Genomes and Genes
Summary: Methods used to study CELLS.
- Lynge E, Antilla A, Arbyn M, Segnan N, Ronco G. What's next? Perspectives and future needs of cervical screening in Europe in the era of molecular testing and vaccination. Eur J Cancer. 2009;45:2714-21 pubmed publisher..Organised vaccination and screening programmes with good record keeping are necessary to optimise the future control of cervical cancer. ..
- Mostert B, Sleijfer S, Foekens J, Gratama J. Circulating tumor cells (CTCs): detection methods and their clinical relevance in breast cancer. Cancer Treat Rev. 2009;35:463-74 pubmed publisher..We have focused on breast cancer as most clinical studies on CTC detection so far have been done in these patients. ..
- Tropé A, Sjøborg K, Nygård M, Røysland K, Campbell S, Alfsen G, et al. Cytology and human papillomavirus testing 6 to 12 months after ASCUS or LSIL cytology in organized screening to predict high-grade cervical neoplasia between screening rounds. J Clin Microbiol. 2012;50:1927-35 pubmed publisher..In addition, the low CIN2+ risk among women with a negative Amplicor HPV test in our study confirms its safe use in a clinical setting. ..
- Kelly R, Patnick J, Kitchener H, Moss S. HPV testing as a triage for borderline or mild dyskaryosis on cervical cytology: results from the Sentinel Sites study. Br J Cancer. 2011;105:983-8 pubmed publisher..Variation in HPV-positive rates results in differing colposcopy workload. ..
- Benevolo M, Vocaturo A, Caraceni D, French D, Rosini S, Zappacosta R, et al. Sensitivity, specificity, and clinical value of human papillomavirus (HPV) E6/E7 mRNA assay as a triage test for cervical cytology and HPV DNA test. J Clin Microbiol. 2011;49:2643-50 pubmed publisher..It is also more efficient than cytology for the triage of HPV DNA-positive women. Nevertheless, its low sensitivity demands a strict follow-up of HPV DNA positive-mRNA negative cases. ..
- Swaby R, Cristofanilli M. Circulating tumor cells in breast cancer: a tool whose time has come of age. BMC Med. 2011;9:43 pubmed publisher..We will also introduce their utility in pharmacodynamic monitoring for rational selection of molecularly targeted therapies and briefly address how they can help elucidate the biology of cancer metastasis. ..
- Esteban M, Wang T, Qin B, Yang J, Qin D, Cai J, et al. Vitamin C enhances the generation of mouse and human induced pluripotent stem cells. Cell Stem Cell. 2010;6:71-9 pubmed publisher..Our results therefore highlight a straightforward method for improving the speed and efficiency of iPSC generation and provide additional insights into the mechanistic basis of the reprogramming process. ..
- Girasole M, Dinarelli S, Boumis G. Structure and function in native and pathological erythrocytes: a quantitative view from the nanoscale. Micron. 2012;43:1273-86 pubmed publisher..As a whole, the collected data enable to describe the entire phenomenon as a sequence of morphological intermediates following one another along the aging path. ..
- Morgan G, Kail M, Hollinshead M, Vaux D. Combined biochemical and cytological analysis of membrane trafficking using lectins. Anal Biochem. 2013;441:21-31 pubmed publisher..Overall, we find that conjugated plant lectins are effective tools for combinatory biochemical and cytological analysis of membrane trafficking of glycoproteins. ..
- Abasolo A, Vargas M, Rios Martin J, Trigo I, Arjona A, Gonzalez Campora R. Application of fluorescence in situ hybridization as a diagnostic tool in melanocytic lesions, using paraffin wax-embedded tissues and imprint-cytology specimens. Clin Exp Dermatol. 2012;37:838-43 pubmed publisher..The probes displayed exceptional discriminative capacity in difficult or ambiguous lesions. To our knowledge, his is the first reported use of imprint-cytology specimens for FISH diagnosis. ..
- Zhang M, Scholer H, Greber B. Rapid and efficient generation of neurons from human pluripotent stem cells in a multititre plate format. J Vis Exp. 2013;:e4335 pubmed publisher..Due to these features, the procedure may serve as a useful platform for further functional investigation as well as for cell-based screening approaches requiring human sensory neurons or neurons of any type. ..
- Gunduz A, Cumurcu T, Demirel E, Akpolat N, Karincaoglu Y. The ocular surface in the Behçet's disease patient. Can J Ophthalmol. 2012;47:429-34 pubmed publisher..05). We found that there was a statistically significant difference between Behçet's disease patients and normal subjects regarding the ocular film layer, but no difference regarding conjunctival surface epithelial morphology. ..
- Waltemath D, Karr J, Bergmann F, Chelliah V, Hucka M, Krantz M, et al. Toward Community Standards and Software for Whole-Cell Modeling. IEEE Trans Biomed Eng. 2016;63:2007-14 pubmed publisher..We, therefore, propose several new WC modeling standards, software, and databases. We anticipate that these new standards and software will enable more comprehensive models. ..
- Gupta P, Rajwanshi A, Nijhawan R, Srinivasan R, Gupta N, Saikia U, et al. Fine needle aspiration in retroperitoneal lesions. APMIS. 2017;125:16-23 pubmed publisher..8%) cases. We believe FNAC is a useful method for an early, rapid, minimally invasive and reliable pre-operative diagnosis for retroperitoneal lesions and can often obviate the need for open surgical biopsy. ..
- Radley A, Schwab R, Tan Y, Kim J, Lo E, Cahan P. Assessment of engineered cells using CellNet and RNA-seq. Nat Protoc. 2017;12:1089-1102 pubmed publisher..Once the raw data have been preprocessed, running CellNet takes only several minutes, whereas the time required to create a completely new CellNet is several hours. ..
- Ghigo C, Mondor I, Jorquera A, Nowak J, Wienert S, Zahner S, et al. Multicolor fate mapping of Langerhans cell homeostasis. J Exp Med. 2013;210:1657-64 pubmed publisher..Altogether, our results demonstrate the general utility of our novel fate-mapping system to follow cell population dynamics in vivo and to establish an alternative model for LC homeostasis. ..
- Budach S, Mueller R. Reproducibility of a semiquantitative method to assess cutaneous cytology. Vet Dermatol. 2012;23:426-e80 pubmed publisher..Based on these results, this semiquantitative method of grading can be recommended for evaluating and monitoring of antimicrobial therapy in daily practice. ..
- Shashikala R, Saikumar A, Ramesh K, Aparana V. Alternaria alternata in a case of mass in the lung. Indian J Med Microbiol. 2013;31:308-10 pubmed publisher..Serum specimen was evaluated for immunoglobulin E specific titres for Alternaria species which was high. Patient was treated with fluconazole for 6 weeks after which the symptoms disappeared and chest X-ray was normal. ..
- Toapanta F, Bernal P, Sztein M. Diverse phosphorylation patterns of B cell receptor-associated signaling in naïve and memory human B cells revealed by phosphoflow, a powerful technique to study signaling at the single cell level. Front Cell Infect Microbiol. 2012;2:128 pubmed publisher..Phosphoflow holds great potential to accelerate vaccine development by identifying signaling profiles in good/poor responders. ..
- Beine B, Diehl H, Meyer H, Henkel C. Tissue MALDI Mass Spectrometry Imaging (MALDI MSI) of Peptides. Methods Mol Biol. 2016;1394:129-150 pubmed publisher..On-tissue digestion and matrix application are described for two different commercially available and commonly used spraying devices: the SunCollect (SunChrom) and the ImagePrep (Bruker Daltonik GmbH). ..
- Meste O, Brau F, Guyon A. Robust estimation of the motile cilia beating frequency. Med Biol Eng Comput. 2015;53:1025-35 pubmed publisher..Such regulations are likely to participate in homeostatic mechanisms regulating CSF movements and brain energy supply. ..
- de Bekker Grob E, de Kok I, Bulten J, van Rosmalen J, Vedder J, Arbyn M, et al. Liquid-based cervical cytology using ThinPrep technology: weighing the pros and cons in a cost-effectiveness analysis. Cancer Causes Control. 2012;23:1323-31 pubmed publisher..Further research is needed to establish whether other LBC systems will be more favorable with regard to cost-effectiveness. ..
- Hoebaus J, Heher P, Gottschamel T, Scheinast M, Auner H, Walder D, et al. Embryonic stem cells facilitate the isolation of persistent clonal cardiovascular progenitor cell lines and leukemia inhibitor factor maintains their self-renewal and myocardial differentiation potential in vitro. Cells Tissues Organs. 2013;197:249-68 pubmed publisher..Isolation of wild-type cardiovascular progenitor cell lines from adolescent and old mice has finally demonstrated the general feasibility of this strategy for the isolation of phenotypically stable somatic stem cell lines. ..
- Grundl D, Zhang X, Messaoud S, Pfister C, Demmel F, Mommer M, et al. Reaction-diffusion modelling for microphysiometry on cellular specimens. Med Biol Eng Comput. 2013;51:387-95 pubmed publisher..It is applicable to any setting of (bio-) sensors involving reaction and diffusion of dissolved gases and particularly H(+) ions in buffered solutions. ..
- Lewis D, Blatchley M, Park K, Gerecht S. O2-controllable hydrogels for studying cellular responses to hypoxic gradients in three dimensions in vitro and in vivo. Nat Protoc. 2017;12:1620-1638 pubmed publisher..Time courses for biological experiments using this hydrogel are variable, and thus they may range from hours to weeks, depending on the application and user end goal. ..
- Scanga L, Maygarden S. Utility of fine-needle aspiration and core biopsy with touch preparation in the diagnosis of renal lesions. Cancer Cytopathol. 2014;122:182-90 pubmed publisher..0 ± 1.3 cm) masses (n = 47). Compared with FNA, CB and TP have higher adequacy and diagnostic yield and provide more diagnostic information. Cytology diagnoses are highly accurate when correlated to surgical specimens. ..
- Renshaw A, Elsheikh T. The value of expert review in prospective trials of automated assisted screening devices. Diagn Cytopathol. 2014;42:117-9 pubmed publisher..Trials without expert consensus review may be compared to those with expert consensus review at the threshold of ASCUS+ but may not be reliable at the threshold of HSIL+ without additional confirmatory data. ..
- Spindler K, Hsu T. Viral disruption of the blood-brain barrier. Trends Microbiol. 2012;20:282-90 pubmed publisher..Viral proteins acting in BBB disruption are described for HIV-1, currently the most studied encephalitic virus; other viruses are also discussed. ..
- Balandya B, Pembe A, Mwakyoma H. Cervical pre-malignant lesions in HIV infected women attending Care and Treatment Centre in a tertiary hospital, Dar es Salaam, Tanzania. East Afr J Public Health. 2011;8:185-9 pubmed
- Ravarino A, Nemolato S, Macciocu E, Fraschini M, Senes G, Faa G, et al. CINtec PLUS immunocytochemistry as a tool for the cytologic diagnosis of glandular lesions of the cervix uteri. Am J Clin Pathol. 2012;138:652-6 pubmed publisher..Of the 16 negative samples, 15 (93.8%) stained negative and only 1 (6.2%) showed several positive clusters of cells. Our study shows that CINtec PLUS is a robust and useful tool for the diagnosis of glandular lesions of the cervix uteri...
- Yuan F, Song L, Liu F, Gu L, Zhang Y. Eukaryotic DNA mismatch repair in vitro. Methods Mol Biol. 2012;920:149-62 pubmed publisher..We validated the yeast cell-free system by the mismatch repair deficient strain (?msh2) and the complementation assay with purified yeast MutS?. ..
- de Freitas G, Gonçalves R, Gralle M. Functional test of PCDHB11, the most human-specific neuronal surface protein. BMC Evol Biol. 2016;16:75 pubmed publisher..In spite of its fast evolution and low intra-human variability, cell-based tests on the only proposed function for PCDHB11 did not indicate a functional change. ..
- Miyaoka Y, Chan A, Judge L, Yoo J, Huang M, Nguyen T, et al. Isolation of single-base genome-edited human iPS cells without antibiotic selection. Nat Methods. 2014;11:291-3 pubmed publisher..This method facilitates efficient induction or reversion of mutations associated with human disease in isogenic human induced pluripotent stem cells. ..
- Griffin M, Hsieh Wilson L. Glycan Engineering for Cell and Developmental Biology. Cell Chem Biol. 2016;23:108-121 pubmed publisher..Here, we describe methods to sculpt glycans on cell surfaces and highlight recent successes in which artificially engineered glycans have been employed to control biological outcomes such as the immune response and stem cellÂ fate. ..
- Martell J, Deerinck T, Lam S, Ellisman M, Ting A. Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. Nat Protoc. 2017;12:1792-1816 pubmed publisher..Notably, the only additional steps required relative to a standard EM sample preparation are cell transfection and a 2- to 45-min staining period with 3,3-diaminobenzidine (DAB) and hydrogen peroxide (H2O2). ..
- Dy M, Kanaya S, Sugiura T. Localized cell stiffness measurement using axial movement of an optically trapped microparticle. J Biomed Opt. 2013;18:111411 pubmed publisher..Results suggest that the proposed optical tweezers scheme can measure the stiffness of a particular cell locale using Hertz model, offering insights about how cells respond to outside mechanical stimulus. ..
- Krebs M, Schumacher K. Live cell imaging of cytoplasmic and nuclear Ca2+ dynamics in Arabidopsis roots. Cold Spring Harb Protoc. 2013;2013:776-80 pubmed publisher..This protocol provides instructions for setting up a CLSM-based experiment to measure cytosolic and nuclear Ca(2+) dynamics in Arabidopsis lines expressing Yellow Cameleon Ca(2+) indicators. ..
- Parsons S, Jurzinsky C, Cuvelier S, Patel K. Studying leukocyte recruitment under flow conditions. Methods Mol Biol. 2013;946:285-300 pubmed publisher..Although these methods are described for interactions between leukocytes and endothelial cells, they are broadly applicable to the study of interactions between many combinations of adhesive substrates and adhesive particles. ..
- Cho C, Amadei G, Breadner D, Luyt L, Lewis J. Discovery of novel integrin ligands from combinatorial libraries using a multiplex "beads on a bead" approach. Nano Lett. 2012;12:5957-65 pubmed publisher..The peptides identified here represent novel integrin-targeted agents that can be used to develop targeted nanomedicines without the risk of increased tumor invasion and metastasis. ..
- Pittman K, Pittman A, Karlson S, Cieplinska T, Sourd P, Redmond K, et al. Body site matters: an evaluation and application of a novel histological methodology on the quantification of mucous cells in the skin of Atlantic salmon, Salmo salar L. J Fish Dis. 2013;36:115-27 pubmed publisher..The results further suggest that salmon exhibit a dynamic repeatable pattern of mucous cell development influenced by sex, diet and possibly strain and season. ..
- Burger R, Kirby D, Glynn M, Nwankire C, O SULLIVAN M, Siegrist J, et al. Centrifugal microfluidics for cell analysis. Curr Opin Chem Biol. 2012;16:409-14 pubmed publisher..In this review we discuss technologies to implement two important steps for cell handling, namely separation and capturing/counting. ..
- Raschbichler V, Lieber D, Bailer S. NEX-TRAP, a novel method for in vivo analysis of nuclear export of proteins. Traffic. 2012;13:1326-34 pubmed publisher..The NEX-TRAP holds the promise of applicability in automated fluorescence imaging for systematic analysis of nuclear export, thereby improving in silico prediction of nuclear export sequences. ..
- Patel D, Rozek L, Colacino J, Van Zomeren Dohm A, Ruffin M, Unger E, et al. Patterns of cellular and HPV 16 methylation as biomarkers for cervical neoplasia. J Virol Methods. 2012;184:84-92 pubmed publisher..2, and LINE1 site 1.2. HPV 16 genome CpG methylation was low except for the L1 region. In general, lower HPV 16 methylation and higher candidate gene methylation levels were associated with higher odds of abnormal cytology. ..
- Jones N, Wakely P, Klemanski D, Al Saif O, Young G, Frankel W, et al. Cytopathologic evaluation of the in situ margin in patients undergoing hepatectomy. Cancer Cytopathol. 2012;120:410-5 pubmed publisher..Given the difficulty of accurately assessing margins after hepatectomy, cytopathologic evaluation may be more reflective of the true margin. Cancer (Cancer Cytopathol) 2012. © 2012 American Cancer Society. ..
- Nacamulli D, Nico L, Barollo S, Zambonin L, Pennelli G, Girelli M, et al. Comparison of the diagnostic accuracy of combined elastosonography and BRAF analysis vs cytology and ultrasonography for thyroid nodule suspected of malignancy. Clin Endocrinol (Oxf). 2012;77:608-14 pubmed publisher..USE and BRAF analysis for thyroid nodule evaluation might reduce the number of unnecessary surgical procedures. ..
- Rossi M, Buratto M, Bruni S, Filieri C, Tagliati F, Trasforini G, et al. Role of ultrasonographic/clinical profile, cytology, and BRAF V600E mutation evaluation in thyroid nodule screening for malignancy: a prospective study. J Clin Endocrinol Metab. 2012;97:2354-61 pubmed publisher..The diagnostic sensitivity for thyroid cancer is significantly increased by BRAF V600E mutation analysis, indicating that the screening for BRAF mutation in FNAB samples has a relevant diagnostic potential. ..
- Mak D, Vais H, Cheung K, Foskett J. Nuclear patch-clamp electrophysiology of Ca2+ channels. Cold Spring Harb Protoc. 2013;2013:885-91 pubmed publisher..This protocol describes in detail all the steps required to successfully obtain nuclear membrane patches, in various configurations, from both the outer and inner nuclear membranes of isolated nuclei. ..
- Lee S, Jung C, Bae J, Jung S, Choi Y, Kang C. Liquid-based cytology improves preoperative diagnostic accuracy of the tall cell variant of papillary thyroid carcinoma. Diagn Cytopathol. 2014;42:11-7 pubmed publisher..It is possible to make a preoperative diagnosis of TCV using LBC. ..
- Kleiman D, Sporn M, Beninato T, CROWLEY M, Nguyen A, Uccelli A, et al. Preoperative BRAF(V600E) mutation screening is unlikely to alter initial surgical treatment of patients with indeterminate thyroid nodules: a prospective case series of 960 patients. Cancer. 2013;119:1495-502 pubmed publisher..Preoperative mutation screening for BRAF(V600E) does not meaningfully improve risk stratification and is unlikely to alter the initial management of patients with indeterminate nodules. ..
- Wongpaiboonwattana W, Stavridis M. Neural differentiation of mouse embryonic stem cells in serum-free monolayer culture. J Vis Exp. 2015;:e52823 pubmed publisher..We provide detailed instructions on media preparation and cell density optimization to allow the process to be applied to most ESC lines and a variety of cell culture vessels. ..