego-Casas T, Leskela S, Muñoz G, Del Castillo F, Garrido P, Palacios J Tags: Biol Proced Online Source Type: research

A New ELISA to Overcome the Pitfalls in Quantification of Recombinant Human Monoclonal Anti-HBs, GC1102, by Commercial Immunoassays.
Abstract 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. As an alternative, we develope...
Source: Biological Procedures Online - October 4, 2018 Category: Molecular Biology Authors: Shin YW, Cho DH, Song GW, Kim SH Tags: Biol Proced Online Source Type: research

microRNA Regulation in Estrogen Receptor-Positive Breast Cancer and Endocrine Therapy.
Abstract 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 ESR1 mRNA, which can confer...
Source: Biological Procedures Online - September 16, 2018 Category: Molecular Biology Authors: Howard EW, Yang X Tags: Biol Proced Online Source Type: research

Targeting of HER3 with Functional Cooperative miRNAs Enhances Therapeutic Activity in HER2-Overexpressing Breast Cancer Cells.
Conclusions: Here, we showed that functional cooperative miRNAs effectively suppressed erbB3 expression. This novel approach targeting of HER3 was able to enhance the therapeutic efficacy of trastuzumab and paclitaxel against HER2-overexpressing breast cancer. PMID: 30093840 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - August 12, 2018 Category: Molecular Biology Authors: Lyu H, Huang J, He Z, Liu B Tags: Biol Proced Online Source Type: research

Real-Time Vital Mineralization Detection and Quantification during In Vitro Osteoblast Differentiation.
Conclusions: The combination of Calcein Green and the real-time imaging station IncuCyte ZOOM can efficiently replace the Alizarin Red method, and allows very accurate and time-saving assessment of the level and the dynamics of matrix mineralization. PMID: 30078998 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - August 10, 2018 Category: Molecular Biology Authors: Serguienko A, Wang MY, Myklebost O Tags: Biol Proced Online Source Type: research

Icariin: a Potential Compound for the Recovery of Tibial Dyschondroplasia Affected Chicken Via Up-Regulating BMP-2 Expression.
Abstract 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. Icariin is a flavonoid, which is isolated from Epimedium pubescens herb, and it has been used to cure different diseases including bone fractures and osteoporosis. Results: We designed this experiment to use icariin for the treatment of TD affect ...
Source: Biological Procedures Online - July 12, 2018 Category: Molecular Biology Authors: Iqbal M, Zhang H, Mehmood K, Li A, Jiang X, Wang Y, Zhang J, Iqbal MK, Rehman MU, Yao W, Yang S, Li J Tags: Biol Proced Online Source Type: research

Optimization of Immunofluorescent Detection of Bone Marrow Disseminated Tumor Cells.
Conclusions: Robust optimization to increase the signal-to-noise ratio of immunofluorescent staining of bone marrow is required in order to achieve the necessary sensitivity and specificity for rare cell detection. Background immunofluorescent staining in bone marrow causes uncertainty and inconsistency among investigators, which can be overcome by systematically addressing each contributing source. Our optimized assay eliminates sources of background signal, and is adaptable to automated staining platforms for high throughput analysis. PMID: 29988526 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - July 12, 2018 Category: Molecular Biology Authors: Axelrod HD, Pienta KJ, Valkenburg KC Tags: Biol Proced Online Source Type: research

Isolation and Semi Quantitative PCR of Na+/H+ Antiporter (SOS1 and NHX) Genes under Salinity Stress in Kochia scoparia.
Conclusion: The results suggest that K.SSOS1 and K.SNHX play an essential role in salt tolerance of K.scoparia and they can be useful to improve salt tolerance in other crops. PMID: 29881329 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - June 9, 2018 Category: Molecular Biology Authors: Fahmideh L, Fooladvand Z Tags: Biol Proced Online Source Type: research

Method for improving the quality of genomic DNA obtained from minute quantities of tissue and blood samples using Chelex 100 resin.
Conclusion: Our method is different from other extraction methods since it uses non-toxic, easily available and inexpensive reagents as well as minimal amounts of blood or tissue samples for the DNA extraction process. Besides its use in sex determination and genotyping in lab animals as described in this paper, it may also have applications in forensic science and diagnostics such as the easy detection of pathogenic DNA in blood. PMID: 29881330 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - June 9, 2018 Category: Molecular Biology Authors: Singh UA, Kumari M, Iyengar S Tags: Biol Proced Online Source Type: research

Use of RNA Immunoprecipitation Method for Determining Sinorhizobium meliloti RNA-Hfq Protein Associations In Vivo.
Conclusions: This article describes the RIP method for determining Sinorhizobium meliloti RNA-Hfq associations in vivo. It is also applicable to other rhizobia living in planta, although some tissue-specific modification related to sample disruption and homogenization may be needed. PMID: 29743820 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - May 12, 2018 Category: Molecular Biology Authors: Gao M, Benge A, Mesa JM, Javier R, Liu FX Tags: Biol Proced Online Source Type: research

Blockade of ITGA2 Induces Apoptosis and Inhibits Cell Migration in Gastric Cancer.
Conclusions: Here, we showed that the mRNA expression levels of ITGA2 comparing to normal tissues significantly increased. In addition, the results revealed that targeting integrin alpha 2 subunit by antibodies did not only inhibit cell migration, but also induce apoptosis effect on gastric cancer cells. Interestingly, higher expression level of ITGA2 led to significant effects on apoptosis progression during anti-ITGA2 antibody treatment, which indicated that ITGA2 expression levels directly correlate with their functionality. Our findings suggest that ITGA2 is a potential therapeutic target for gastric cancer. PMID:...
Source: Biological Procedures Online - May 12, 2018 Category: Molecular Biology Authors: Chuang YC, Wu HY, Lin YL, Tzou SC, Chuang CH, Jian TY, Chen PR, Chang YC, Lin CH, Huang TH, Wang CC, Chan YL, Liao KW Tags: Biol Proced Online Source Type: research

DNA Area and NETosis Analysis (DANA): a High-Throughput Method to Quantify Neutrophil Extracellular Traps in Fluorescent Microscope Images.
Conclusions: DANA provides a means to quantify DNA decondensation and the frequency of NET-like structures using a variety of different fluorescent markers in a rapid, reliable, simple, high-throughput, and cost-effective manner making it optimal to assess NETosis in a variety of conditions. PMID: 29618953 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - April 8, 2018 Category: Molecular Biology Authors: Rebernick R, Fahmy L, Glover C, Bawadekar M, Shim D, Holmes CL, Rademacher N, Potluri H, Bartels CM, Shelef MA Tags: Biol Proced Online Source Type: research

Treatment of Advanced Non-small-Cell Lung Cancer with Qi-Nourishing Essence-Replenishing Chinese Herbal Medicine Combined with Chemotherapy.
Conclusion: Qi-nourishing essence-replenishing Chinese herbal medicine combined with chemotherapy improves survival of advanced NSCLC patients with essence and qi deficiency. PMID: 29618954 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - April 8, 2018 Category: Molecular Biology Authors: Gong Y, Xu Z, Jin C, Deng H, Wang Z, Zhou W, Zhang M, Zhao X, Wang L Tags: Biol Proced Online Source Type: research

Silhouette Scores for Arbitrary Defined Groups in Gene Expression Data and Insights into Differential Expression Results.
Conclusion: Silhouettes is useful for exploring data with predefined group labels. It would help provide both an objective evaluation of HSC dendrograms and insights into the DE results with regard to the compared groups. PMID: 29507534 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - March 7, 2018 Category: Molecular Biology Authors: Zhao S, Sun J, Shimizu K, Kadota K Tags: Biol Proced Online Source Type: research

High-Sensitivity and High-Resolution In Situ Hybridization of Coding and Long Non-coding RNAs in Vertebrate Ovaries and Testes.
Conclusions: This high-sensitivity and high-resolution in situ hybridization is applicable to many vertebrate species and to various tissues and organs and will be useful for studies on the subcellular regulation of gene expression at the level of RNA localization. PMID: 29507535 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - March 7, 2018 Category: Molecular Biology Authors: Takei N, Nakamura T, Kawamura S, Takada Y, Satoh Y, Kimura AP, Kotani T Tags: Biol Proced Online Source Type: research

Visualisation of Multiple Tight Junctional Complexes in Human Airway Epithelial Cells.
Conclusions: The present study demonstrates the importance of a personalised approach to optimise staining for the visualisation of different tight junction proteins. Of significance, the workflow, once optimised, can readily be translated into primary airway epithelial cell air-liquid interface cultures where it can be used to assess barrier integrity in chronic lung diseases. PMID: 29434527 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - February 14, 2018 Category: Molecular Biology Authors: Buckley AG, Looi K, Iosifidis T, Ling KM, Sutanto EN, Martinovich KM, Kicic-Starcevich E, Garratt LW, Shaw NC, Lannigan FJ, Larcombe AN, Zosky G, Knight DA, Rigby PJ, Kicic A, Stick SM Tags: Biol Proced Online Source Type: research

Antitumor Efficacy of Human Monocyte-Derived Dendritic Cells: Comparing Effects of two Monocyte Isolation Methods.
Conclusions: Overall, both the MACS and the EasySep isolation immunomagnetic technologies provide monocytes that differentiate into viable and functional MoDCs. In our experimental settings, resting EasySep_MoDCs showed a higher basal level of maturation but show less responsivity to stimuli. On the other hand, MACS_MoDCs, when stimulated with tumor antigens, showed better ability to stimulate Th1 responses and to induce T cell cytotoxicity against tumor cells. Thus, monocyte isolation techniques crucially affect MoDCs' function and, therefore, should be carefully selected to obtain the desired functionality. PMID: 29...
Source: Biological Procedures Online - February 14, 2018 Category: Molecular Biology Authors: Marques GS, Silva Z, Videira PA Tags: Biol Proced Online Source Type: research

Gibson Deletion: a novel application of isothermal in vitro recombination.
Conclusions: Gibson Deletion is a novel, easy and convenient application of isothermal in vitro assembly, that performs with high efficiency and can be implemented for a broad range of applications. PMID: 29375275 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - January 30, 2018 Category: Molecular Biology Authors: Kalva S, Boeke JD, Mita P Tags: Biol Proced Online Source Type: research

Cancer chemoprevention and therapy using chinese herbal medicine.
Abstract 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 number of naturally occurring products from Chinese herbs extracts exhibit strong inhibitory properties against carcinogenesis, including CHM single-herb extracts, CHM-derived active components, and CHM formulas (the polyherbal combinations), which regulate JAK/STAT, MAPK, and NF-ҡB pathways. The present review aims to report the cancer-preventive effect of CHM with evidence from cell-line, animal, epide...
Source: Biological Procedures Online - January 13, 2018 Category: Molecular Biology Authors: Jiao L, Bi L, Lu Y, Wang Q, Gong Y, Shi J, Xu L Tags: Biol Proced Online Source Type: research

Maintaining RNA Integrity for Transcriptomic Profiling of Ex Vivo Cultured Limbal Epithelial Stem Cells after Fluorescence-Activated Cell Sorting (FACS).
Conclusion: In this study, we developed a reliable FACS-based procedure using ethanol as a fixative that would support accurate isolation of limbal epithelial progenitor subpopulations along with RNA yield and quality sufficient to enable deep transcriptomic profiling. PMID: 29255379 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - December 21, 2017 Category: Molecular Biology Authors: Liu L, Nielsen FM, Riis SE, Emmersen J, Fink T, Hjortdal JØ, Bath C, Zachar V Tags: Biol Proced Online Source Type: research

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.
Conclusions: A modified-sandwich ELISA for the quantification of TFF3 dimeric form was established. The established ELISA will be a valuable tool for facilitating the investigation of the physiological roles and the diagnostic values of TFF3 in oral diseases. The concept of this modified-sandwich ELISA may be applied for the determination of other homodimeric peptides of interest. PMID: 29151819 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - November 21, 2017 Category: Molecular Biology Authors: Khummuang S, Phanphrom W, Laopajon W, Kasinrerk W, Chaiyarit P, Pata S Tags: Biol Proced Online Source Type: research

SV40 Large T Antigen Disrupts Embryogenesis of Canine and Porcine Somatic Cell Nuclear Transfer Embryo.
CONCLUSIONS: Although lifespan-extended canine and porcine cells via SV40LT exhibit no apparent transforming changes, they are inappropriate for use as nuclei donors for SCNT because of their aneuploidy. PMID: 29075153 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - October 28, 2017 Category: Molecular Biology Authors: Eun K, Hwang SU, Jeong YW, Seo S, Lee SY, Hwang WS, Hyun SH, Kim H Tags: Biol Proced Online Source Type: research

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.
Abstract 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 extended non-overlapping sequence at the 3' end of the primer increases the PCR amplification efficiency and the capacity of multi-site mutagenesis. Here, we introduced silent restriction sites in the primers used in this PCR-based SDM method by utilizing SDM-Assist software to generate mutants of Helicobacter pylori neutrophil-activating protein (HP-NAP), whose gene has low GC content. The HP-NAP m...
Source: Biological Procedures Online - October 1, 2017 Category: Molecular Biology Authors: Kuo TY, Tsai CC, Fu HW Tags: Biol Proced Online Source Type: research

Efficient and inexpensive transient expression of multispecific multivalent antibodies in Expi293 cells.
CONCLUSIONS: This protocol is the first describing transfection of the human Expi293 cells with PEI. It can be used to generate functional multi-specific antibodies in high amounts. The use of biological drugs, and in particular multispecific antibodies, is rapidly increasing, hence improved protocols such as the one presented here are highly valuable. PMID: 28932173 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - September 23, 2017 Category: Molecular Biology Authors: Fang XT, Sehlin D, Lannfelt L, Syvänen S, Hultqvist G Tags: Biol Proced Online Source Type: research

An Assessment of Fixed and Native Chromatin Preparation Methods to Study Histone Post-Translational Modifications at a Whole Genome Scale in Skeletal Muscle Tissue.
CONCLUSIONS: Our findings suggest that the preparation of muscle chromatin for ChIP-seq in cross-linked conditions can compromise the systematic analysis of broad histone marks. Therefore, native chromatin preparation should be preferred to cross-linking when a ChIP experiment has to be performed on skeletal muscle tissue, particularly when a broad source signal is considered. PMID: 28855851 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - September 1, 2017 Category: Molecular Biology Authors: David SA, Piégu B, Hennequet-Antier C, Pannetier M, Aguirre-Lavin T, Crochet S, Bordeau T, Couroussé N, Brionne A, Bigot Y, Collin A, Coustham V Tags: Biol Proced Online Source Type: research

Cell Counting and Viability Assessment of 2D and 3D Cell Cultures: Expected Reliability of the Trypan Blue Assay.
CONCLUSIONS: The main aim of this study was to make researchers aware of potential measurement errors when TB is used with a haemocytometer for counting and viability measurements in 2D and 3D cultures. We believe that these results can help researchers to determine whether the expected reliability of the TB assay is compliant with their applications. PMID: 28814944 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - August 19, 2017 Category: Molecular Biology Authors: Piccinini F, Tesei A, Arienti C, Bevilacqua A Tags: Biol Proced Online Source Type: research

An Initial Investigation of an Alternative Model to Study rat Primordial Germ Cell Epigenetic Reprogramming.
CONCLUSIONS: This study suggests that the protocol used here can be a potential method to study the wide DNA demethylation that takes place during PGC reprogramming. PMID: 28785173 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - August 9, 2017 Category: Molecular Biology Authors: Cantão IH, Tesser RB, Stumpp T Tags: Biol Proced Online Source Type: research

3D Printer Generated Tissue iMolds for Cleared Tissue Using Single- and Multi-Photon Microscopy for Deep Tissue Evaluation.
CONCLUSIONS: Taken together, with iMolds it is now possible to image cleared tissue in clearing medium while limiting movement and being able to relocate precise anatomical and cellular locations on sequential imaging events in any basic laboratory. This system provides great potential for screening widespread effects of therapeutics and disease across entire organ systems. PMID: 28690429 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - July 12, 2017 Category: Molecular Biology Authors: Miller SJ, Rothstein JD Tags: Biol Proced Online Source Type: research

Pre-Microporation Improves Outcome of Pancreatic Islet Labelling for Optical and (19)F MR Imaging.
CONCLUSIONS: For labelling of pancreatic islets using poly(lactic-co-glycolic acid) nanoparticles, the modified microporation procedure with low voltage was found to be safer than the standard microporation procedure. The modified procedure was fast, however, efficiency was lower compared to endocytosis. PMID: 28674481 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - July 6, 2017 Category: Molecular Biology Authors: Herynek V, Gálisová A, Srinivas M, van Dinther EAW, Kosinová L, Ruzicka J, Jirátová M, Kriz J, Jirák D Tags: Biol Proced Online Source Type: research

Performances of Different Fragment Sizes for Reduced Representation Bisulfite Sequencing in Pigs.
CONCLUSIONS: In this study, our results demonstrated that selections of fragment sizes could affect the numbers and sequencing depth of detected CpG sites as well as the cost-efficiency. No single solution of RRBS is optimal in all circumstances for investigating genome-scale DNA methylation. This work provides the useful knowledge on designing and executing RRBS for investigating the genome-wide DNA methylation in tissues from pigs. PMID: 28596713 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - June 10, 2017 Category: Molecular Biology Authors: Yuan XL, Zhang Z, Pan RY, Gao N, Deng X, Li B, Zhang H, Sangild PT, Li JQ Tags: Biol Proced Online Source Type: research

Comparison of transepithelial resistance measurement techniques: Chopsticks vs. Endohm.
CONCLUSION: Our study indicates the importance of using a single approach when seeking to measure and compare the TER values of cultured cell lines. PMID: 28490975 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - May 13, 2017 Category: Molecular Biology Authors: Sheller RA, Cuevas ME, Todd MC Tags: Biol Proced Online Source Type: research

LncRNAs and immunity: watchdogs for host pathogen interactions.
Abstract 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...
Source: Biological Procedures Online - May 4, 2017 Category: Molecular Biology Authors: Mumtaz PT, Bhat SA, Ahmad SM, Dar MA, Ahmed R, Urwat U, Ayaz A, Shrivastava D, Shah RA, Ganai NA Tags: Biol Proced Online Source Type: research

Methylated DNA/RNA in Body Fluids as Biomarkers for Lung Cancer.
Abstract 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. We also discuss the emerging r...
Source: Biological Procedures Online - March 25, 2017 Category: Molecular Biology Authors: Lu Y, Li S, Zhu S, Gong Y, Shi J, Xu L Tags: Biol Proced Online Source Type: research

Auxin Extraction and Purification Based on Recombinant Aux/IAA Proteins.
CONCLUSION: This work validated the potential of Aux/IAA proteins to extract and purify IAA from crude plant extracts once we refined the techniques for these processes. PMID: 28100961 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - January 20, 2017 Category: Molecular Biology Authors: Su Y, Luo W, Chen X, Liu H, Hu Y, Lin W, Xiao L Tags: Biol Proced Online Source Type: research