Sensitivity of Neuroblastoma and Induced Neural Progenitor Cells to High-Intensity THz Radiation.

THz radiation induces a variety of processes in cells and has attracted the attention of researchers in recent decades. Here, data on the effects of high-intensity terahertz (THz) radiation on human directly reprogrammed neural progenitor cells (drNPCs) and on neuroblastoma cells (SK-N-BE (2)) were obtained for the first time. The results demonstrated that the exposure of non-tumor and tumor cells to broadband (0.1-3 THz) THz pulses with the intensity of 21 GW/cm2 and the electric field strength of 2.8 MV/cm for 30 min induced neither a noticeable genotoxic effect nor a statistically significant change in the proliferative activity and cell differentiation. It was also shown that the combined effect of THz radiation and salinomycin, a promising antitumor agent, on neuroblastoma cells did not enhance the genotoxic effect of this antibiotic. However, further studies involving chemotherapy drugs and other exposure parameters are warranted to introduce this new concept into anti-tumor clinical practice and to enhance the efficacy of the existing approaches.

Controlled hatching at the prescribed site using femtosecond laser for zona pellucida drilling at the early blastocyst stage.

PURPOSE: To study whether the application of femtosecond laser pulses for zona pellucida (ZP) drilling of blastocysts at the embryonic or abembryonic poles can promote hatching to start immediately through the hole formed and ensure high hatching rates and embryo viability. METHODS: Mouse blastocyst (E3.5) ZP were microdissected with femtosecond laser pulses (514-nm wavelength, 280-fs pulse duration, 2.5-kHz repetition rate) close to the trophoblast or inner cell mass (ICM). The sizes of the holes formed were in the range of 4.5-8.5 µm. Additional longitudinal incisions (5-7-µm long) on either side of the hole were created to determine whether hatching had started at the correct position. Embryos post-laser-assisted ZP drilling and intact embryos were cultured under standard conditions for 2 days; embryo quality was assessed twice daily. The hatching rates and in vitro and in vivo implantation rates (only for embryos with ZP dissected close to the ICM) were estimated. RESULTS: Femtosecond laser-assisted ZP drilling at the early blastocyst stage facilitated embryo hatching to start at the artificial opening with probability approaching 100%. Despite the artificial opening's small size, no embryo trapping during hatching was observed. Both experimental groups had higher hatching rates than the control groups (93.3-94.7% vs. 83.3-85.7%, respectively). The in vitro implantation rate was comparable with that of the control group (92.3% vs. 95.4%). No statistically significant differences were obtained in the in vivo implantation rates between the experimental and control groups. CONCLUSIONS: Blastocyst-stage femtosecond laser microsurgery of ZP is fast and delicate and enables the hatching process to be initiated in a controlled manner through a relatively small opening, with no embryo trapping.

Femtosecond laser is effective tool for zona pellucida engraving and tagging of preimplantation mammalian embryos.

PURPOSE: Our purpose was to study whether application of femtosecond laser pulses for alphanumeric code marking in the volume of zona pellucida (ZP) could be effective and reliable approach for direct tagging of preimplantation embryos. METHODS: Femtosecond laser pulses (wavelength of 514 nm, pulse duration of 280 fs, repetition rate of 2.5 kHz, pulse energy of 20 nJ) were applied for precise alphanumeric code engraving on the ZP of mouse embryos at the zygote stage for individual embryo marking and their accurate identification. Embryo quality assessment every 24 h post laser-assisted marking as well as immunofluorescence staining (for ICM/TE cell number ratio calculation) were performed. RESULTS: Initial experiments have started with embryo marking in a single equatorial plane. The codes engraved could be clearly recognized until the thinning of the ZP prior to hatching. Since embryo may change its orientation during the ART cycle, multi-plane code engraving seems to be more practical for simplifying the process of code searching and embryo identification. We have marked the ZP in three planes, and no decrease in developmental rates as well as no morphological changes of embryos post laser-assisted engraving have been observed as compared to control group embryos. CONCLUSIONS: Our results demonstrate the suitability of femtosecond laser as a novel tool for noninvasive embryo tagging, enabling embryo identification from day 0.5 post coitum to at least early blastocyst stage. Thus, the versatility and the potential use of femtosecond lasers in the field of developmental biology and assisted reproduction have been shown.

Guidelines for the functional annotation of microRNAs using the Gene Ontology.

MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual).

Application of comparative biology in GO functional annotation: the mouse model.

The Gene Ontology (GO) is an important component of modern biological knowledge representation with great utility for computational analysis of genomic and genetic data. The Gene Ontology Consortium (GOC) consists of a large team of contributors including curation teams from most model organism database groups as well as curation teams focused on representation of data relevant to specific human diseases. Key to the generation of consistent and comprehensive annotations is the development and use of shared standards and measures of curation quality. The GOC engages all contributors to work to a defined standard of curation that is presented here in the context of annotation of genes in the laboratory mouse. Comprehensive understanding of the origin, epistemology, and coverage of GO annotations is essential for most effective use of GO resources. Here the application of comparative approaches to capturing functional data in the mouse system is described.

Studying the genotoxic effects of high intensity terahertz radiation on fibroblasts and CNS tumor cells.

The data is obtained on the effect of high-intensity pulses of terahertz (THz) radiation with a broad spectrum (0.2-3 THz) on cell cultures. We have evaluated the threshold exposure parameters of THz radiation causing genotoxic effects in fibroblasts. Phosphorylation of histone H2AX at Ser 139 (γH2AX) was chosen as a marker for genotoxicity and a quantitative estimation of γH2AX foci number in fibroblasts was performed after cell irradiation with THz pulses for 30 min. No genotoxic effects of THz radiation were observed in fibroblasts unless peak intensity and electric field strength exceeded 21 GW cm-2 and 2.8 MV cm-1 , respectively. In tumor cell lines (neuroblastoma (SK-N-BE (2)) and glioblastoma (U87)), exposure to THz pulses with peak intensity of 21 GW cm-2 for 30 min caused no morphological changes as well as no statistically significant increase in histone phosphorylation foci number.

Concept annotation in the CRAFT corpus.

BACKGROUND: Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. RESULTS: This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released). Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. CONCLUSIONS: As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens), our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection), the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are freely available at http://bionlp-corpora.sourceforge.net/CRAFT/index.shtml.

From Zygote to Blastocyst: Application of Ultrashort Lasers in the Field of Assisted Reproduction and Developmental Biology.

Although the use of lasers in medical diagnosis and therapies, as well as in fundamental biomedical research is now almost routine, advanced laser sources and new laser-based methods continue to emerge. Due to the unique ability of ultrashort laser pulses to deposit energy into a microscopic volume in the bulk of a transparent material without disrupting the surrounding tissues, the ultrashort laser-based microsurgery of cells and subcellular components within structurally complex and fragile specimens such as embryos is becoming an important tool in developmental biology and reproductive medicine. In this review, we discuss the mechanisms of ultrashort laser pulse interaction with the matter, advantages of their application for oocyte and preimplantation embryo microsurgery (e.g., for oocyte/blastomere enucleation and embryonic cell fusion), as well as for nonlinear optical microscopy for studying the dynamics of embryonic development and embryo quality assessment. Moreover, we focus on ultrashort laser-based approaches and techniques that are increasingly being applied in the fundamental research and have the potential for successful translation into the IVF (in vitro fertilization) clinics, such as laser-mediated individual embryo labelling and controlled laser-assisted hatching.

Effects of high intensity non-ionizing terahertz radiation on human skin fibroblasts.

For the first time, the data have been obtained on the effects of high-intensity terahertz (THz) radiation (with the intensity of 30 GW/cm2, electric field strength of 3.5 MV/cm) on human skin fibroblasts. A quantitative estimation of the number of histone Н2АХ foci of phosphorylation was performed. The number of foci per cell was studied depending on the irradiation time, as well as on the THz pulse energy. The performed studies have shown that the appearance of the foci is not related to either the oxidative stress (the cells preserve their morphology, cytoskeleton structure, and the reactive oxygen species content does not exceed the control values), or the thermal effect of THz radiation. The prolonged irradiation of fibroblasts also did not result in a decrease of their proliferative index.

Application of femtosecond laser microsurgery in assisted reproductive technologies for preimplantation embryo tagging.

Femtosecond laser pulses were applied for precise alphanumeric code engraving on the zona pellucida (ZP) of mouse zygotes for individual embryo marking and their identification. The optimal range of laser pulse energies required for safe ZP microsurgery has been determined. ZP was marked with codes in three different planes to simplify the process of embryo identification. No decrease in developmental rates and no morphological changes of embryos post laser-assisted engraving have been observed. ZP thickness of embryos post laser-assisted code engraving has been shown to differ significantly from that of control group embryos at the hatching stage. Due to moderate ZP thinning as compared to its initial width at 0.5 dpc (days post coitum), readability of the code degrades slightly and it still remains recognizable even at hatching stage. Our results demonstrate that application of femtosecond laser radiation could be an effective approach for noninvasive direct embryo tagging, enabling embryo identification for the whole period of preimplantation development.