Copy number variation (CNV) is a prevalent form of critical genetic variation that leads to an abnormal number of copies of large genomic regions in a cell. Microarray-based comparative genome ...hybridization (arrayCGH) or genotyping arrays have been standard technologies to detect large regions subject to copy number changes in genomes until most recently high-resolution sequence data can be analyzed by next-generation sequencing (NGS). During the last several years, NGS-based analysis has been widely applied to identify CNVs in both healthy and diseased individuals. Correspondingly, the strong demand for NGS-based CNV analyses has fuelled development of numerous computational methods and tools for CNV detection. In this article, we review the recent advances in computational methods pertaining to CNV detection using whole genome and whole exome sequencing data. Additionally, we discuss their strengths and weaknesses and suggest directions for future development.
•Edamame at different drying times were evaluated using a hyperspectral imaging technique.•Mean and entropy features were extracted from the reflectance images for prediction coupled with partial ...least squares.•Hyperspectral image features are useful for predicting color and moisture content during drying process.
Dried soybean is among the most popular snack foods consumed in numerous countries, and its quality has received considerable attention from processors and consumers. Color and moisture content are two critical parameters used to evaluate dried soybean quality. This study thus aimed to develop regression models for predicting the color and moisture content of soybeans simultaneously during the drying process using a hyperspectral imaging technique. Hyperspectral reflectance images were acquired from fresh and dried soybeans over the spectral region between 400 and 1000nm for 270 samples. After the automatic segmentation of soybean images at each wavelength based on an active contour model, mean reflectance and image entropy parameters were extracted and tested separately and in combination for predicting the color and moisture content of the processed soybeans. Predicting models were built using the partial least squares regression method. Better prediction results for both color and moisture content were achieved using the mean reflectance data (with correlation coefficients or RP=0.862 and root-mean-square errors of prediction or RMSEP=1.04 for color, as well as RP=0.971 and RMSEP=4.7% for moisture content) than when using entropy data (RP=0.839 and RMSEP=1.14 for color, as well as RP=0.901 and RMSEP=9.2% for moisture content). However, the integration of mean reflectance and entropy data did not show significant improvements in predicting the color or moisture content. Overall, a simple hyperspectral imaging technique involving rapid image preprocessing and single spectral features showed significant potential in measuring the color and moisture content of soybeans simultaneously during the drying process.
Next generation sequencing (NGS) technologies allow us to explore virus interactions with host genomes that lead to carcinogenesis or other diseases; however, this effort is largely hindered by the ...dearth of efficient computational tools. Here, we present a new tool, VirusFinder, for the identification of viruses and their integration sites in host genomes using NGS data, including whole transcriptome sequencing (RNA-Seq), whole genome sequencing (WGS), and targeted sequencing data. VirusFinder's unique features include the characterization of insertion loci of virus of arbitrary type in the host genome and high accuracy and computational efficiency as a result of its well-designed pipeline. The source code as well as additional data of VirusFinder is publicly available at http://bioinfo.mc.vanderbilt.edu/VirusFinder/.
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•Cu(II) enhanced the nZVT corrosion to release the low valence tungsten species.•Low valence tungsten species accelerated copper-redox cycling by a direct reduction pathway.•Cu(II) ...was also reduced through an indirect reduction pathway driven by active hydrogen atoms.•The formed Cu(I) was confirmed as the main effective activator for PMS.•OH, SO4−, and O2− were responsible for TC removal in the nZVT/Cu(II)/PMS system.
This work presented a new strategy to activate peroxymonosulfate (PMS) by the addition of nano-zero-valent tungsten (nZVT) via accelerating the redox cycles of Cu(II)/Cu(I), which induce the consecutive generation of highly reactive oxygen species ultimately. The oxidation capacity of the nZVT/Cu(II)/PMS process and the detailed mechanisms of PMS activation were investigated with tetracycline (TC) as the targeted pollutant. Our results indicated that about 70% TC removal was obtained in the nZVT/Cu(II)/PMS system in 15 min with an initial pH of 4.6. In addition, hydroxyl radicals (OH), sulfate radicals (SO4−), and superoxide radicals (O2−) were identified as the reactive oxygen species (ROSs) attributed to rapid TC decomposition according to the quenching studies and EPR technology. The effective component that was responsible for PMS activation and ROSs generation was ascertained to be the resulting Cu(I), which derived from the direct reduction pathway driven by epigenetic low valence tungsten species and the indirect reduction pathway driven by active hydrogen atoms. Further, the presence of Cu(II) significantly accelerated the corrosion of the nZVT powders, leading to the accumulation of low valence tungsten species and the decrease in the mean diameter of the ZVT nanoparticles. There was no obvious change of the composition and structure between the original and residual nZVT powders, as evidenced by XPS and XRD analysis. The degradation process of TC included the cleavage of specific functional groups, the ring-opening reactions and the hydroxylation process. This study provided theoretical significance in applying zero-valent metals to activate PMS through a cupric/cuprous redox cycling mechanism.
Finding the longest common subsequence (LCS) of multiple strings is an NP-hard problem, with many applications in the areas of bioinformatics and computational genomics. Although significant efforts ...have been made to address the problem and its special cases, the increasing complexity and size of biological data require more efficient methods applicable to an arbitrary number of strings. In this paper, we present a new algorithm for the general case of multiple LCS (or MLCS) problem, i.e., finding an LCS of any number of strings, and its parallel realization. The algorithm is based on the dominant point approach and employs a fast divide-and-conquer technique to compute the dominant points. When applied to a case of three strings, our algorithm demonstrates the same performance as the fastest existing MLCS algorithm designed for that specific case. When applied to more than three strings, our algorithm is significantly faster than the best existing sequential methods, reaching up to 2-3 orders of magnitude faster speed on large-size problems. Finally, we present an efficient parallel implementation of the algorithm. Evaluating the parallel algorithm on a benchmark set of both random and biological sequences reveals a near-linear speedup with respect to the sequential algorithm.
In this paper, we present locomotion learning for an Anguilliform robotic fish using a central pattern generator (CPG) approach. First, we give the overall structure of the CPG. Different from a ...traditional CPG that contains only coupled oscillators, our CPG consists of coupled Andronov-Hopf oscillators, an artificial neural network (ANN), and an outer amplitude modulator. Coupled oscillators, which possess a limit-cycle character, are used to generate inputs to excite the ANN. The ANN serves as a learning mechanism, from which we can obtain desired waveforms. By inputting different signals to the ANN, different desired locomotion patterns can be obtained. Outer amplitude modulator resizes the amplitudes of the ANN outputs according to task specifications. The CPG possess temporal scalability, spatial scalability, and phase-shift property; thus, we can obtain desired amplitudes, oscillation frequencies, and phase differences by tuning corresponding parameters. By extracting the swimming pattern from a real fish and using the CPG approach, we successfully generate a new swimming pattern and apply it to the robotic fish. The new pattern reserves the swimming characters of the real fish, and it is more suitable to be applied to the robotic fish. By using the new pattern, the robotic fish can perform both forward locomotion and backward locomotion, which are validated by experiments.
Oxidized sodium alginate is a handily modifiable polysaccharide owing to the pendant aldehyde groups which can form dynamic covalent bonds with amines, acylhydrazines, etc., providing oxidized sodium ...alginate-based hydrogels with stimuli-responsive properties. However, due to the stiffness and, in particular, the hydrophobicity of sodium alginate dialdehyde at low pH, the mechanical performance and pH stimuli responsiveness of oxidized sodium alginate-based hydrogels are still strictly limited. Herein, we report a new strategy to build an injectable, dual responsive, and self-healing hydrogel based on oxidized sodium alginate and hydrazide-modified poly(ethyleneglycol) (PEG). The hydrazide-modified PEG, referred to as PEG-DTP, acts as a macromolecule crosslinker. We found that the presence of PEG-DTP reduces the hydrophobicity of oxidized sodium alginate at low pH so effectively that even a pH-induced reversible sol-gel transitions can be realized. Meanwhile, the disulfide bonds in PEG-DTP endows the hydrogel with the other reversible sol-gel transitions by redox stimuli. In particular, due to the softness of PEG-DTP chains, mechanical performance was also enhanced significantly. Our results indicate we can easily integrate multi-stimuli responsiveness, injectability, and self-healing behavior together into an oxidized sodium alginate-based hydrogel merely by mixing an oxidized sodium alginate solution with PEG-DTP solution in certain proportions.
Mycelia growth inhibition of Colletotrichum gloeosporioides exposed to VOCs from biological control agents TB09, TB30, TB52, and TB72, in vitro (left) and in vivo (right). Display omitted
► Volatiles ...produced by two Bacillus strains inhibited anthracnose pathogen. ► Mycelial growth of Colletotrichum gloeosporioides was suppressed. ► Anthracnose on mango fruit was reduced. ► Four volatiles can inhibit mycelia growth in vitro completely.
Four bacterial strains of Bacillus spp. which were antagonistic to the mango anthracnose pathogen were isolated and screened. Among them, TB09 and TB72 were identified by 16S rDNA sequence as Bacillus pumilus and Bacillus thuringiensis, respectively. In vitro, the anthracnose fungus showed 88.87% and 80.07% of mycelia growth inhibitions in presence of B. pumilus and B. thuringiensis, respectively and in vivo, the inhibitions of the disease were 94.28% and 87.06%, respectively. Based on the Gas Chromatography–Mass Spectrometer (GC–MS) analysis, 11 volatile compounds produced by B. pumilus and B. thuringiensis were identified. Among them, five volatiles showed better inhibition effects on the pathogens. 2-nonanone, β-benzeneethanamine, 2-decanone completely inhibited mycelia growth in vitro at a concentration of 100μLL−1, and thymol inhibited growth at concentrations of 50mgL−1 and 100mgL−1. The inhibition rate of 40μLL−1 artificial mixture of 5 volatiles was 98.75% in the plate test. The results showed that the two screened antagonistic bacteria, and some of their produced volatiles and artificial mixtures could be promising control methods for anthracnose in harvested mango fruit.
The fundamental metabolic decision of a cell, the balance between respiration and fermentation, rests in part on expression of the mitochondrial genome (mtDNA) and coordination with expression of the ...nuclear genome (nuDNA). Previously we described mtDNA copy number depletion across many solid tumor types (Reznik et al., 2016). Here, we use orthogonal RNA-sequencing data to quantify mtDNA expression (mtRNA), and report analogously lower expression of mtRNA in tumors (relative to normal tissue) across a majority of cancer types. Several cancers exhibit a trio of mutually consistent evidence suggesting a drop in respiratory activity: depletion of mtDNA copy number, decreases in mtRNA levels, and decreases in expression of nuDNA-encoded respiratory proteins. Intriguingly, a minority of cancer types exhibit a drop in mtDNA expression but an increase in nuDNA expression of respiratory proteins, with unknown implications for respiratory activity. Our results indicate suppression of respiratory gene expression across many cancer types.
Background:
Baicalin (BCL), a candidate drug for ischemic stroke, has been indicated to protect neurons by promoting brain-derived neurotrophic factor (BDNF). However, the cellular source of BDNF ...release promoted by baicalin and its detailed protective mechanism after ischemia/reperfusion remains to be studied. The aim of this study was to investigate the neuroprotective mechanisms of baicalin against oxygen–glucose deprivation/reoxygenation (OGD/R) in a neuron–astrocyte coculture system and to explore whether the BDNF-TrkB pathway is involved.
Methods and Results:
A neuron–astrocyte coculture system was established to elucidate the role of astrocytes in neurons under OGD/R conditions. The results demonstrated that astrocytes became reactive astrocytes and released more BDNF in the coculture system to attenuate neuronal apoptosis and injury after OGD/R. BCL maintained the characteristics of reactive astrocytes and obviously increased the expression of cyclic AMP response element-binding protein (CREB) and the levels of BDNF in the coculture system after OGD/R. To further verify whether BDNF binding to its receptor tyrosine kinase receptor B (TrkB) was required for the neuroprotective effect of baicalin, we examined the effect of ANA-12, an antagonist of TrkB, on NA system injury, including oxidative stress, inflammation, and apoptosis induced by OGD/R. The results showed that treatment of NA systems with ANA-12 significantly attenuated the neuroprotection of BCL. The phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) and mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase (ERK) pathways are two important downstream cascades of signaling pathways activated by BDNF binding to TrkB. We investigated the expressions of TrkB, PI3K, Akt, MAPK, and ERK. The results demonstrated that baicalin significantly increased the expressions of TrkB, PI3K/AKT, and MAPK/ERK.
Conclusion:
The neuroprotective effects of baicalin against oxidative stress, inflammation, and apoptosis were improved by astrocytes, mainly mediated by increasing the release of BDNF and its associated receptor TrkB and downstream signaling regulators PI3K/Akt and MAPK/ERK1/2.
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