Extracting transcription factor binding sites from unaligned gene sequences with statistical models

<p>Abstract</p> <p>Background</p> <p>Transcription factor binding sites (TFBSs) are crucial in the regulation of gene transcription. Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used to identify potential regulatory sequences, but the procedure can only map the probable protein-DNA interaction loci within 1–2 kb resolution. To find out the exact binding motifs, it is necessary to build a computational method to examine the ChIP-chip array binding sequences and search for possible motifs representing the transcription factor binding sites.</p> <p>Results</p> <p>We developed a program to find out accurate motif sites from a set of unaligned DNA sequences in the yeast genome. Compared with MDscan, the prediction results suggest that, overall, our algorithm outperforms MDscan since the predicted motifs are more consistent with previously known specificities reported in the literature and have better prediction ranks. Our program also outperforms the constraint-less Cosmo program, especially in the elimination of false positives.</p> <p>Conclusion</p> <p>In this study, an improved sampling algorithm is proposed to incorporate the binomial probability model to build significant initial candidate motif sets. By investigating the statistical dependence between base positions in TFBSs, the method of dependency graphs and their expanded Bayesian networks is combined. The results show that our program satisfactorily extract transcription factor binding sites from unaligned gene sequences.</p

The Effect of Substituent on Molecules That Contain a Triple Bond Between Arsenic and Group 13 Elements: Theoretical Designs and Characterizations

The effect of substitution on the potential energy surfaces of RE13≡AsR (E13 = group 13 elements; R = F, OH, H, CH3, and SiH3) is determined using density functional theory (M06‐2X/Def2‐TZVP, B3PW91/Def2‐TZVP, and B3LYP/LANL2DZ+dp). The computational studies demonstrate that all triply bonded RE13≡AsR species prefer to adopt a bent geometry that is consistent with the valence electron model. The theoretical studies also demonstrate that RE13≡AsR molecules with smaller substituents are kinetically unstable, with respect to the intramolecular rearrangements. However, triply bonded R′E13≡AsR′ species with bulkier substituents (R′ = SiMe(SitBu3)2, SiiPrDis2, and NHC) are found to occupy the lowest minimum on the singlet potential energy surface, and they are both kinetically and thermodynamically stable. That is to say, the electronic and steric effects of bulky substituents play an important role in making molecules that feature an E13≡As triple bond as viable synthetic target

Orthogonal Constant-Amplitude Sequence Families for System Parameter Identification in Spectrally Compact OFDM

In rectangularly-pulsed orthogonal frequency division multiplexing (OFDM) systems, constant-amplitude (CA) sequences are desirable to construct preamble/pilot waveforms to facilitate system parameter identification (SPI). Orthogonal CA sequences are generally preferred in various SPI applications like random-access channel identification. However, the number of conventional orthogonal CA sequences (e.g., Zadoff-Chu sequences) that can be adopted in cellular communication without causing sequence identification ambiguity is insufficient. Such insufficiency causes heavy performance degradation for SPI requiring a large number of identification sequences. Moreover, rectangularly-pulsed OFDM preamble/pilot waveforms carrying conventional CA sequences suffer from large power spectral sidelobes and thus exhibit low spectral compactness. This paper is thus motivated to develop several order-I CA sequence families which contain more orthogonal CA sequences while endowing the corresponding OFDM preamble/pilot waveforms with fast-decaying spectral sidelobes. Since more orthogonal sequences are provided, the developed order-I CA sequence families can enhance the performance characteristics in SPI requiring a large number of identification sequences over multipath channels exhibiting short-delay channel profiles, while composing spectrally compact OFDM preamble/pilot waveforms.Comment: 15 pages, 4 figure

Spatiotemporal expression of the serine protease inhibitor, SERPINE2, in the mouse placenta and uterus during the estrous cycle, pregnancy, and lactation

<p>Abstract</p> <p>Background</p> <p>SERPINE2, also known as glia-derived nexin or protease nexin-1, belongs to the serine protease inhibitor (SERPIN) superfamily. It is one of the potent serpins that modulates the activity of the plasminogen activator (PA) and was implicated in tissue remodeling. In this study, we investigated the expression patterns of SERPINE2 in the mouse placenta and uterus during the estrous cycle, pregnancy, and lactation.</p> <p>Methods</p> <p>SERPINE2 was purified from mouse seminal vesicle secretion using liquid chromatography (LC) and identified by LC/tandem mass spectrometry. The antiserum against the SERPINE2 protein was raised in rabbits. To reveal the uterine and placental expression of SERPINE2, tissues at various stages were collected for real-time PCR quantification, Western blotting, and immunohistochemical staining.</p> <p>Results</p> <p>Serpine2 mRNA was the major PA inhibitor in the placenta and uterus during the estrous cycle, pregnancy, and lactation, although Serpine1 mRNA had higher expression levels than Serpine2 mRNA in the placenta. Plat seemed to be the major PA in the mouse uterus and placenta. Antiserum against the SERPINE2 protein specifically recognized two forms of SERPINE2 and an extra 75-kDa protein, which was probably a complex of SERPINE2 with a certain protease, from among thousands of protein components in the tissue extract as demonstrated by Western blotting. In the uterus, SERPINE2 was primarily localized in luminal and glandular epithelial cells but it also was detected in circular and longitudinal smooth muscle cells during the estrous cycle and lactation. It was prominently expressed in decidual stroma cells, the metrial gland, and endometrial epithelium of the pregnant uterus. In the placenta, SERPINE2 was expressed in trophoblasts of the labyrinth and spongiotrophoblasts. However, its expression was remarkably reduced in giant cells which existed in the giant cell-decidual junction zone. In contrast, prominent expression of SERPINE2 seemed to be detected on clusters of glycogen cells near the junction zone. In addition, yolk sac membranes also showed high expression of SERPINE2.</p> <p>Conclusions</p> <p>These findings indicate that SERPINE2 is a major PA inhibitor in the placenta and uterus during the estrous cycle, pregnancy, and lactation. It may participate in the PA-modulated tissue remodeling process in the mouse placenta and uterus.</p

Glass-Embedded Fan-Out Antenna-in-Packaging for 5G Millimeter Wave Applications

The paper proposes a novel Antenna-in-Packaging (AiP) structure design for 60 GHz, millimeter wave WiFi applications. In the AiP design, single- or double-sided glass redistribution layers were embedded in a typical fan-out (FO) packaging structure to introduce design flexibility and to improve the radiation properties of the antenna. ANSYS-HFSS software was employed for electromagnetic (EM) characteristic simulations on the fan-out AiP (FO_AiP) design. To improve antenna radiation performance, single factor analyses were first performed to study the impact of each of the design parameters. A consecutive procedure followed to find more suitable combinations of the design parameters. As a result, two typical glass-embedded FO_AiP structures - one with 7.6 GHz bandwidth plus 4.7 dB gain and upward radiation, and another with 5.3 GHz bandwidth plus 5.2 dB gain and downward radiation, are proposed for the 60 GHz applications