Different Effects of Hypnotics and Stimulants on Sleep Between Wild Type and Sleep-less Flies

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Genome-wide identification and annotation of HIF-1α binding sites in two cell lines using massively parallel sequencing

We identified 531 and 616 putative HIF-1α target sites by ChIP-Seq in the cancerous cell line DLD-1 and the non-cancerous cell line TIG-3, respectively. We also examined the positions and expression levels of transcriptional start sites (TSSs) in these cell lines using our TSS-Seq method. We observed that 121 and 48 genes in DLD-1 and TIG-3 cells, respectively, had HIF-1α binding sites in proximal regions of the previously reported TSSs that were up-regulated at the transcriptional level. In addition, 193 and 123 of the HIF-1α target sites, respectively, were located in proximal regions of previously uncharacterized TSSs, namely, TSSs of putative alternative promoters of protein-coding genes or promoters of putative non-protein-coding transcripts. The hypoxic response of DLD-1 cells was more significant than that of TIG-3 cells with respect to both the number of target sites and the degree of induced changes in transcript expression. The Nucleosome-Seq and ChIP-Seq analyses of histone modifications revealed that the chromatin formed an open structure in regions surrounding the HIF-1α binding sites, but this event occurred prior to the actual binding of HIF-1α. Different cellular histories may be encoded by chromatin structures and determine the activation of specific genes in response to hypoxic shock. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11568-011-9150-9) contains supplementary material, which is available to authorized users

FOXO3a-dependent regulation of Puma in response to cytokine/growth factor withdrawal

Puma is an essential mediator of p53-dependent and -independent apoptosis in vivo. In response to genotoxic stress, Puma is induced in a p53-dependent manner. However, the transcription factor driving Puma up-regulation in response to p53-independent apoptotic stimuli has yet to be identified. Here, we show that FOXO3a up-regulates Puma expression in response to cytokine or growth factor deprivation. Importantly, dysregulated Akt signaling in lymphoid cells attenuated Puma induction upon cytokine withdrawal. Our results suggest that Puma, together with another BH3 only member, Bim, function as FOXO3a downstream targets to mediate a stress response when PI3K/Akt signaling is down-regulated

Heterogeneous hydraulic properties of an insular aquifer clarified by a tidal response method with simple decomposition techniques

Two simple frequency decomposition techniques were used as part of a tidal response method to derive the hydraulic diffusivities of a freshwater-lens aquifer. Digital high-pass filtering can separate the tidal components of diurnal and shorter periods from longer-period components. Discrete Fourier transform can be used to isolate a specific tidal component. These techniques are easy to practice using the built-in functions of spreadsheet software. The applied techniques were each optimized for the frequencies of known major tidal components. Isolation of the specific tidal signals helps to reduce the errors of a basic tidal response method that uses in its calculations the amplitude attenuation and phase lag of a simple sinusoidal wave of groundwater fluctuations. Another advantage of the present tidal method is the utilization of two groundwater time series collected from near-shore and relatively inland sites affected by the same ocean tide. The method does not use surface-water observation, thus avoiding errors derived from generally possible surface-water/groundwater boundary effects.The tidal response method with simple decomposition techniques was used to investigate the aquifer properties of an uplifted limestone island located in a subtropical region of Japan. A freshwater lens is the principal water resource for this island and its sustainable development is desired. Significant hydraulic layering has not been reported in the limestone aquifer. Pairs of groundwater-level time-series data collected by simultaneous observations at near-shore and inland sites were analysed by the tidal response method. The results demonstrated heterogeneous aquifer diffusivity on the island, typically with larger values in the southeastern coastal part than in the northwestern coastal part, which is consistent with the planar distribution of the entire freshwater lens and the position of its maximum thickness that are slightly biased toward the northwestern side.</p

Axonal-Transport-Mediated Gene Transduction in the Interior of Rat Bone

BACKGROUND: Gene transduction has been considered advantageous for the sustained delivery of proteins to specific target tissues. However, in the case of hard tissues, such as bone, local gene delivery remains problematic owing to anatomical accessibility limitations of the target sites. METHODOLOGY/PRINCIPAL FINDINGS: Here, we evaluated the feasibility of exogenous gene transduction in the interior of bone via axonal transport following intramuscular administration of a nonviral vector. A high expression level of the transduced gene was achieved in the tibia ipsilateral to the injected tibialis anterior muscle, as well as in the ipsilateral sciatic nerve and dorsal root ganglia. In sciatic transection rats, the gene expression level was significantly lowered in bone. CONCLUSIONS/SIGNIFICANCE: These results suggest that axonal transport is critical for gene transduction. Our study may provide a basis for developing therapeutic methods for efficient gene delivery into hard tissues

Recommendations related to the analytical equivalence assessment of gene panel testing

Advances in cancer genome care over the past few years have included the development of gene panel testing for various biomarkers. This article summarizes issues and provides recommendations related to analytical performance evaluations for new oncology gene panels. The scope of these recommendations includes comprehensive genomic profiling assays related to gene panel testing that uses histological or serum specimens to detect gene mutations. As a research project of the Japan Agency for Medical Research and Development Research on Regulatory Science of Pharmaceuticals and Medical Devices, we convened the working group committee that consisted of more than 30 experts from academia, industry, and government. We have discussed the points that should be considered to allow maximal simplification of assessments using clinical specimens in evaluating accuracy and limit of detection in equivalence and analytical performance for three years. We provide recommendations specific to each type of gene mutation as well as to reference standards or specimens used for evaluations. In addition, in order to facilitate the discussion on the analytical performance of gene panel tests by multidisciplinary tumor boards of hospitals, the present recommendations also describe the items that companies are expected to provide information on in their packaging inserts and reports, and the items that are expected to be discussed by multidisciplinary tumor boards. Our working group document will be important for participants in multidisciplinary tumor boards including medical oncologists and genome scientists, and developers of gene panels not only in Japan but also in other countries

DBTSS provides a tissue specific dynamic view of Transcription Start Sites

DataBase of Transcription Start Sites (DBTSS) is a database which contains precise positional information for transcription start sites (TSSs) of eukaryotic mRNAs. In this update, we included 330 million new tags generated by massively sequencing the 5′-end of oligo-cap selected cDNAs in humans and mice. The tags were collected from normal fetal or adult human tissues, including brain, thymus, liver, kidney and heart, from 6 human cell lines in 21 diverse growth conditions as well as from mouse NIH3T3 cell line: altogether 31 different cell types or culture conditions are represented. This unprecedented increase in depth of data now allows DBTSS to faithfully represent the dynamically changing landscape of TSSs in different cell types and conditions, during development and in the course of evolution. Differential usage of alternative 5′-ends across cell types and conditions can be viewed in a series of new interfaces. Promoter sequence information is now displayed in a comparative genomics viewer where evolutionary turnover of the TSSs can be evaluated. DBTSS can be accessed at http://dbtss.hgc.jp/

Dominant-negative constructs of human 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 and -4: effect on the expression of endogenous 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase mRNA

Expression of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase (PFKFB), a key regulatory enzyme of glycolysis, is significantly increased in different malignant tumors provides a potential mechanism of enhanced glycolysis and cancer cell proliferation. We created dominant-negative constructs of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase-3 and -4 (dnPFKFB-3 and dnPFKFB-4) cDNA for suppression of strongly enhanced expression endogenous PFKFB-3 and PFKFB-4. We introduce point mutation in ATP-binding domain of 6-phosphofructo-2-kinase part of PFKFB-3 as well as PFKFB-4 cDNA for suppression of 6-phosphofructo-2-kinase activity in the products of dnPFKFB-3 and dnPFKFB-4 expression. Cancer cells were stable transfected with these dominant-negative constructs for suppression of endogenous PFKFB-3 and PFKFB-4 expression and cell proliferation. We have shown that PFKFB-3 expression in pancreatic cancer cell line Panc1, stable transfected by dnPFKFB-3, was significantly reduced in normal as well as in hypoxic conditions. Pancreatic cancer cells proliferation, stable transfected by dnPFKFB-3 or dnPFKFB-4, was also reduced. Results of this investigation demonstrate possibility to apply the dominant-negative constructs of PFKFB-3 and PFKFB-4 for suppression of glycolysis and tumor cells proliferation via reduction of endogenous PFKFB expression.Експресія 6-фосфофрукто-2-кінази/фруктозо-2,6-бісфосфатази (PFKFB), ключового регуляторного ензиму гліколізу, різко зростає в різних злоякісних пухлинах, що розкриває можливий механізм посиленого гліколізу в ракових клітинах та їх проліферації. Ми створили домінантнегативні конструкції кДНК 6-фосфофрукто-2-кінази/фруктозо-2,6-бісфосфатази-3 та -4 (dnPFKFB-3 та dnPFKFB-4) для пригнічення посиленої експресії ендогенних PFKFB-3 та PFKFB-4. Для цього вводили точкові мутації в АТР-зв’язувальний домен 6-фосфофрукто-2-кінази як PFKFB-3, так і PFKFB-4 кДНК для пригнічення 6-фосфо-фрукто-2-кіназної активності у продуктах експресії цих конструкцій. Проводили трансфекцію ракових клітин цими домінантнегативними конструкціями для пригнічення експресії ендогенних PFKFB-3 і PFKFB-4 та проліферації клітин. Встановлено, що експресія PFKFB-3 в клітинах карциноми підшлункової залози лінії Panc1, стабільно трансфекованих dnPFKFB-3, знижується як у нормальних умовах, так і за гіпоксії. У клітинах з посиленою експресією dnPFKFB-4 спостерігали пригнічення ендогенних як PFKFB-4, так і PFKFB-3. Проліферація клітин карциноми підшлункової залози, стабільно трансфекованих як dnPFKFB-3, так і dnPFKFB-4, знижується. Результати цих досліджень показують можливість використання домінантнегативних конструкцій PFKFB-3 та PFKFB-4 для зменшення інтенсивності гліколізу та проліферації ракових клітин шляхом зниження експресії ендогенних PFKFB.Экспрессия 6-фосфофрукто-2-киназы/фруктозо-2,6-бисфосфатазы (PFKFB), ключевого регуляторного энзима гликолиза, резко возрастает в различных злокачественных опухолях, что раскрывает возможный механизм усиленного гликолиза в раковых клетках и их пролиферации. Мы создали доминантнегативные конструкции кДНК 6-фосфофрукто-2-киназы/фруктозо-2,6-бисфосфатазы-3 и -4 (dnPFKFB-3 и dnPFKFB-4) для угнетения усиленной экспрессии эндогенных PFKFB-3 и PFKFB-4. Для этого вводили точечные мутации в АТР-связывающий домен 6-фосфофрукто-2-киназы как PFKFB-3, так и PFKFB-4 для угнетения 6-фосфофрукто-2-киназной активности в продуктах экспрессии этих конструкций. Проводили трансфекцию раковых клеток этими доминантнегативными конструкциями для угнетения экспрессии эндогенных PFKFB-3, а также пролиферации клеток. Установлено, что экспрессия PFKFB-3 в клетках карциномы поджелудочной железы линии Panc1, стабильно трансфецированных dnPFKFB-3, снижается как в нормальных условиях, так и при гипоксии. В клетках с усиленной экспрессией dnPFKFB-4 наблюдали угнетение эндогенных как PFKFB-4, так и PFKFB-3. Пролиферация клеток карциномы поджелудочной железы, стабильно трансфецированных как dnPFKFB-3, так и dnPFKFB-4, снижается. Результаты этих исследований показывают возможность использования доминантнегативных конструкций PFKFB-3 и PFKFB-4 для уменьшения интенсивности гликолиза и пролиферации раковых клеток путем снижения экспрессии эндогенных PFKFB