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.
Conclusions: The results revealed that nsp1 as a virulence factor and crucial agent in spreading of the COVID-19 among the society can be a potential target for the future epidemiology, drug, and vaccine studies. PMID: 32336957 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - April 29, 2020 Category: Molecular Biology Authors: Zolfaghari Emameh R, Nosrati H, Taheri RA Tags: Biol Proced Online Source Type: research

Caco-2 Cells for Measuring Intestinal Cholesterol Transport - Possibilities and Limitations.
Conclusions: The Caco-2 cell line is widely used in the scientific community as model for the intestinal epithelium, although with highly divergent protocols. The herein provided information and protocols can be a common basis for researchers intending to use Caco-2 cells in the context of cellular cholesterol homeostasis. PMID: 32308567 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - April 22, 2020 Category: Molecular Biology Authors: Hiebl V, Schachner D, Ladurner A, Heiss EH, Stangl H, Dirsch VM Tags: Biol Proced Online Source Type: research

High-Resolution Confocal Fluorescence Imaging of Serine Hydrolase Activity in Cryosections - Application to Glioma Brain Unveils Activity Hotspots Originating from Tumor-Associated Neutrophils.
Conclusions: Our study advances the ABPP methodology to tissue sections, enabling high-resolution confocal fluorescence imaging of global SH activity in anatomically preserved complex native cellular environment. To achieve global portrait of SH activity throughout the section, a probe with broad reactivity towards the SH family members was employed. As ABPP requires no a priori knowledge of the identity of the target, we envisage no imaginable reason why the presently described approach would not work for sections regardless of species and tissue source. PMID: 32190011 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - March 20, 2020 Category: Molecular Biology Authors: Aaltonen N, Singha PK, Jakupović H, Wirth T, Samaranayake H, Pasonen-Seppänen S, Rilla K, Varjosalo M, Edgington-Mitchell LE, Kasperkiewicz P, Drag M, Kälvälä S, Moisio E, Savinainen JR, Laitinen JT Tags: Biol Proced Online Source Type: research

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.
Conclusion: For patients with LAC, ACT combined with CHMF after radical surgery can prolong the DFS time especially in the early stage, and reduces the chemotherapy-related toxic and side effects. Trial Registration: NCT01441752. Registered 14 July, 2011. PMID: 32140080 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - March 7, 2020 Category: Molecular Biology Authors: Wang Q, Jiao L, Wang S, Chen P, Bi L, Zhou D, Yao J, Li J, Wang L, Chen Z, Jia Y, Zhang Z, Shen W, Zhu W, Xu J, Gao Y, Xu L, Gong Y Tags: Biol Proced Online Source Type: research

Exploring G Protein-Coupled Receptor Signaling in Primary Pancreatic Islets.
Conclusions: Detection of the second messengers IP1, cAMP, and calcium, can be used to reliably analyze GPCR activation in intact islets. PMID: 32082084 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - February 23, 2020 Category: Molecular Biology Authors: Röthe J, Kraft R, Schöneberg T, Thor D Tags: Biol Proced Online Source Type: research

A microcarrier-based spheroid 3D invasion assay to monitor dynamic cell movement in extracellular matrix.
Conclusions: In all, the microcarrier-based spheroids 3D model allows exploration of adherent cell invasion in a fast and highly reproducible way, and provides informative results on dynamic cell behavior in vitro. PMID: 32021568 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - February 6, 2020 Category: Molecular Biology Authors: Liu H, Lu T, Kremers GJ, Seynhaeve ALB, Ten Hagen TLM Tags: Biol Proced Online Source Type: research

Analytical Validation of Telomere Analysis Technology ® for the High-Throughput Analysis of Multiple Telomere-Associated Variables.
Conclusions: Analytical validation of TAT shows that is a robust and reliable technique for the characterization of a detailed telomere profile in large cell populations. The combination of high-throughput imaging and software workflows allows for the collection of a large number of telomere-associated variables from each sample, which can then be used in epidemiological and clinical studies. PMID: 31956299 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - January 22, 2020 Category: Molecular Biology Authors: de Pedro N, Díez M, García I, García J, Otero L, Fernández L, García B, González R, Rincón S, Pérez D, Rodríguez E, Segovia E, Najarro P Tags: Biol Proced Online Source Type: research

Glycosaminoglycans from Co-Products of «Scyliorhinus canicula»: Extraction and Purification in Reference to the European Pharmacopoeia Requirement.
Conclusion: The extracted and purified active ingredient is perfectly conform to the tests described by the Ph. Eur. The results suggest that the co-product of Scyliorhinus canicula would be a perfect source of molecules of pharmacological interest, obtained by a simple and non-agressive process. PMID: 31908599 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - January 9, 2020 Category: Molecular Biology Authors: Talmoudi N, Ghariani N, Sadok S Tags: Biol Proced Online Source Type: research

Application of a New Multiplexed Array for Rapid, Sensitive, Simultaneous and Quantitative Assessment of Spliced and Unspliced XBP1.
Conclusions: The XBP1 biochip enables isoform specific quantification of protein level changes upon activation and inhibition of IRE1α RNase activity, using a routine clinical methodology. As such it provides a research tool and potential clinical tool with a quantified, simultaneous, rapid output that is not available from any other published method. PMID: 31807121 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - December 7, 2019 Category: Molecular Biology Authors: Creedican S, Talty A, Fitzgerald SP, Samali A, Richardson C, Gorman AM, Martin K Tags: Biol Proced Online Source Type: research

Cell-Wide Survey of Amide-Bonded Lysine Modifications by Using Deacetylase CobB.
Conclusions: We developed a method that was capable of monitoring and quantifying amide-bonded lysine modifications in cells of different origins. PMID: 31798349 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - December 6, 2019 Category: Molecular Biology Authors: Wei Y, Yang WJ, Wang QJ, Lin PC, Zhao JY, Xu W, Zhao SM, He XD Tags: Biol Proced Online Source Type: research

Manipulating osa-MIR156f Expression by D18 Promoter to Regulate Plant Architecture and Yield Traits both in Seasonal and Ratooning Rice.
Conclusion: Our results indicated that the manipulation of osa-MIR156f expression may have application significance in rice genetic breeding. This study developed a novel strategy to regulate plant architecture and grain yield potential both in the seasonal and ratooning rice. PMID: 31700499 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - November 10, 2019 Category: Molecular Biology Authors: Liu Q, Su Y, Zhu Y, Peng K, Hong B, Wang R, Gaballah M, Xiao L Tags: Biol Proced Online Source Type: research

Comprehensive Transcriptomic Analysis of Mouse Gonadal Development Involving Sexual Differentiation, Meiosis and Gametogenesis.
Conclusion: Taken together, our findings have enriched the gonadal transcriptome database and provided novel candidate genes and avenues to research the molecular mechanisms of sexual differentiation, meiosis, and gametogenesis. Supplementary information: Supplementary information accompanies this paper at 10.1186/s12575-019-0108-y. PMID: 31636514 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - October 24, 2019 Category: Molecular Biology Authors: Wang J, Tian GG, Zheng Z, Li B, Xing Q, Wu J Tags: Biol Proced Online Source Type: research

DNA Methylation Validation Methods: a Coherent Review with Practical Comparison.
Šálek C, Remešová H Abstract 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...
Source: Biological Procedures Online - October 5, 2019 Category: Molecular Biology Authors: Šestáková Š, Šálek C, Remešová H Tags: Biol Proced Online Source Type: research

MBEC Versus MBIC: the Lack of Differentiation between Biofilm Reducing and Inhibitory Effects as a Current Problem in Biofilm Methodology.
Conclusion: The assessment of pre-treatment biofilms contributes to a standardized use of biofilm susceptibility endpoint parameters, which is urgently needed to improve the clinical validity of future anti-biofilm assays. PMID: 31528123 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - September 20, 2019 Category: Molecular Biology Authors: Thieme L, Hartung A, Tramm K, Klinger-Strobel M, Jandt KD, Makarewicz O, Pletz MW Tags: Biol Proced Online Source Type: research

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.
Conclusions: These results all indicated that the method for determination of residual DNA in biological products expressed from CHO cells is sensitive, accurate and robust. PMID: 31496923 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - September 11, 2019 Category: Molecular Biology Authors: Zheng W, Jiang L, Lei Q, Yang J, Gao X, Wang W, Zhang Y, Kong T, Chen Q, Li G Tags: Biol Proced Online Source Type: research

Genetic Manipulation of MicroRNAs in the Silk Gland of Silkworm, Bombyx Mori.
Conclusions: A practical technical system was established for studying the functions of miRNAs in silk gland of Bombyx mori. Our research provides methodological support for the functional study of miRNAs and other noncoding RNAs in the silk gland and more organs in other species. PMID: 31427900 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - August 22, 2019 Category: Molecular Biology Authors: Wang W, Wang X, Li X, Pu Q, Luo C, Xu L, Peng X, Liu S Tags: Biol Proced Online Source Type: research

Immunostick Test for Detecting ζ-Globin Chains and Screening of the Southeast Asian α-Thalassemia 1 Deletion.
Conclusion: In this study, a novel simple immunostick test for the screening of (--(SEA)) α-thalassemia 1 carriers was presented. The developed immunostick test, within a single test, contains both positive and negative internal procedural controls. PMID: 31388336 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - August 9, 2019 Category: Molecular Biology Authors: Pata S, Pongpaiboon M, Laopajon W, Munkongdee T, Paiboonsukwong K, Pornpresert S, Fucharoen S, Kasinrerk W Tags: Biol Proced Online Source Type: research

Exploiting Differential Gene Expression to Discover Ionic and Osmotic-Associated Transcripts in the Halophyte Grass Aeluropus littoralis.
Conclusion: Differential regulation of these TDFs was observed in root and shoot which confirm their role in salt stress tolerance and provide initial insights into the transcriptome of A. littoralis. Expression pattern of ionic and osmotic-related TDFs at A. littoralis can be taken as an indication of their functional relevance at different salt and drought stresses. PMID: 31337987 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - July 26, 2019 Category: Molecular Biology Authors: Fatemi F, Hashemi-Petroudi SH, Nematzadeh G, Askari H, Abdollahi MR Tags: Biol Proced Online Source Type: research

Automated macrophage counting in DLBCL tissue samples: a ROF filter based approach.
Conclusions: ROF based approach is successfully applied to detection of IHC stained macrophages in DLBCL tissue samples. The method competes well with existing commercial software kits. In difference to them, it is fully automated, externally repeatable, independent on training data and completely documented. Comparison with gene expression data indicates that image morphometry constitutes an independent source of information about antibody-polarized macrophage occurence and distribution. PMID: 31303867 [PubMed] (Source: Biological Procedures Online)
Source: Biological Procedures Online - July 16, 2019 Category: Molecular Biology Authors: Wagner M, Hänsel R, Reinke S, Richter J, Altenbuchinger M, Braumann UD, Spang R, Löffler M, Klapper W Tags: Biol Proced Online Source Type: research

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